@article {pmid40633701,
year = {2025},
author = {Mokgokong, SP and Hassim, A and Mafuna, T and Turner, WC and van Heerden, H and Lekota, KE},
title = {Comparative genomics of Bacillus anthracis A and B-clades reveals genetic variation in genes responsible for spore germination.},
journal = {Genomics},
volume = {},
number = {},
pages = {111074},
doi = {10.1016/j.ygeno.2025.111074},
pmid = {40633701},
issn = {1089-8646},
abstract = {Bacillus anthracis, the causative agent of anthrax, is composed of three genetic clades (A, B, and C). Clade-A is the most common and distributed worldwide, B-clade has a narrow geographic distribution, and C-Clade is rare. South Africa's Kruger National Park (KNP) has high diversity of B. anthracis, with strains from A and B clades described from its northernmost region, Pafuri. We employed whole genome sequencing to investigate the genomic diversity of B. anthracis strains isolated from animal carcasses (n = 34) during the 2012-2015 outbreaks. Whole-genome single-nucleotide polymorphism (wgSNP) analysis assigned the 2012-2015 B. anthracis genomes to the A-clade branch, distributed across the branch's two minor sub-clades A.Br.005/006. Additionally, pan-genomic analysis distinguished the A- and B-clade genomes, identifying unique accessory genes. Notable genetic differences include the biosynthetic spore cell wall genes; long-chain fatty acid CoA ligases (FaD13), Bacillus collagen-like protein of anthracis (BclA) involved in the exosporium germination, as well as a truncated murein DD-endopeptidase (mepH) found in the pXO2 plasmid of the B-clade strains. The tryptophan synthase subunit alpha gene (trpA), which results in a pseudogene in B-clade genomes separates the A- and B-clade genomes. These differences in biosynthetic cell wall genes suggest variation in adaptability or cell growth of the B-clade strains in the environment, further influenced by the truncation of the trpA gene involved in spore germination. The A.Br.005/006-clade strains in KNP exhibit higher genetic diversity, which may enhance their resilience to environmental stressors. In contrast, the KNP B-clade (B.Br.001/002) strains show limited genetic variation, potentially reducing their adaptability. This pattern is evident through whole-genome SNP analysis and pan-genomics investigating the evolution of B. anthracis.},
}

@article {pmid40631900,
year = {2025},
author = {Migicovsky, Z},
title = {Genomic resources for crop wild relatives are critical for perennial fruit breeding and conservation.},
journal = {American journal of botany},
volume = {},
number = {},
pages = {e70068},
doi = {10.1002/ajb2.70068},
pmid = {40631900},
issn = {1537-2197},
abstract = {Many perennial fruit crops are clonally propagated, resulting in uniform fruit quality but increasing vulnerability to pests, diseases, and climate change. In contrast, closely related crop wild relatives (CWRs) continue to evolve in response to these pressures and are a valuable source of adaptive traits. Despite their potential, CWRs are underutilized in perennial fruit breeding. Efficient and accurate introgression of traits from CWRs during perennial fruit breeding will require the use of genomics. Genomics-assisted breeding begins with genetic mapping, such as genome-wide association studies, to identify markers predictive of traits of interest. For diverse species such as CWRs, a pangenomic approach that incorporates multiple species as a reference is often necessary. Continued use of CWRs in fruit breeding also depends on their conservation, both in situ (in natural habitats) and ex situ (off-site). Ex situ collections can also be used for genetic mapping, further supporting genomics-assisted plant breeding efforts. Ultimately, breeding and conservation of perennial fruit crops are complementary goals that benefit from the development and application of genomic resources.},
}

@article {pmid40631467,
year = {2025},
author = {Fan, W and Liao, Z and Gu, M and Zhang, Y and Lei, W and Zhang, Y and Li, H and Yan, J and Xiao, Y and Lin, H and Jin, S and Yu, Y and Fang, J and Ye, N and Wang, P},
title = {Pan-Genome of Jasminum sambac Reveals the Genetic Diversity of Different Petal Morphology and Aroma-Related Genes.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70013},
doi = {10.1111/1755-0998.70013},
pmid = {40631467},
issn = {1755-0998},
support = {2022YFD2101102//National Key Research and Development Program of China/ ; 2023J01508//Natural Science Foundation of Fujian Province/ ; },
abstract = {Jasmine (Jasminum sambac) is globally renowned for its distinct fragrance and ornamental appeal, existing primarily in three floral morphologies: single-petal, double-petal and multi-petal. De novo sequencing and chromosome-level genome assembly were performed on two distinct jasmine varieties: 'Yuanye' double-petal and 'Bijian' multi-petal jasmines. These assemblies, along with three previously published genomes, were integrated to construct a pan-genome framework that comprehensively encompasses both the core and variable genomic components of jasmine. A substantial number of structural variations (SVs) and single nucleotide polymorphisms (SNPs) had been identified, of which 89.5% were insertions/deletions (size ≥ 50 bp), whereas gene families also exhibited significant contractions and expansions, revealing the high complexity and dynamics of the jasmine genomes. Comparative genomic approaches further revealed multiple transcription factor families associated with aromatic biosynthesis, floral organogenesis and environmental adaptability. Key genes involved in the formation of jasmine scent, with a particular focus on the variation in copy number and expression levels of critical enzyme genes responsible for the production of four major volatile terpenoids and benzyl acetate, thereby elucidating the genetic basis of jasmine aroma diversity. Additionally, within the MADS-box gene family, the PI and AP3 subfamilies are hypothesized to play crucial roles in the development of floral organs. Through the integration of these comprehensive data, a pan-genome website for jasmine was developed to facilitate data download and visualise genomic variations via a genome browser (https://www.pan-jasmine.cn/). In summary, this work provides valuable genomic resources for the genetic enhancement and marker-assisted breeding of jasmine.},
}

@article {pmid40629470,
year = {2025},
author = {Wang, W and Liu, Q and Zhao, Q and Zhu, Z and Wen, W and Zhang, Z and Li, X},
title = {Homologous recombination and evolutionary arms race drive the adaptive evolution of African swine fever virus.},
journal = {Veterinary research},
volume = {56},
number = {1},
pages = {142},
pmid = {40629470},
issn = {1297-9716},
support = {2023YFD1800500//National Key Research and Development Program of China/ ; JSSCTD202224//Jiangsu Innovative and Entrepreneurial Talent Team Project/ ; D18007//the 111 Project/ ; },
mesh = {*African Swine Fever Virus/genetics/physiology ; *Evolution, Molecular ; *Genome, Viral ; *Homologous Recombination ; Animals ; Swine ; African Swine Fever/virology ; Biological Evolution ; Phylogeny ; },
abstract = {African Swine Fever Virus (ASFV) is a highly contagious pathogen responsible for substantial economic losses in swine populations worldwide. Despite extensive research, the mechanisms underlying the genomic evolution of ASFV remain poorly understood. In this study, we conducted a comprehensive analysis of ASFV evolutionary strategies by examining 252 complete ASFV genomes. Our pan-genome analysis categorizes ASFV genes into core and non-core categories, with core genes predominantly locate in the central region of the genome, while non-core genes are primarily situated at the variable genomic termini, exhibiting higher rates of genetic loss and diversification. Gene synteny analysis revealed that ASFV inherited a portion of its core gene repertoire from the common ancestor of the Asfarviridae family, establishing its central genomic framework, and acquired virus-specific genes that contributed to its distinct genetic identity during divergence. Homologous recombination analysis identified 76 genes exhibiting strong recombination signals, emphasizing the critical role of recombination in ASFV evolution. Additionally, 9 genes were found to be under positive selection, highlighting the influence of the host-virus evolutionary arms race in shaping ASFV genome, particularly in terms of immune evasion and host interaction. These findings underscore the dynamic evolutionary forces driving ASFV adaptive evolution and provide important implications for understanding the virus global spread and the development of effective control measures.},
}

*African Swine Fever Virus/genetics/physiology
*Evolution, Molecular
*Genome, Viral
*Homologous Recombination
Animals
Swine
African Swine Fever/virology
Biological Evolution
Phylogeny

@article {pmid40629160,
year = {2025},
author = {Kundu, P and Thorat, SA and Kiran, A and Goel, K and Zinta, G},
title = {Plant-derived triterpenoid saponins: multifaceted roles and bioengineering prospects.},
journal = {Plant cell reports},
volume = {44},
number = {8},
pages = {172},
pmid = {40629160},
issn = {1432-203X},
support = {MLP-178//CSIR/ ; },
mesh = {*Saponins/metabolism/chemistry/biosynthesis/pharmacology ; *Triterpenes/metabolism/chemistry ; *Plants/metabolism ; *Bioengineering/methods ; Biosynthetic Pathways ; Humans ; },
abstract = {Saponins are plant secondary metabolites synthesized through the triterpenoid biosynthetic pathway by a series of modifications, including acylation, glycosylation, and oxidation of β-amyrin, a product of 2,3-oxidosqualene. They are classified into triterpenoid saponins and steroidal saponins, exhibiting diverse bioactivities and applications in the pharmaceuticals, agriculture, cosmetics, and food industries. Beyond their industrial relevance, saponins play a crucial role in plant defense, stress tolerance, and shaping of rhizosphere microbiota. Despite their significant potential, plant-derived triterpenoid saponins remain underexplored. Additionally, their biosynthesis in plants is limited and requires rigorous exploration to decipher novel biotechnological approaches to enhance their production. In this review, we provide a comprehensive update on the types of triterpenoid saponins, the regulation of their biosynthesis pathway, defense responses, therapeutic activities, biotechnological interventions, and the challenges associated with the large-scale production of saponins. Also, we explicitly provide an update on strategies for synthesizing saponins in microbial cells and in vitro plant systems. Thus, this review provides a foundation for further research on plant-derived triterpenoid saponins, their diverse therapeutic activities, their critical role in defense responses, and the development of novel methods to increase saponin production for human health, industrial, and agricultural applications.},
}

*Saponins/metabolism/chemistry/biosynthesis/pharmacology
*Triterpenes/metabolism/chemistry
*Plants/metabolism
*Bioengineering/methods
Biosynthetic Pathways
Humans

@article {pmid40627207,
year = {2025},
author = {Elufisan, TO and Rosas-García, NM},
title = {Whole genome sequence analysis of pigmented Bacillus inaquosorum LBA001 revealed biosynthetic gene clusters for a variety of secondary metabolites.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {8},
pages = {107},
pmid = {40627207},
issn = {1572-9699},
support = {Apoyos CI//IPN/ ; },
mesh = {*Bacillus/genetics/metabolism/classification/isolation & purification ; Phylogeny ; Whole Genome Sequencing ; *Genome, Bacterial ; *Multigene Family ; *Secondary Metabolism/genetics ; *Pigments, Biological/biosynthesis/genetics ; *Biosynthetic Pathways/genetics ; Soil Microbiology ; Base Composition ; },
abstract = {The strain Bacillus inaquosorum LBA001 was isolated from a soil sample as a potential entomopathogenic bacteria; and produces a brown pigment at each growth on LB (Luria-Bertani) agar. We investigated its biochemical and physiological characteristics using the standard bacteriological technique. The whole genome sequencing was used to explore its genetic composition and metabolic capabilities. We used whole genome sequencing to examine the role of its genetic makeup and its potential metabolic capacity. The whole genome assembly resulted in one scaffold with a GC content of 43.19% and a genome size of about 4.3 Mb. The Prokka annotation showed 4,149 coding sequences and full sets of ribosomal RNA (5S, 16S, and 23S). The pan genome analysis identified 192 core genes among the strains compared with numerous accessory genes in individual strains. Phylogenetic analysis confirmed that it belongs to the B. inaquosorum clade, as it has much in common with B. inaquosorum KCTC 13249[ T]. AntiSMASH indicated that LBA001 contains certain groups of biosynthetic genes such as bacilysin, surfactin, fengycin, bacillaene, and pulcherriminic acid among others. The predicted proteome of LBA001 was subjected to BLAST-based homology searches against reference pigment gene database. The analysis identified 23 high-confidence pigment biosynthesis genes, with five different types of pigments in seven distinct colors. Numerous CAZymes in LBA00 were predicted, suggesting its potential applications in biotechnology and agriculture. The identification of potential antibiotic resistance genes in LBA001 genome reflected its adaptive characteristics. These findings will add to our understanding of B. inaquosorum metabolic versatility and its potential as a beneficial source of bioactive compounds.},
}

*Bacillus/genetics/metabolism/classification/isolation & purification
Phylogeny
Whole Genome Sequencing
*Genome, Bacterial
*Multigene Family
*Secondary Metabolism/genetics
*Pigments, Biological/biosynthesis/genetics
*Biosynthetic Pathways/genetics
Soil Microbiology
Base Composition

@article {pmid40625851,
year = {2025},
author = {Karberg, KA},
title = {The ever-evolving world of microbes: the current state of microbial taxonomy, genome evolutionary dynamics, and the potential impact on the future of agricultural microbials risk assessment.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {13},
number = {},
pages = {1620652},
pmid = {40625851},
issn = {2296-4185},
abstract = {Risk assessment frameworks for plant agricultural biotechnology products have been in place for decades, focused on the evaluation of living biotechnology products created through genetic engineering. These products contain genetic material from outside the breeder's gene pool, which is often from different taxa or represents "novel combinations of genetic material". These products are typically considered to be "genetically modified" (GM) organisms in regulatory jurisdictions. However, in the microbial world, particularly among Bacteria and Archaea, the rapid expansion of genome sequence databases shows that natural microbial innovation primarily occurs through the natural exchange of genetic material from various sources, even from different taxa. This means that many microbes can be considered naturally occurring GM organisms. This raises the question of whether labeling a microbe as GM is always scientifically relevant for risk assessment. In most regulatory frameworks, being classified as GM significantly impacts the registration path, especially for microbes intended for environmental release. A more effective and science-based regulatory approach would assess the actual functions of a microbe rather than relying on the uncertain classification of its genetic material. This would benefit regulators, developers, and society by promoting the use of microbial technologies for agricultural use.},
}

@article {pmid40623120,
year = {2025},
author = {Dong, X and Jiao, D and Xue, H and Fan, S and Wei, C},
title = {APAV: An advanced pangenome analysis and visualization toolkit.},
journal = {PLoS computational biology},
volume = {21},
number = {7},
pages = {e1013288},
doi = {10.1371/journal.pcbi.1013288},
pmid = {40623120},
issn = {1553-7358},
abstract = {Traditional pangenome analysis focuses on gene presence/absence variations (gene PAVs). However, the current methods for gene PAV analysis are insensitive to detect small but valuable mutations within gene regions, and they overlook variations in intergenic regions. Additionally, the visual inspection of PAVs is an important but time-consuming step for pangenome analysis and result interpretation. To address these issues, we present APAV, an advanced toolkit designed for comprehensive PAV analysis and visualization. It integrates gene element-level PAV analysis and provides PAV analysis for arbitrary given regions in a genome. The resulted PAV profile can be visualized and investigated interactively with reports in HTML format, enabling researchers to conveniently verify sequencing read depth, target region coverage, and intervals of absence for each PAV. Furthermore, APAV offers various subsequent analysis and visualization functions based on the PAV profile table, including basic statistics, sample clustering, genome size estimation, and phenotype association analysis. We demonstrated the capability of APAV with pangenome analysis of tumor genomes and rice genomes. Performing PAV analysis at the element level not only provides more accurate information about the variations but also uncovers a larger number of variations for the phenotype-genotype association studies. In the rice genome analysis, we identified over twenty thousand distributed genes and more than fifty thousand distributed genetic elements. In the tumor genome analysis, element-level analysis revealed approximately three times as many phenotype-related genes as gene-level analysis. This indicates that altering the PAV unit from genes to smaller segments or elements can lead to more biological insights.},
}

@article {pmid40616976,
year = {2025},
author = {González-Cruz, M and Reyes-Gastellou, A and Castelán-Vega, JA and Monterrubio-López, GP and Jiménez-Alberto, A and Aparicio-Ozores, G and Ribas-Aparicio, RM},
title = {In silico development of a broad-spectrum vaccine against ESKAPE pathogens.},
journal = {Journal of molecular graphics & modelling},
volume = {140},
number = {},
pages = {109120},
doi = {10.1016/j.jmgm.2025.109120},
pmid = {40616976},
issn = {1873-4243},
abstract = {Antimicrobial-resistant ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter cloacae) have significantly restricted therapeutic alternatives for critical infections, consequently contributing to increase the severity and mortality of infectious illnesses that represent a significant global health challenge. Vaccination as a preventive measure can be crucial in substantially reducing bacterial infections and is potentially effective against antibiotic-resistant bacteria. This study shows the design of an epitope-based vaccine capable of neutralizing shared antigenic determinants present among the ESKAPE pathogens. The pangenome of the ESKAPE pathogens was analyzed to extract the core proteome. This approach facilitated reverse vaccinology analysis to identify antigenic proteins within this bacterial group. The study revealed similar structures in porins OmpA, OprD, and TolC, as well as the collagen-binding adhesins Acm and Cna. These proteins were then utilized to predict T-cell and B-cell epitopes, selecting those with their best physicochemical properties, antigenicity, non-allergenicity, and lack of toxicity. Additionally, epitopes located on the surface of the antigens and capable of coupling with HLA molecules were prioritized. In this computational approach, we engineered a construct incorporating the adjuvant RS09, a TLR4 agonist, and immunogenic epitopes connected by linkers. We assessed the stability of their interaction with pattern recognition receptors of the immune system through molecular docking and molecular dynamics simulations. The in silico immune simulation demonstrated that the vaccine could trigger humoral and cell-mediated immune responses. The resulting construct potentially represents an effective and safe vaccine candidate to prevent infections caused by the ESKAPE group.},
}

@article {pmid40616241,
year = {2025},
author = {Dhaouadi, S and Vinchira-Villarraga, D and Bijarniya, S and Webster, AJ and Dorati, F and Brady, C and Arnold, DL and Rabiey, M and Jackson, RW},
title = {A Sucrose-Utilisation Gene Cluster Contributes to Colonisation of Horse Chestnut by Pseudomonas syringae pv. aesculi.},
journal = {Molecular plant pathology},
volume = {26},
number = {7},
pages = {e70116},
pmid = {40616241},
issn = {1364-3703},
support = {//JAAB/ ; },
mesh = {*Pseudomonas syringae/genetics/pathogenicity/metabolism/growth & development ; *Sucrose/metabolism ; *Plant Diseases/microbiology ; *Multigene Family/genetics ; *Aesculus/microbiology ; Virulence/genetics ; Plant Leaves/microbiology ; },
abstract = {Pseudomonas syringae pathovar aesculi (E-Pae) causes bleeding canker disease in the woody tissue of European horse chestnut (HC). Comparative genomic analysis of E-Pae with a related leaf-infecting strain (I-Pae) and other P. syringae strains identified candidate virulence genes for colonisation of woody tissue, including a sucrose uptake and utilisation system (scrYABCDBR cluster) found in 162 of 206 P. syringae strains spanning the pangenome. Growth analysis using sucrose as sole carbon source showed that I-Pae (lacking the gene cluster) was unable to grow whereas E-Pae could grow. P. savastanoi pv. phaseolicola 1448A and P. syringae pv. morsprunorum R15244 were compromised in growth despite the presence of the gene cluster. Sucrose utilisation assays using scrB and scrY mutants and complemented strains confirmed the importance of the cluster for sucrose metabolism in vitro. Pathogenicity assays in HC revealed the sucrose gene cluster is important for symptom development in the woody tissue. While the scr genes contribute to disease causation, they were not essential for pathogen fitness when compared to hrpL and hopAB1 mutants. E-Pae caused disease symptoms in HC leaves, suggesting the strain has the potential to infect leaves as well. However, it was notable that the scrB mutant of E-Pae caused increased disease symptoms, possibly highlighting a niche adaptation strategy for I-Pae to cause leaf spots in HC as well as constraining E-Pae to predominantly infect the woody tissue.},
}

*Pseudomonas syringae/genetics/pathogenicity/metabolism/growth & development
*Sucrose/metabolism
*Plant Diseases/microbiology
*Multigene Family/genetics
*Aesculus/microbiology
Virulence/genetics
Plant Leaves/microbiology

@article {pmid40611899,
year = {2025},
author = {Pokharel, SK and Shehata, N and Ahearne, A and Knehans, T and Bailey, CB and Boudreau, PD and Stevens, DC},
title = {Establishing Conserved Biosynthetic Gene Clusters of the Phylum Myxococcota.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40611899},
issn = {2692-8205},
support = {P20 GM130460/GM/NIGMS NIH HHS/United States ; R01 GM149795/GM/NIGMS NIH HHS/United States ; },
abstract = {A surge in sequenced myxobacteria catalyzed by advancements in long read genome and metagenome sequencing has provided sufficient data to scrutinize the conserved biosynthetic gene clusters (BGCs) within the phylum Myxococcota. Provided the utility of myxobacteria in environmental nutrient cycles and discovery of novel therapeutic leads, we sought to determine any conserved specialized metabolism in the phylum. Using a pan-genome approach to analyze eleven genera and 195 sequenced genomes including ten newly reported myxobacterial isolate, we observed five conserved BGCs. All five clusters encode for characterized metabolites with established ecological roles for four of the metabolites, and none of the metabolites are known toxins. Validation of our approach was done by analyzing Myxococcota genera without sufficient, sequenced representatives for pan-genome analysis to observe the presence/absence of these five clusters. This approach enabled observation of genus-level conservation of BGCs with varying degrees of confidence due to diversity of sequenced species within each genus. The indigoidine BGC typically found in Streptomyces spp. was notably conserved in Melittangium; heterologous expression of the core biosynthetic gene bspA in Escherichia coli and subsequent detection of indigoidine confirmed the identity of the indigoidine cluster. Conserved BGCs in myxobacteria reveal maintenance of biosynthetic pathways and cognate metabolites with ecological roles as chemical signals and stress response; these observations suggest competitive specialization of secondary metabolism and toxin production in myxobacteria.},
}

@article {pmid40608406,
year = {2025},
author = {Ito, K and Ito, Y},
title = {Comparative genomic analysis of Latilactobacillus sakei strains provides new insights into their association with different niche adaptations.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {7},
pages = {},
pmid = {40608406},
issn = {1465-2080},
mesh = {*Genome, Bacterial ; Phylogeny ; *Adaptation, Physiological/genetics ; Plasmids/genetics ; *Latilactobacillus sakei/genetics/classification/physiology/growth & development/metabolism ; Genomics ; Carbohydrate Metabolism/genetics ; Fermentation ; Genetic Variation ; },
abstract = {Latilactobacillus sakei, a lactic acid bacterium in diverse environments such as fermented foods, meat and the human gastrointestinal tract, exhibits significant genetic diversity and niche-specific adaptations. This study conducts a comprehensive comparative genomic analysis of 29 complete L. sakei genomes to uncover the genetic mechanisms underlying these adaptations. Phylogenetic analysis divided the species into three distinct clades that did not correlate with the source of isolation and did not suggest any niche-specific evolutionary direction. The pan-genome analysis revealed a substantial core genome alongside a diverse genetic repertoire, indicating both high genetic conservation and adaptability. Predicted growth rates based on codon use bias analysis suggest that L. sakei strains have an overall faster growth rate and may be able to efficiently dominate in competitive environments. Plasmid analysis revealed a variety of plasmids carrying genes essential for carbohydrate metabolism, enhancing L. sakei's ability to thrive in various fermentation substrates. It was also found that the number of genes belonging to the GH1 family amongst sugar metabolism-related genes present on chromosomes and plasmids varies between strains and that AA1, which is involved in alcohol oxidation, has been acquired from plasmids. blast analysis revealed that some strains have environmental adaptation gene clusters of cell surface polysaccharides that may mediate attachment to food and mucosa. The knowledge gleaned from this study lays a solid foundation for future research aimed at harnessing the genetic traits of L. sakei strains for industrial and health-related applications.},
}

*Genome, Bacterial
Phylogeny
*Adaptation, Physiological/genetics
Plasmids/genetics
*Latilactobacillus sakei/genetics/classification/physiology/growth & development/metabolism
Genomics
Carbohydrate Metabolism/genetics
Fermentation
Genetic Variation

@article {pmid40608125,
year = {2025},
author = {León-Lemus, A and Martínez-García, M and Cabirol, N and Campos, JE and Monsalvo-Reyes, A},
title = {Draft genome sequence and comparative genomic analysis of Halomonas salifodinae strain A2 isolated from the Zapotitlán Salinas Valley, Puebla, Mexico.},
journal = {Extremophiles : life under extreme conditions},
volume = {29},
number = {2},
pages = {28},
pmid = {40608125},
issn = {1433-4909},
mesh = {*Halomonas/genetics/isolation & purification/classification ; *Genome, Bacterial ; Mexico ; Phylogeny ; },
abstract = {In this study, we report the draft genome sequence of strain A2. The genome size was 3.8 Mbp, the GC content was 67.4%, and it was predicted to contain 3520 protein-coding genes, 62 tRNA genes, 8 rRNA genes, and 4 snRNA genes. Phylogenetic analysis of the 16S rRNA gene in different databases suggests that strain A2 belongs to Halomonas salifodinae. Also, Multilocus Sequence Typing analysis confirms that A2 is closely related to H. salifodinae. Phylogenomic of the core genes and comparative genomic analysis using the Average Nucleotide Identity, digital DNA-DNA Hybridization, Average Amino acid Identity, the Percentage of Conserved Proteins values indicators, and the Genome Taxonomy Database indicates that strain A2 is identified as H. salifodinae and suggest that this species has a closer phylogenetic relationship with the genus Bisbaumannia than with Halomonas. The pangenomic analysis of A2 against 100 reference genomes of described Halomonas and another related genus shows 136,122 genes that comprise the pangenome with 317 core genes, 3457 shell genes, 132,332 accessory genome genes, and 691 unique genes. A2 has 261 signature genes that it shares only with Bisbaumannia and Halomonas salifodinae. For strain A2 we found 29 genes for secretion systems, 23 genes for Na[+] and K[+] ion transport, 6 Biosynthetic Gene Clusters groups, a total of 12 genomic islands, an 8.2 kb gene prophage region, 15 regions associated with CRISPR and one CAS-TypeIF cas gene cluster region, 12 genes of biotechnological importance, 38 unique genes essential for adaptability and biotechnological relevance, as well as, 35 genes for the synthesis of compatible solutes. Comparative genomics analysis shows that strain A2 has multiple unique genetic features that could be useful for biotechnological applications. The result of this study places the species Halomonas salifodinae in a very close relationship with the genus Bisbaumannia than with Halomonas, so its reclassification to the genus Bisbaumannia is proposed for future validation.},
}

*Halomonas/genetics/isolation & purification/classification
*Genome, Bacterial
Mexico
Phylogeny

@article {pmid40601639,
year = {2025},
author = {Tareq, MMI and Biswas, S and Rahman, FA and Siam, LS and Tauhida, SJ and Ahmed, S and Shovon, HJ and Ahmed, M and Jerin, KA and Hasan, MN},
title = {Development of a potential vaccine against Capripox virus implementing reverse vaccinology and pan-genomic immunoinformatics.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0326310},
pmid = {40601639},
issn = {1932-6203},
mesh = {*Capripoxvirus/immunology/genetics ; Animals ; *Viral Vaccines/immunology ; Epitopes, T-Lymphocyte/immunology ; Epitopes, B-Lymphocyte/immunology ; Vaccinology/methods ; Computational Biology/methods ; *Poxviridae Infections/prevention & control/immunology/veterinary/virology ; *Vaccine Development ; Sheep ; Goats ; Viral Proteins/immunology/chemistry/genetics ; Immunoinformatics ; },
abstract = {CPXV is responsible for animal diseases affecting cattle (Lumpy Skin Disease), sheep (Sheeppox), and goats (Goatpox). During outbreaks, these diseases have huge socio-economic effects. Now, no vaccination that is effective against sheeppox, goatpox, and lumpy skin disease is available. This work used an immunoinformatic methodology to discover possible targets for vaccination against CPXV. After the 122 CPXV proteins were obtained from the Vipr database, several investigations into the proteins' virulence, antigenicity, toxicity, solubility, and IFN-g activity were carried out. Three outer membrane and extracellular proteins were selected to predict their B-cell and T-cell epitopes based on certain distinctive features. These epitopes exhibit conservation across three species, namely Sheeppox virus (SPPV), Goatpox virus (GTPV), and Lumpy skin disease virus (LSDV) of CPXV. This will provide more comprehensive immunity against diverse virus strains worldwide. Nine MHC-I, MHC-II, and B-cell epitopes were selected to generate multi-epitope vaccine constructions. These constructs were linked using AAY, GPGPG, and KK linkers and 50S ribosomal protein L7/L12 adjuvants to enhance the immunogenicity of the vaccines. Molecular modeling and structural validation enabled the production of vaccine constructs with high-quality 3D structures. CPXV (Protein A35, Protein Resolve A22, and Scaffold Protein) was selected for further analysis because of its varied immunological and physiochemical properties (Number of Amino Acids, Molecular Weight (Daltons), Theoretical pI Aliphatic index, Grand average of hydropathicity (GRAVY), Instability index GC content, and CAI value) and docking scores. The bacterial expression system showed notable gene expression for the CPXV-V5 vaccine, as shown by computational cloning analysis. Molecular dynamics (MD) simulations revealed structural stability and long-term epitope visibility, implying strong immune responses after delivery. These results suggest that the developed vaccines might be quite safe and effective in practical settings, and they offer a solid foundation for further experimental verification.},
}

*Capripoxvirus/immunology/genetics
Animals
*Viral Vaccines/immunology
Epitopes, T-Lymphocyte/immunology
Epitopes, B-Lymphocyte/immunology
Vaccinology/methods
Computational Biology/methods
*Poxviridae Infections/prevention & control/immunology/veterinary/virology
*Vaccine Development
Sheep
Goats
Viral Proteins/immunology/chemistry/genetics
Immunoinformatics

@article {pmid40600140,
year = {2025},
author = {Shahed, K and Islam, SI and Sangsawad, P and Jung, WK and Permpoonpattana, P and Linh, NV},
title = {Benchmarking pangenome dynamics and horizontal gene transfer in Mycobacterium marinum evolution.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1537826},
pmid = {40600140},
issn = {1664-302X},
abstract = {Horizontal gene transfer (HGT) is a key driver of microbial evolution, promoting genetic diversity and contributing to the emergence of antibiotic resistance. This study explores the pangenome dynamics and HGT in Mycobacterium marinum (M. marinum), a close relative of Mycobacterium tuberculosis. Multiple pangenome datasets were analyzed to quantify gene gain, loss, and pangenome openness, utilizing Panstripe and a Generalized Linear Model (GLM) framework to assess gene presence/absence across strains. Additionally, a comparative benchmarking analysis of gene ontology (GO) annotations were conducted using eggNOG and InterProScan to evaluate their functional annotation accuracy. Our findings demonstrated significant differences in gene gain and loss rates, suggesting variations in annotation accuracy and the presence of mobile genetic elements (MGE). Single nucleotide polymorphisms (SNPs) were also identified, highlighting the genetic variability that may impact strain-specific traits such as pathogenicity and antibiotic resistance. Pangenome of M. marinum was characterized as highly open, with substantial variability in gene content, reflecting ongoing genetic exchange and adaptability. Functional annotation benchmarking demonstrated that eggNOG and InterProScan provided complementary insights, with each tool excelling in distinct strengths of gene function identification. Overall, these findings highlight the complex interplay between HGT, pangenome evolution, and antibiotic resistance in M. marinum, and the analytical framework presented here provides a robust approach for future studies aiming to inform therapeutic interventions and vaccine development.},
}

@article {pmid40598134,
year = {2025},
author = {He, RS and Zhao, R and Lin, JJ and Li, Y and Kong, XZ and Xu, JX and Wu, JH and Bu, XJ and Zhang, YJ and Sun, Y},
title = {Construction of the graph genomes of Takifugu provides novel insights into the genomic mechanisms of population structure and migratory traits.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {195},
pmid = {40598134},
issn = {1741-7007},
support = {31871964, 31801738, 32302320//National Natural Science Foundation of China/ ; CARS-01-40//National Rice Industry Technology System Project/ ; 202003a06020009//Major Science and Technology Projects in Anhui Province/ ; },
mesh = {Animals ; *Takifugu/genetics/physiology ; *Genome ; *Genetic Variation ; *Animal Migration ; Gene Flow ; },
abstract = {BACKGROUND: The genus Takifugu includes highly valued fish species known for their delicate flavor, making them popular in multiple countries. However, many species from this genus face significant threats. In order to better understand the genetic diversity and evolutionary dynamics of Takifugu, a syntelog-based pan-genome and graph genome were constructed using the data of seven Takifugu species.

RESULTS: The analysis of 28,085 syntelog groups (SGs) composed of protein-coding genes revealed that only 57.3% of the SGs were shared among all individuals, whereas the remaining genes presented presence-absence variation (PAV) across the seven genomes. Using the graph genome as a reference, a population of 160 Takifugu individuals was analyzed, from which 20,133,471 SNPs, 4,606,141 Indels, and 152,200 SVs were identified. The gene flow analysis revealed directional gene flow from Takifugu bimaculatus and Takifugu flavidus to Takifugu oblongus. Notably, a 51-bp insertion in the ABCB9 gene differed significantly in frequency between the two migratory populations, suggesting the potential role of this gene in the migratory behavior of these species. Additionally, the expression profiles from 13 tissues or organs (brain, gallbladder, gill, gonad, heart, kidney, liver, muscle, pituitary, skin, spleen, stomach, and swim bladder) revealed a unique expression pattern in the liver, with the tissue-specific genes exhibiting evolutionary conservation to varying degrees. The highest proportion of core genes was found in the pituitary, whereas the lowest was found in the spleen.

CONCLUSIONS: This study provides comprehensive genomic resources that enhance the understanding of the genetic diversity and evolutionary dynamics of Takifugu species. The findings offer insights for research on both breeding and conservation of Takifugu.},
}

Animals
*Takifugu/genetics/physiology
*Genome
*Genetic Variation
*Animal Migration
Gene Flow

@article {pmid40594904,
year = {2025},
author = {Sayem, M and Rafi, MA and Mishu, ID and Mahmud, Z},
title = {Comprehensive genomic analysis reveals virulence and antibiotic resistance genes in a multidrug-resistant Bacillus cereus isolated from hospital wastewater in Bangladesh.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22915},
pmid = {40594904},
issn = {2045-2322},
mesh = {*Bacillus cereus/genetics/pathogenicity/isolation & purification/drug effects ; *Wastewater/microbiology ; Bangladesh ; *Drug Resistance, Multiple, Bacterial/genetics ; Phylogeny ; Hospitals ; Virulence/genetics ; Genome, Bacterial ; Whole Genome Sequencing ; Genomics/methods ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Humans ; },
abstract = {Hospital wastewater represents a significant reservoir for antimicrobial-resistant bacteria, including multidrug-resistant (MDR) Bacillus cereus, a pathogen of growing concern due to its potential impact on public health and environmental safety. This study characterizes the genomic features, antimicrobial resistance (AMR) mechanisms, and virulence potential of Bacillus cereus MBC, isolated from hospital wastewater in Dhaka, Bangladesh. Using whole-genome sequencing (WGS) and advanced bioinformatics, we analyzed the isolate's taxonomy, phylogenetics, functional annotation, and biosynthetic potential. The genome, spanning 5.6 Mb with a GC content of 34.84%, contained 5,881 protein-coding sequences, including 1,424 hypothetical proteins, and 28 genes associated with AMR. Phylogenetic analysis revealed a close genetic relationship with Bacillus cereus ATCC 14579, sharing virulence factors such as hemolysin BL (HBL), non-hemolytic enterotoxin (NHE), and cytotoxin K (CytK), all contributing to its pathogenicity. The ability to form biofilms further enhances the strain's persistence and resistance in hospital environments. AMR profiling identified genes conferring resistance to beta-lactams (e.g., BcI, BcII, BcIII), tetracyclines (tetB(P)), glycopeptides (vanY), and fosfomycin, highlighting the bacterium's capacity to resist a wide array of antibiotics. Functional annotation revealed metabolic pathways involved in iron acquisition and the biosynthesis of siderophores such as petrobactin and bacillibactin, reinforcing the bacterium's adaptability in nutrient-limited environments. Mobile genetic elements, including prophages, CRISPR-Cas systems, and transposable elements, suggest significant horizontal gene transfer (HGT), enhancing genetic plasticity and resistance spread. Pangenomic analysis, involving 125 B. cereus strains, revealed a high degree of genetic diversity and close relationships with strains from clinical, food, and agricultural environments, emphasizing the overlap between clinical and environmental reservoirs of resistance. The strain's isolation from hospital wastewater underscores the complex interplay between environmental contaminants and bacterial evolution, which fosters MDR traits. Our findings underscore the urgent need for enhanced genomic surveillance and wastewater management strategies to mitigate the spread of MDR B. cereus and AMR genes in hospital environments.},
}

*Bacillus cereus/genetics/pathogenicity/isolation & purification/drug effects
*Wastewater/microbiology
Bangladesh
*Drug Resistance, Multiple, Bacterial/genetics
Phylogeny
Hospitals
Virulence/genetics
Genome, Bacterial
Whole Genome Sequencing
Genomics/methods
Anti-Bacterial Agents/pharmacology
Virulence Factors/genetics
Humans

@article {pmid40594015,
year = {2025},
author = {Zaman, N and Gul, K and Khurram, K and Azam, SS},
title = {Molecular insights into pangenome localization and constructs design for Hemophilus influenza vaccine.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22316},
pmid = {40594015},
issn = {2045-2322},
mesh = {Humans ; Molecular Dynamics Simulation ; *Haemophilus influenzae/immunology/genetics ; Bacterial Proteins/immunology/genetics/chemistry ; *Genome, Bacterial ; *Influenza Vaccines/immunology/genetics ; *Influenza, Human/prevention & control/immunology ; Epitopes/immunology/genetics ; },
abstract = {Haemophilus influenza, a major contributor to respiratory infections such as pneumonia, meningitis, sinusitis, chronic bronchitis, and acute otitis, poses a significant public health challenge, driven by rising antibiotic resistance particularly among the non-typeable H. influenza (NTHi) strains given their ability to evade immune surveillance. To address this, we employed a comprehensive immunoinformatics pipeline integrated with extensive pan-genome analysis of 59 strains of H. influenzae to design a novel multiepitope vaccine (MEV) candidate targeting most virulent and clinically significant proteins. Key surface exposed and virulence associated proteins, including Protein E, PilA, Protein D, P4, TolC, YadA, and HifC were prioritized based on their roles in bacterial adhesion, immune evasion, biofilm formation, and nutrient acquisition. Advanced in silico epitope prediction and verification strategies were utilized to map highly immunogenic regions across these proteins, followed by codon optimization to enhance expression efficiency in human systems. To further stabilize the vaccine construct, we performed disulfide engineering to enhance structural integrity and resilience. Comprehensive validation through in silico immune simulations, molecular dynamics (MD) simulations and binding free energy calculations confirmed the structural stability, immunogenic potential, and strong receptor affinity of the MEV candidate. Phylogenetic and virulence factor analysis further corroborated the broad coverage of the pathogenic relevance of the selected proteins. Together, our integrative approach presents a robust pipeline for rational vaccine design, offering a promising avenue toward combating multidrug resistant and immune evasive H. influenza strains.},
}

Humans
Molecular Dynamics Simulation
*Haemophilus influenzae/immunology/genetics
Bacterial Proteins/immunology/genetics/chemistry
*Genome, Bacterial
*Influenza Vaccines/immunology/genetics
*Influenza, Human/prevention & control/immunology
Epitopes/immunology/genetics

@article {pmid40591735,
year = {2025},
author = {Xie, Z and Zheng, H and Cheng, S and Yu, H and Yu, X and Wang, C and Wang, J and Yao, B and Jiang, X and Hu, Y and Jian, A and He, X and Gao, J and Chen, M and Chen, Y and Zhu, Y and Ren, Y and Cheng, Z and Lei, C and Lin, Q and Wang, X and Guo, X and Tian, Y and Liu, S and Liu, X and Jiang, L and Wu, C and Zhu, S and Zhao, Z and Wan, J},
title = {Chromosomal translocations are a significant driver of hybrid sterility in rice.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyaf126},
pmid = {40591735},
issn = {1943-2631},
abstract = {Hybrid sterility is a major barrier in exploiting hybrid vigor in rice grains produced by crossing distantly related parents. While genetic mechanisms such as the killer-protector system have been extensively studied, novel systems underlying hybrid sterility remain poorly characterized. Here, a novel hybrid sterility system governed by two tightly pseudolinked loci SGA1 (on chromosome 1) and SGA2 (on chromosome 2) is reported, which induces semi-sterility in male and female gametes during hybridization between the indica and japonica subspecies. Chromosomal translocations were proposed as the basis for pseudolinkage and unbiased segregation, supported by cytological evidence of meiotic quadrivalent configurations and translocation breakpoint sequences. Gametophytic sterility was identified as the primary driver of dual male-female semi-sterility in translocated heterozygotes. Furthermore, large-segment chromosomal translocations are found to be widespread in rice. Analysis of 120 pangenomic rice accessions revealed that chromosomal translocations are prevalent among cultivars, with one-third exhibiting large translocations (>500-kb). Translocation breakpoints were mainly localized in intergenic and intronic regions, and the disrupted genes were identified as predominantly transposons and retrotransposons. Besides, large translocations were validated through sequence analysis and phenotypic assays. Overall, this study establishes chromosomal translocations as a critical driver of hybrid sterility and provides new insights into heterosis constraints.},
}

@article {pmid40586540,
year = {2025},
author = {Bulka, O and Edwards, EA},
title = {Complete metagenome-assembled genome sequence of Solidesulfovibrio sp. DCME from a dichloromethane dechlorinating microbial community.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0051525},
doi = {10.1128/mra.00515-25},
pmid = {40586540},
issn = {2576-098X},
abstract = {Here, we announce the closed genome of Solidesulfovibrio sp. DCME, assembled from metagenomic sequencing of an anaerobic dichloromethane mineralizing enrichment culture. The Solidesulfovibrio genus is known to cycle hydrogen, a key process for facilitating dichloromethane mineralization, which nominates this microbe as an important player in its microbial community.},
}

@article {pmid40586315,
year = {2025},
author = {Schulman, AH and Hartung, F and Smulders, MJM and Sundström, JF and Wilhelm, R and Rognli, OA and Metzlaff, K},
title = {Proposed EU NGT legislation in light of plant genetic variation.},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/pbi.70228},
pmid = {40586315},
issn = {1467-7652},
support = {210021//Jane ja Aatos Erkon Säätiö/ ; },
abstract = {The European Commission (EC) proposal for New Genomic Techniques (NGTs) of July 2023 specifies that Category 1 NGT (NGT1) plants, which are considered equivalent to conventional plants, that is those obtainable by conventional plant breeding or mutagenesis, may differ from the recipient or parental plant by no more than 20 insertions, which cannot be longer than 20 bp; deletions can be no more than 20 but of any size. Here, we examine the proposed 20/20 NGT1 limit against the background of the theoretical considerations and older data used to frame it and in light of recent data from highly contiguous long-read assemblies for reference genomes and pangenomes. We find that current genomic data indicate that natural variation in germplasm used by breeders is much greater than earlier understood and that both conventional breeding and mutagenesis can introduce genomic changes that are both more extensive in size and more frequent than the NGT Category 1 '20 insertions of maximum 20 bp' limit would allow. Furthermore, natural variation also scales with genome size and complexity, a factor not considered in the EC proposal. We conclude that the proposed cut-offs under which an NGT plant is considered equivalent to conventional plants do not align with what is observed in nature, conventional breeding and mutagenesis. Updating the 20/20 rule to broader limits would facilitate breeding for climate resilience, farming sustainability and nutritional security, while ensuring that NGT1 plants are equivalent to conventional ones.},
}

@article {pmid40585573,
year = {2025},
author = {Isobe, S},
title = {Unlocking the potential of genetic resources in the Pangenome era.},
journal = {Breeding science},
volume = {75},
number = {1},
pages = {1},
pmid = {40585573},
issn = {1344-7610},
}

@article {pmid40585572,
year = {2025},
author = {Sato, K},
title = {Genetic resources and pangenome analysis of barley.},
journal = {Breeding science},
volume = {75},
number = {1},
pages = {13-20},
pmid = {40585572},
issn = {1344-7610},
abstract = {Barley (Hordeum vulgare) is widely cultivated, ranking fourth in cultivation area among cereal crops worldwide. Many wild and cultivated barley accessions have been collected and preserved in crop genebanks throughout the world. Barley has a large genome (~5 Gbp) that has recently been sequenced and assembled at the chromosome level by the international research community. The community also is sequencing accessions representing the diversity of both domesticated and wild barley to provide genome-wide genotyping information for pangenome analysis. Given that the pangenome represents the universe of genome sequences existing in a species, the long-term goal of this project is to obtain high-quality genome sequences of the major barley accessions worldwide. As each accession is annotated, the capacity to explore structural differences is enhanced by the increased understanding of the diversity of the barley genome, which will facilitate efficient development of cultivars for human consumption. This review describes our current knowledge of barley genome diversity and proposes future directions for basic and applied research of the barley pangenome.},
}

@article {pmid40585571,
year = {2025},
author = {Aoyagi Blue, Y and Iimura, H and Sato, MP and Shirasawa, K},
title = {The impact of telomere-to-telomere genome assembly in the plant pan-genomics era.},
journal = {Breeding science},
volume = {75},
number = {1},
pages = {3-12},
pmid = {40585571},
issn = {1344-7610},
abstract = {Advances in sequencing technologies have enabled the determination of genome sequences of multiple lines within a single species. Comparative analysis of multiple genome sequences reveals all genes present within a species, providing insight into the genetic mechanisms that lead to the establishment of species. Highly accurate pan-genome analysis requires telomere-to-telomere gapless genome assembly, providing an ultimate genome sequence that covers all chromosomal regions without any undetermined nucleotide sequences. This review describes the genome sequencing technologies and sophisticated bioinformatics required for telomere-to-telomere gapless genome assembly, as well as a genetic mapping that can evaluate the accuracy of telomere-to-telomere genome assembly. Pan-genome analyses may contribute to the understanding of genetic mechanisms not only within a single species but also across species.},
}

@article {pmid40585570,
year = {2025},
author = {Shigita, G and Tanaka, K and Kato, K},
title = {Current and future pangenomic research in cucurbit crops.},
journal = {Breeding science},
volume = {75},
number = {1},
pages = {34-50},
doi = {10.1270/jsbbs.24048},
pmid = {40585570},
issn = {1344-7610},
abstract = {Pangenomics is the exploration and characterization of the full spectrum of genetic variation within a species or a given taxonomic clade. Driven by the accelerating decline in sequencing costs and the widespread adoption of long-read sequencing technologies, the "wave" of pangenomics is now hitting various major crops, uncovering substantial intraspecific diversity previously underestimated and neglected. This includes crops belonging to the gourd family (Cucurbitaceae), such as cucumber (Cucumis sativus), melon (Cucumis melo), watermelon (Citrullus lanatus), wax gourd (Benincasa hispida), and bottle gourd (Lagenaria siceraria), all of which are important on a global or regional scale. In this review, we consolidate the findings from all nine pangenomic studies reported as of June 2024, on the five cucurbit crops listed above. This summarizes the current state of pangenomics in the family. We then highlight remaining knowledge gaps for each crop, and propose further research to fill these gaps. Finally, we discuss how pangenomics will shape the future of crop breeding and expand the framework of crop genetic resources in synergy with other technological advances. These insights would apply not only to cucurbits but also to crops across diverse families.},
}

@article {pmid40585569,
year = {2025},
author = {Yoshikawa, T and Sato, Y},
title = {Usage of wild Oryza germplasms for breeding in pan-genomics era.},
journal = {Breeding science},
volume = {75},
number = {1},
pages = {51-60},
doi = {10.1270/jsbbs.24050},
pmid = {40585569},
issn = {1344-7610},
abstract = {One approach to sustainable agricultural production in a changing global environment is the effective utilization of unutilized germplasms. Among these, crop wild relatives (CWRs) represent valuable germplasms that retain the diversity lost during domestication. The genus Oryza has two cultivated species and 22 wild species. One of the cultivated species, Oryza sativa, produces the rice that is the staple food for half of the world's population. We are responsible for the maintenance and distribution of wild Oryza genetic resources held by Japan's National Institute of Genetics (NIG). The NIG has collected the genome sequences of numerous wild Oryza accessions, aiming at understanding and promoting the utilization of Oryza germplasm for both basic and applied sciences, such as breeding. The genome information of many wild Oryza germplasms deciphered by multiple groups is publicly available in databases, allowing for pangenome analysis. This review mainly introduces the wild Oryza genetic resources held by the NIG, discusses the genome diversity revealed through genome sequencing, presents new attempts to utilize wild Oryza germplasm as novel resources enabled by genome sequencing, and discusses the challenges in further effectively utilizing wild Oryza germplasm in breeding.},
}

@article {pmid40585568,
year = {2025},
author = {Chapman, MA},
title = {Novel breeding resources for the underutilised legume, lablab, based on a pangenome approach.},
journal = {Breeding science},
volume = {75},
number = {1},
pages = {61-66},
doi = {10.1270/jsbbs.24055},
pmid = {40585568},
issn = {1344-7610},
abstract = {Individuals across a species exhibit substantial presence-absence variation, to the extent that a reference genome from a single individual only contains a subset of the species' genome. Cataloguing genome regions absent from a reference genome can therefore reveal novel genome regions, and some of this variation can be adaptive. In this work, existing short sequencing reads for the underutilised crop lablab (Lablab purpureus (L.) Sweet) were used to identify regions of the genome absent from the reference genome. Lablab is made up of two distinct gene pools, each with wild and domesticated types therefore represents an opportunity to identify gene pool-specific variation. Approximately 7.7% of the reads from eight accessions failed to map to the lablab reference genome (cv. Highworth), putatively being novel, and these were assembled and collapsed into between 735 and 12,304 contigs. Four samples were focussed on (one each wild and domesticated from each of the gene pools) and the novel contigs compared, to identify those present only in subsets of samples. Whilst the number of contigs containing sequenced with similarity to known genes in other legumes was low, there were some enriched gene ontology (GO) terms that could relate to adaptive differences between the groups and therefore contain novel genes for future lablab breeding. The approached used here has potential use in any other species.},
}

@article {pmid40579690,
year = {2025},
author = {Huang, G and Li, L and Cao, X and Lin, H},
title = {Alfalfa pan-genome unveiled-a breakthrough in alfalfa genomics-assisted breeding.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {40579690},
issn = {1869-1889},
}

@article {pmid40577690,
year = {2025},
author = {Tanaka, T and Haraguchi, Y and Todoroki, T and Saisho, D and Abiko, T and Kai, H},
title = {Reference-based chromosome-scale assembly of Japanese barley (Hordeum vulgare ssp. vulgare) cultivar Hayakiso 2.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {},
number = {},
pages = {},
doi = {10.1093/dnares/dsaf016},
pmid = {40577690},
issn = {1756-1663},
abstract = {Current advances in next generation sequencing (NGS) technology and assembling programs permits construct chromosome-level genome assemblies in various plants. In contrast to resequencing, the genome sequences provide comprehensive annotation data useful for plant genetics and breeding. Herein, we constructed a reference-based genome assembly of winter barley (H. vulgare ssp. vulgare) cv. 'Hayakiso 2' using long and short read NGS data and barley reference genome sequences from 'Morex.' We constructed 'Hayakiso 2' genome sequences covering 4.3 Gbp with 55,477 genes. Comparative genomics revealed that 14,106 genes had orthologs to two barley data, wheat (A, B and D homoeologs, respectively), and rice. From the GO analysis, 2,494 orthologs against wheat and rice but not two barley contained agricultural important genes, such as "response to biotic and abiotic stress" and "metabolic process". Phylogenetic analysis using 76 pangenome data indicated that 'Hayakiso 2' was clustered into Japanese-type genomes with unique alleles. 'Hayakiso 2' genome sequences showed known genes related to flowering and facilitated barley breeding through the development of various markers related to agronomically important alleles such as tolerance to various types of biotic and abiotic stress. Therefore, 'Hayakiso 2' genome sequences will be used for the further barley breeding.},
}

@article {pmid40573859,
year = {2025},
author = {Zhang, W and Zhou, L and Ni, D and Ni, J and Song, F and Yang, L and Zhang, D},
title = {Genetic Analysis of Lodging Resistance in 1892S Based on the T2T Genome: Providing a Genetic Approach for the Improvement of Two-Line Hybrid Rice Varieties.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
pmid = {40573859},
issn = {2223-7747},
support = {U21A20211//National Natural Science Foundation of China/ ; },
abstract = {Successfully breeding high-yield, lodging-resistant hybrid rice varieties is critical for ensuring food security. Two-line hybrid rice system plays an essential role in rice breeding, and 1892S, an important two-line sterile line, has contributed significantly to the development of over 100 hybrid rice varieties with superior agronomic traits, including lodging resistance. Despite its importance, a comprehensive understanding of the genomic basis underlying these traits in 1892S has been lacking due to the limitations of short-read sequencing technologies. To address this gap, we utilized advanced telomere-to-telomere (T2T) genome assembly techniques to generate a high-quality, gap-free genome of 1892S-the final genome comprises 12 complete chromosomes with 40,560 protein-coding genes. Comparative genomic analysis identified multiple known lodging resistance genes, including SD1, Sdt97, SBI, OsFBA2, APO1, and OsTB1, with unique allelic variations that may enhance resistance. The pan-genome analysis identified 2347 strain-specific genes in 1892S, further supporting its unique genetic advantages. This study represents the complete T2T genome assembly of a two-line sterile line and provides novel insights into the genetic foundation of lodging resistance in hybrid rice. This study highlights the genetic potential of 1892S in hybrid rice breeding and provides a model for the genomic analysis of other two-line sterile lines, offering valuable insights for improving in hybrid rice, including traits lodging resistance, yield stability, and adaptability, which are crucial for global food security.},
}

@article {pmid40572210,
year = {2025},
author = {Wang, Y and Hao, J and Gu, J and Wu, J and Zhang, Y and Liang, T and Bai, H and Cao, Q and Jiang, J and Li, L and Cao, X},
title = {Genome-Driven Functional Validation of Bacillus amyloliquefaciens Strain MEPW12: A Multifunctional Endophyte for Sustainable Sweet Potato Cultivation.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572210},
issn = {2076-2607},
support = {32471584//National Natural Science Foundation of China/ ; 32030072//National Natural Science Foundation of China/ ; KYCX22_2814//Postgraduate Research and Practice Innovation Program of Jiangsu Province/ ; },
abstract = {Sweet potato (Ipomoea batatas (L.) Lam.), as an important crop, is rich in polyphenols, vitamins, minerals, and other nutrients in its roots and leaves and is gradually gaining popularity. The use of endophytic bacteria to improve the quality of sweet potato can protect the environment and effectively promote the sustainable development of the sweet potato industry. In this study, 12 strains of endophytic bacteria were isolated from sweet potato. Through nitrogen fixation, phosphorus solubilization, indoleacetic acid production, siderophore production, ACC deaminase production, and carboxymethyl cellulose production, three strains with multiple biological activities were screened out. Among them, MEPW12 had the most plant growth-promoting functions. In addition, MEPW12 promoted host chlorophyll accumulation and inhibited pathogen growth and colonization in sweet potato roots and can utilize various carbon sources and salts for growth. It can also grow in extreme environments of high salt and weak acid. MEPW12 was identified as Bacillus amyloliquefaciens with a genome size of 3,928,046 bp and a GC content of 46.59%. After the annotation of multiple databases, it was found that MEPW12 had multiple enzymatic activities and metabolic potential. Comparative genomics and pan-genomics analyses revealed that other Bacillus sp. strains of MEPW12 have similar functions. However, due to adaptation to different growth environments, there are still genomic differences and changes. Inoculation with MEPW12 induced the high expression of IbGH3.10, IbERF1, and other genes, thereby promoting the growth of sweet potatoes. Bacillus amyloliquefaciens strain MEPW12 is a sweet potato endophyte with multiple growth-promoting functions, which can promote the growth of sweet potato seedlings. This study provides new microbial resources for developing microbial agents and improving the quality of sweet potatoes.},
}

@article {pmid40572063,
year = {2025},
author = {Shi, J and Su, H and He, S and Dai, S and Mao, H and Wu, D},
title = {Pan-Genomic Insights into Rumen Microbiome-Mediated Short-Chain Fatty Acid Production and Regulation in Ruminants.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572063},
issn = {2076-2607},
abstract = {The rumen microbiome represents a cornerstone of ruminant digestive physiology, orchestrating the anaerobic fermentation of plant biomass into short-chain fatty acids (SCFAs)-critical metabolites underpinning host energy metabolism, immune function, and environmental sustainability. This comprehensive review evaluates the transformative role of pan-genomics in deciphering the genetic and metabolic networks governing SCFA production in the rumen ecosystem. By integrating multi-omics datasets, pan-genomic approaches unveil unprecedented layers of microbial diversity, enabling precise identification of core functional genes and their dynamic contributions to carbohydrate degradation and SCFA biosynthesis. Notable advancements include the following: mechanistic insights into microbial community assembly and metabolic pathway regulation, highlighting strain-specific adaptations to dietary shifts; precision interventions for optimizing feed efficiency, such as rationally designing microbial consortia and screening novel feed additives through pan-genome association studies; and sustainability breakthroughs, demonstrating how targeted modulation of rumen fermentation can simultaneously enhance production efficiency and mitigate methane emissions. This synthesis underscores the potential of pan-genomics to revolutionize ruminant nutrition, offering a blueprint for developing next-generation strategies that reconcile agricultural productivity with environmental stewardship. The translational applications discussed herein position pan-genomics as a critical tool for advancing animal science and fostering a resilient livestock industry.},
}

@article {pmid40567591,
year = {2025},
author = {Rozanova, IV and Vodiasova, EA},
title = {Modern methods in peach (Prunus persica) genome research.},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {29},
number = {3},
pages = {358-369},
doi = {10.18699/vjgb-25-39},
pmid = {40567591},
issn = {2500-0462},
abstract = {Peach (Prunus persica (L.) Batsch) is one of the main agricultural stone fruit crops of the family Rosaceae. Modern breeding is aimed at improving the quality of the fruit, extending the period of its production, increasing its resistance to unfavorable environmental conditions and reducing the total cost of production of cultivated varieties. However, peach breeding is an extremely long process: it takes 10-15 years from hybridization of the parental forms to obtaining fruit-bearing trees. Research into peach varieties as donors of desirable traits began in the 1980s. The first version of the peach genome was presented in 2013, and its appearance contributed to the identification and localization of loci, followed by the identification of candidate genes that control the desired trait. The development of NGS has accelerated the development of methods based on the use of diagnostic DNA markers. Approaches that allow accelerating classical breeding processes include marker-oriented selection (MOS) and genomic selection. In order to develop DNA markers associated with the traits under investigation, it is necessary to carry out preliminary mapping of loci controlling economically desirable traits and to develop linkage maps. SNP-chip approaches and genotyping by sequencing (GBS) methods are being developed. In recent years, genome-wide association analysis (GWAS) has been actively used to identify genomic loci associated with economically important traits, which requires screening of large samples of varieties for hundreds and thousands of SNPs. Study on the pangenome has shown the need to analyze a larger number of samples, since there is still not enough data to identify polymorphic regions of the genome. The aim of this review was to systematize and summarize the major advances in peach genomic research over the last 40 years: linkage and physical map construction, development of different molecular markers, full genome sequencing for peach, and existing methods for genome-wide association studies with high-density SNP markers. This review provides a theoretical basis for future GWAS analysis in order to identify high-performance markers of economically valuable traits for peach and to develop genomic selection of this crop.},
}

@article {pmid40565594,
year = {2025},
author = {Saccone, S and Brancato, D and Bruno, F and Coniglio, E and Sturiale, V and Federico, C},
title = {Origin and Evolution of Genes in Eukaryotes: Mechanisms, Dynamics, and Functional Implications.},
journal = {Genes},
volume = {16},
number = {6},
pages = {},
pmid = {40565594},
issn = {2073-4425},
mesh = {Humans ; *Evolution, Molecular ; Animals ; *Eukaryota/genetics ; Gene Duplication ; Gene Transfer, Horizontal ; Selection, Genetic ; },
abstract = {The origin and evolution of genes are central themes in evolutionary biology and genomics, shedding light on how molecular innovations shape biological complexity and adaptation. This review explores the principal mechanisms underlying gene emergence in eukaryotes, including gene duplication, de novo gene birth, horizontal gene transfer, viral gene domestication, and exon shuffling. We examine the population dynamics that govern the fixation of new genes, their functional integration, and the selective forces acting upon them-from purifying selection to adaptive innovation. Examples such as NOTCH2NL and SRGAP2C, which originated through recent segmental duplications followed by neofunctionalization, illustrate how duplicate-derived de novo genes can play a key role in human brain development. In addition, we highlight the emerging relevance of nuclear architecture in determining the evolutionary fate of new genes, offering a spatial dimension to gene innovation. We also discuss methodological approaches for detecting new genes and inferring selection, and finally, we highlight the emerging role of the human pangenome in revealing hidden gene diversity and its implications for evolutionary and biomedical research. Understanding gene innovation not only enhances our grasp of evolutionary processes but also informs clinical studies on disease susceptibility and human uniqueness.},
}

Humans
*Evolution, Molecular
Animals
*Eukaryota/genetics
Gene Duplication
Gene Transfer, Horizontal
Selection, Genetic

@article {pmid40560760,
year = {2025},
author = {Sia, CM and Ambrose, RL and Valcanis, M and Andersson, P and Ballard, SA and Howden, BP and Williamson, DA and Pearson, JS and Ingle, DJ},
title = {Distinct adaptation and epidemiological success of different genotypes within Salmonella enterica serovar Dublin.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {40560760},
issn = {2050-084X},
support = {GNT1174555//National Health and Medical Research Council/ ; SMRF22008//Sylvia and Charles Viertel Charitable Foundation/ ; GNT1196103//National Health and Medical Research Council/ ; GNT1195210//National Health and Medical Research Council/ ; Medical Research Future Fund FSPGN000045//Australian Government/ ; },
mesh = {*Salmonella enterica/genetics/drug effects/pathogenicity/classification ; Humans ; *Salmonella Infections/microbiology/epidemiology ; *Genotype ; Virulence ; Plasmids/genetics ; Genome, Bacterial ; Serogroup ; Phylogeny ; Australia/epidemiology ; Genomic Islands ; Drug Resistance, Bacterial ; *Adaptation, Physiological ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Salmonella Dublin is a host-adapted, invasive nontyphoidal Salmonella (iNTS) serovar that causes bloodstream infections in humans and demonstrates increasing prevalence of antimicrobial resistance (AMR). Using a global dataset of 1303 genomes, coupled with in vitro assays, we examined the evolutionary, resistance, and virulence characteristics of S. Dublin. Our analysis revealed strong geographical associations between AMR profiles and plasmid types, with highly resistant isolates confined predominantly to North America, linked to IncC plasmids co-encoding AMR and heavy metal resistance. By contrast, Australian isolates were largely antimicrobial-susceptible, reflecting differing AMR pressures. We identified two phylogenetically distinct Australian lineages, ST10 and ST74, with a small number of ST10 isolates harbouring a novel hybrid plasmid encoding both AMR and mercuric resistance. Whereas the ST10 lineage remains globally dominant, the ST74 lineage was less prevalent. ST74 exhibited unique genomic features including a larger pan genome compared to ST10 and the absence of key virulence loci, including Salmonella pathogenicity island (SPI)-19 which encodes a type VI secretion system (T6SS). Despite these genomic differences, the ST74 lineage displayed enhanced intracellular replication in human macrophages and induced less pro-inflammatory responses compared with ST10, suggesting alternative virulence strategies that may support systemic dissemination of ST74. The Vi antigen was absent in all ST10 and ST74 genomes, highlighting challenges for serotyping and vaccine development, and has implications for current diagnostic and control strategies for S. Dublin infections. Collectively, this study represents the most comprehensive investigation of S. Dublin to date and, importantly, has revealed distinct adaptations of two genotypes within the same serovar, leading to different epidemiological success. The regional emergence and evolution of distinct S. Dublin lineages highlight the need to understand the divergence of intra-serovar virulence mechanisms which may impact the development of effective control measures against this important global pathogen.},
}

*Salmonella enterica/genetics/drug effects/pathogenicity/classification
Humans
*Salmonella Infections/microbiology/epidemiology
*Genotype
Virulence
Plasmids/genetics
Genome, Bacterial
Serogroup
Phylogeny
Australia/epidemiology
Genomic Islands
Drug Resistance, Bacterial
*Adaptation, Physiological
Anti-Bacterial Agents/pharmacology

@article {pmid40559531,
year = {2025},
author = {Ajmi, N and Duman, M and Ay, H and Saticioglu, IB},
title = {Genomic and Pangenomic Insights into Aeromonas salmonicida subsp. oncorhynchi subsp. nov.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
pmid = {40559531},
issn = {2076-0817},
support = {TGA-2024-1797//Research Fund of Bursa Uludag University/ ; },
mesh = {*Aeromonas salmonicida/genetics/classification/isolation & purification/pathogenicity ; Animals ; Phylogeny ; *Genome, Bacterial ; Virulence Factors/genetics ; *Oncorhynchus mykiss/microbiology ; Genomics ; *Fish Diseases/microbiology ; *Gram-Negative Bacterial Infections/microbiology/veterinary ; Whole Genome Sequencing ; Plasmids/genetics ; },
abstract = {The strain A-9[T], isolated from Oncorhynchus mykiss (rainbow trout) in a Turkish aquaculture facility, was characterized through integrated phenotypic, phylogenetic, and genomic analyses. Whole-genome sequencing revealed a 5.21 Mb circular chromosome (GC content: 58.16%) and three plasmids encoding proteins for mobilization and toxin-antitoxin systems. Multilocus phylogenetic analysis (MLPA) using seven housekeeping genes supported the distinct lineage of A-9[T]. Digital DNA-DNA hybridization (77.6-78.6%) and average nucleotide identity values (96.59-97.58%) confirmed taxonomic divergence from all currently recognized A. salmonicida subspecies. Comparative proteomic and pangenomic analyses identified 328 strain-specific genes, including virulence factors, secretion system components (Type II and Type VI), and efflux-related proteins. Although genes encoding Type III secretion systems and biofilm formation were absent, A-9[T] harbored a broad virulence gene repertoire and resistance determinants, including OXA-956, cphA5, and FOX-20, supporting a multidrug-resistant phenotype. Based on its genomic, phenotypic, and functional distinctiveness, we propose the novel taxon Aeromonas salmonicida subsp. oncorhynchi subsp. nov. (type strain A-9[T] = LMG 33538[T] = DSM 117494[T]), expanding the taxonomic landscape of the A. salmonicida complex and offering insights into fish-associated bacterial evolution.},
}

*Aeromonas salmonicida/genetics/classification/isolation & purification/pathogenicity
Animals
Phylogeny
*Genome, Bacterial
Virulence Factors/genetics
*Oncorhynchus mykiss/microbiology
Genomics
*Fish Diseases/microbiology
*Gram-Negative Bacterial Infections/microbiology/veterinary
Whole Genome Sequencing
Plasmids/genetics

@article {pmid40558202,
year = {2025},
author = {Chaichana, N and Suwannasin, S and Boonsan, J and Yaikhan, T and Klaysubun, C and Singkhamanan, K and Wonglapsuwan, M and Pomwised, R and Konglue, S and Chema, R and Saivaew, M and Surachat, K},
title = {Genomic Characterization and Safety Evaluation of Enterococcus lactis RB10 Isolated from Goat Feces.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
pmid = {40558202},
issn = {2079-6382},
abstract = {Background: The genus Enterococcus includes a diverse group of bacteria that are commonly found in the gastrointestinal tracts of humans and animals, as well as in various environmental habitats. Methods: In this study, Enterococcus lactis RB10, isolated from goat feces, was subjected to comprehensive genomic and functional analysis to assess its safety and potential as a probiotic strain. Results: The genome of E. lactis RB10, with a size of 2,713,772 bp and a GC content of 38.3%, was assembled using Oxford Nanopore Technologies (ONT). Genome annotation revealed 3375 coding sequences (CDSs) and highlighted key metabolic pathways involved in carbohydrate, protein, and amino acid metabolism. The strain was susceptible to important antibiotics, including ampicillin, chloramphenicol, tetracycline, and vancomycin, but exhibited resistance to aminoglycosides, a common trait in Enterococcus species with non-hemolytic activity. Genomic analysis further identified two intrinsic antimicrobial resistance genes (ARGs). The strain also demonstrated antimicrobial activity against Bacillus cereus DMST 11098 and Salmonella Typhi DMST 22842, indicating pathogen-specific effects. Key genes for adhesion, biofilm formation, and stress tolerance were also identified, suggesting that RB10 could potentially colonize the gut and compete with pathogens. Moreover, the presence of bacteriocin and secondary metabolite biosynthetic gene clusters suggests its potential for further evaluation as a biocontrol agent and gut health promoter. Conclusions: However, it is important to note that E. lactis RB10 was isolated from goat feces, a source that may harbor both commensal and opportunistic bacteria, and therefore additional safety assessments are necessary. While further validation is needed, E. lactis RB10 exhibits promising probiotic properties with low pathogenic risk, supporting its potential use in food and health applications.},
}

@article {pmid40556891,
year = {2025},
author = {Chekole, WS and Potgieter, L and Adamu, H and Sternberg-Lewerin, S and Tessema, TS and Magnusson, U},
title = {Genomic insights into antimicrobial resistance and virulence of E. coli in central Ethiopia: a one health approach.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1597580},
pmid = {40556891},
issn = {1664-302X},
abstract = {Antimicrobial resistance is a global threat causing millions of deaths annually. The study aimed to identify antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence genes (VGs) and track their dissemination among E. coli isolates. Seventy-seven isolates from calves, environments, and human sources were studied. The study involved WGS sequencing, bacterial strains characterized; pan genome, multi-locus sequence typing, and serotyping using O-, and H-typing. The ARGs, VGs, and MGEs were identified using ABRicate against selected respective databases. A maximum likelihood SNP (single nucleotide polymorphism) tree was constructed and visualized with an interactive tree of life (IToL). Descriptive statistics were used to analyze the data. Seventy-seven of the isolates were identified as E. coli, later grouped into 5 clades and four known phylogroups. ST10 and O16:H48 were most prevalent in 12 and 42 isolates, respectively. There were about 106 unique ARGs detected between 1.3% and 91.9%, with 57 detected in 40% of isolates. In terms of ARGs, the most common were bla-ampH (90.9%), bla-AmpC1 (89.6%), tet(A) (84.4%), mdf(A) (81.8%), aph(3")-Ib (79%), sul2 (79%), aph(6)-Id (75%), and bla-PBP (70%). It was found that 95 percent (96/106) of ARGs came from at least two sources. The majority of detected ARGs exhibited high concordance between phenotypic resistance and ARGs profiles (JSI ≥ 0.5). In eight isolates, mutations in the gyrA (3) and par-C/E (5) genes led to ciprofloxacin and nalidixic acid resistance. The most common co-occurrences of ARG and MGE were Tn3 with bla-TEM-105 (34), Int1 with sul1 (13), and dhfr7 (11). Meanwhile, the most frequently detected VGs (n ≥ 71 isolates) included elfA-G, fimB-I, hcpA-C, espL, ibeC, entA, fepA-C, ompA, ecpA-E, fepD, fes, and ibeB. Nearly, 88.3% (128/1450) VGs were shared in isolates from at least two sources. ETEC (53.2%), EAEC (22.1%), and STEC (14.3%) were the three most frequently predicted pathotypes. Despite significant ST diversity, ARGs and VGs showed an extensive distribution among the study groups. These findings suggest limited clonal transmission of isolates. In comparison, the wide distribution of ARGs and VGs may be attributed to horizontal gene transfer driven by similar antibiotic selection pressures in the study area.},
}

@article {pmid40554012,
year = {2025},
author = {Qi, Y and Patel, MH and Lu, SY and Skory, CD},
title = {Genomic insights into persistence, antibiotic resistance, and intraspecific diversity of lactic acid bacterial contaminants at corn dry-grind fuel ethanol facilities.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132836},
doi = {10.1016/j.biortech.2025.132836},
pmid = {40554012},
issn = {1873-2976},
abstract = {During fuel ethanol production, fermenter tanks are persistently contaminated by lactic acid bacteria (LAB), lowering ethanol yields and causing costly shutdowns for cleaning. In this study, whole-genome sequencing was conducted for 156 Lactiplantibacillus plantarum, Levilactobacillus brevis, Limosilactobacillus fermentum, and Limosilactobacillus mucosae isolates previously obtained in a two-year longitudinal study at a U.S. Midwest corn dry-grind fuel ethanol production facility. Striking similarity between genomes for isolates collected during different years reveal the strong ability of LAB strains to persist in bioethanol fermentation facilities. Furthermore, comparison of bioethanol contaminant genomes and previously published genomes in the same species from other environments showed a smaller, closed pangenome for bioethanol contaminants, indicating their specialization for this niche. Additionally, 39 genomes contained a putative plasmid or transposable element encoding for resistance to the antibiotic virginiamycin, frequently used by fermentation facilities to control LAB contamination. Finally, comparison of L. fermentum isolates that strongly inhibited Saccharomyces cerevisiae fermentation and less inhibitory isolates suggest there may be genetic and metabolic changes underlying these differences. To our knowledge, this study represents the first large-scale genomic analysis for LAB contaminants of bioethanol production, providing new insights into the biology of industrial microbial contaminants that have enormous economic impact.},
}

@article {pmid40553877,
year = {2025},
author = {Saleem, S and Amin, W and Bhatti, F and Majid, M and Fazal, A},
title = {Nucleic acid-based strategies to mitigate stripe rust disease of wheat for achieving global food security - A review.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {145353},
doi = {10.1016/j.ijbiomac.2025.145353},
pmid = {40553877},
issn = {1879-0003},
abstract = {Wheat (Triticum aestivum), being a global staple crop, is critical in ensuring food security due to its significant nutritional value. However, it faces numerous challenges from both biotic and abiotic stresses, with fungal diseases being particularly detrimental to yield. Among these, wheat stripe rust, caused by the fungal pathogen Puccinia striiformis, poses a severe threat to wheat. Globally, 5.47 million tons of grains are lost due to the stripe rust pathogen, equivalent to a loss of USD 979 million annually; almost 88 % of the world's wheat production is susceptible to stripe rust. This review accentuates the global extensive distribution of stripe rust, detailing its causes and impact on crop productivity and mitigating approaches following traditional, genomic, and post-genomics. The mitigation approaches to wheat stripe rust have been mainly categorized into primitive (pre-genomic), modern (genomic), and next-generation (post-genomic) approaches. The primitive approaches include traditional breeding, phenotypic selection, and exotic germplasm to introduce resistance leads to early success in disease management. The advanced genomic era, with tools like QTL mapping, GWAS, marker-assisted selection, and high-throughput sequencing to deploy resistance genes, helps in precise mapping and developing high-throughput genotyping for large-scale screening and introgression of multiple resistant genes. The gene-editing approaches, including CRISPR/Cas9, RNAi, and epigenomics, now enable precise gene editing and regulation for durable resistance, together with multi-omics techniques, to identify resistant pathways and biomarkers with enhanced understanding of host-pathogen interactions and resistance mechanisms. Climate change events like shifts in rainfall patterns and rising temperatures expand the rust-prone area and pose more challenges in developing durable rust-resistant cultivars. Furthermore, the review explores using wheat's valuable genetic resources and integrating AI-based technologies to enhance stripe rust resistance by analyzing large datasets, including pathogen evolution and growth stages, allowing for timely interventions of the stripe rust epidemic. The role of multiomics approaches, particularly genomics and transcriptomics, in unraveling the genetic basis of stress tolerance is highlighted. A forward-looking framework is proposed, emphasizing the use of interdisciplinary methodologies, including big data, multi-omics, and AI-driven approaches, that hold immense promise to revolutionize wheat protection with the development of climate-resilient wheat genotypes and ensure real-time disease monitoring and precision-resistant strategies against the evolving rust pathogen.},
}

@article {pmid40553094,
year = {2025},
author = {Dobhal, S and Hugouvieux-Cotte-Pattat, N and Arizala, D and Sari, GB and Chuang, SC and Alvarez, AM and Arif, M},
title = {Dickeya ananatis sp. nov., pectinolytic bacterium isolated from pineapple (Ananas comosus).},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {6},
pages = {},
doi = {10.1099/ijsem.0.006822},
pmid = {40553094},
issn = {1466-5034},
mesh = {*Ananas/microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Nucleic Acid Hybridization ; Bacterial Typing Techniques ; Genome, Bacterial ; Sequence Analysis, DNA ; *Dickeya/classification/genetics/isolation & purification ; Multilocus Sequence Typing ; Hawaii ; Malaysia ; Plant Diseases/microbiology ; },
abstract = {Species clustering within Dickeya zeae has been recently identified as complex, encompassing validly published names, including Dickeya oryzae and Dickeya parazeae, with some strains potentially delineating new species. In this study, genomes of strains isolated from bacterial heart rot of pineapple (Ananas comosus var. comosus) on Oahu, Hawaii, along with two strains from pineapple in Malaysia, were sequenced. Orthologous average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among the sequenced genomes ranged from 98.93 to 99.9% and 91.8 to 99.9%, respectively, supporting the classification of seven strains within the same species. Comparisons of ANI and dDDH values between these seven strains and type strains of D. zeae, D. parazeae and D. oryzae ranged from 94.4-95.9% to 57.2-66.5%, respectively. These values fall below the proposed boundaries for species designation, supporting the delineation of a novel species. Phylogenetic analyses, including 16S rRNA, gapA, multi-locus sequence analysis of ten housekeeping genes, whole genome and pangenome analyses, were concordant and revealed a distinct monophyletic clade, separating these strains from other members of the D. zeae complex, with D. oryzae as the closest relative. Notably, a nitrogen fixation gene cluster comprising 28 genes, similar to the Klebsiella spp. nitrogenase gene cluster, was found in the genome of the 7 pineapple strains. Based on polyphasic approaches, including ANI, dDDH, biochemical, physiological and phylogenomic analyses, we propose the reclassification into a new species of the five pineapple strains from Hawaii A5391, A5410[T], A5611, A6136 and A6137, together with the two pineapple strains from Malaysia CFBP 1272 and CFBP 1278, previously classified as D. zeae. We propose the name Dickeya ananatis sp. nov. for this taxon, represented by the type strain A5410[T] (=ICMP 25020[T]=LMG 33197[T]).},
}

*Ananas/microbiology
*Phylogeny
RNA, Ribosomal, 16S/genetics
DNA, Bacterial/genetics
Nucleic Acid Hybridization
Bacterial Typing Techniques
Genome, Bacterial
Sequence Analysis, DNA
*Dickeya/classification/genetics/isolation & purification
Multilocus Sequence Typing
Hawaii
Malaysia
Plant Diseases/microbiology

@article {pmid40552806,
year = {2025},
author = {Beebe, MA and Paredes-Sabja, D and Kociolek, LK and Rodríguez, C and Sorg, JA},
title = {Phenotypic analysis of various Clostridioides difficile ribotypes reveals consistency among core processes.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0096425},
doi = {10.1128/aem.00964-25},
pmid = {40552806},
issn = {1098-5336},
abstract = {Clostridioides difficile infections (CDI) cause almost 300,000 hospitalizations per year, of which ~15%-30% are the result of recurring infections. The prevalence and persistence of CDI in hospital settings have resulted in an extensive collection of C. difficile clinical isolates and their classification, typically by ribotype. While much of the current literature focuses on one or two prominent epidemic ribotypes (e.g., RT027), recent years have seen several other ribotypes dominate the clinical landscape (e.g., RT106 and RT078). Some ribotypes are associated with severe disease and/or increased recurrence rates, but why certain ribotypes are more prominent or harmful than others remains unknown. Because C. difficile has a large, open pan-genome, this observed relationship between ribotype and clinical outcome could be a result of the genetic diversity of C. difficile. Thus, we hypothesize that the core biological processes of C. difficile are conserved across ribotypes/clades. We tested this hypothesis by observing the growth kinetics, sporulation, germination, production of toxin A and toxin B, bile acid sensitivity, bile salt hydrolase activity, and surface motility of 15 strains belonging to various ribotypes spanning each known C. difficile clade. In viewing these phenotypes across each strain, we see that core phenotypes (growth, germination, sporulation, and resistance to bile salt toxicity) are remarkably consistent across clades/ribotypes. This suggests that variations observed in the clinical setting may be due to unidentified factors in the accessory genome or due to unknown host factors.IMPORTANCEClostridioides difficile infections impact thousands of individuals every year, many of whom experience recurring infections. Clinical studies have reported an unexplained correlation between some clades/ribotypes of C. difficile and disease severity/recurrence. Here, we demonstrate that C. difficile strains across major clades/ribotypes are consistent in their core phenotypes. This suggests that such phenotypes are not responsible for variations in disease severity/recurrence and are ideal targets for the development of therapeutics meant to treat C. difficile-related infections.},
}

@article {pmid40552804,
year = {2025},
author = {Eichelman, MC and Meyer, MM},
title = {Assessing the conservation and targets of putative sRNAs in Streptococcus pneumoniae.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0325224},
doi = {10.1128/spectrum.03252-24},
pmid = {40552804},
issn = {2165-0497},
abstract = {UNLABELLED: RNA regulators are often found in regulatory networks and mediate growth and virulence in bacteria. Small RNAs (sRNAs) are non-coding RNAs that modulate translation initiation and mRNA degradation by base pairing. To better understand the role of sRNAs in pathogenicity, several studies identified sRNAs in Streptococcus pneumoniae; however, little functional characterization has followed. This study's goals are to (i) survey putative sRNAs in S. pneumoniae; (ii) assess the conservation of these sRNAs; and (iii) examine their predicted targets. Three previous studies in S. pneumoniae identified 287 putative sRNAs by high-throughput sequencing. This study narrows the candidates down to 58 putative sRNAs. BLAST analysis indicates that the 58 sequences are highly conserved across the S. pneumoniae pangenome, and 25 are identified sporadically in other Streptococcus species. However, only two have corresponding sequences identified across several Streptococcus species. We used four RNA-target prediction programs to predict targets for each of the 58 putative sRNAs. Across all probable predictions, six sRNAs have overlapping targets predicted by multiple programs, four targeting numerous transposase-encoding transcripts. sRNAs targeting transposase-encoding transcripts display nearly identical and perfect base pairing. One sRNA, M63 (Spd_sr37), has several probable targets in the CcpA regulon, a network responsible for global catabolite repression, suggesting a possible biological function in carbon metabolism control. Each M63-target interaction exhibits unique base pairing, increasing confidence in the biological relevance of the result. This study produces a list of S. pneumoniae putative sRNAs whose predicted targets suggest functional significance in transposon and carbon metabolism regulation.

IMPORTANCE: Previous studies identified many small RNA candidates in Streptococcus pneumoniae, several of which were hypothesized to play a role in S. pneumoniae virulence. Due to the differing sequencing methods, diverse inclusion criteria, S. pneumoniae strain differences, as well as limited follow-up, it is unclear to what extent candidates identified in different studies have overlapping sequences and functions, and their biological relevance remains ambiguous. This research aims to consolidate the candidate sRNAs across these studies and focuses attention on those that are likely to be regulatory and associated with virulence. This study's findings enhance our knowledge of the conservation of small regulatory RNAs across the many Streptococcus pneumoniae strains and highlight a handful that appear likely to have a role in growth or virulence.},
}

@article {pmid40549295,
year = {2025},
author = {Bhat, T and Kumar, M and Ballamoole, KK and Deekshit, VK and Gollapalli, P},
title = {Pangenome-based network analysis of Acinetobacter baumannii reveals the landscape of conserved therapeutic targets.},
journal = {Molecular diversity},
volume = {},
number = {},
pages = {},
pmid = {40549295},
issn = {1573-501X},
abstract = {The increasing prevalence of Acinetobacter baumannii infections and its severity demand the acute necessity for innovative therapeutic targets against it. This study employs comprehensive pangenome analysis to investigate 124 A. baumannii multidrug-resistant strains, to determine the most promising therapeutic targets derived from its core genome. Nucleotide diversity analysis of core and variable gene clusters identified key polymorphisms, suggesting significant evolutionary adaptation. Our findings revealed significant presence/absence variation (PAV) in resistance genes across strains, with 97 antimicrobial drug resistance genes identified. Two gene clusters, cluster-288 and cluster-566, harbored resistance-related genes encoding for beta-lactamase and multidrug efflux pump, respectively, were identified from the core genome that plays a pivotal role in conferring multidrug resistance. The functional enrichment analysis of these gene clusters highlighted key proteins, such as penicillin-binding proteins and outer membrane efflux proteins, as potential targets for drug design. Furthermore, we analyzed the physicochemical properties, virulence potential, active site prediction, and predicted conserved motifs. Structural predictions via 3D modeling and molecular dynamics simulations revealed high stability of key proteins, with RMSD values of 0.52 nm for outer membrane channel subunit AdeK and 0.85 nm for beta-lactamase, suggesting these proteins' potential as novel drug targets and their structural integrity under physiological conditions. Principal component analysis (PCA) highlighted distinct motion patterns within these proteins, providing insights into their functional dynamics. This research contributes to ongoing efforts to combat antibiotic resistance through innovative approaches in drug design and therapeutic interventions.},
}

@article {pmid40545607,
year = {2025},
author = {Yu, Z and Lei, T and Yi, X and Hao, Y and Wu, S and Xiao, Z and Qu, J and Li, S and Wang, L and Li, Y and Zhang, L and Pan, Y and Wang, Y and Gou, L and Jiao, Y and Wang, J},
title = {LGRPv2: A high-value platform for the advancement of Fabaceae genomics.},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/pbi.70220},
pmid = {40545607},
issn = {1467-7652},
support = {32470676//National Natural Science Foundation of China/ ; 32170236//National Natural Science Foundation of China/ ; 31501333//National Natural Science Foundation of China/ ; C2020209064//Hebei Natural Science Foundation/ ; C2024209014//Hebei Natural Science Foundation/ ; H2023209084//Hebei Natural Science Foundation/ ; 246Z2508G//Central Guiding Local Science and Technology Development Fund Project/ ; ZD-YG-202313-23//Key Research Project of North China University of Science and Technology/ ; },
abstract = {Fabaceae, as one of the most diverse angiosperm families, plays a crucial role in maintaining global ecosystems and advancing human civilization. With the rapid accumulation of legume genomes, we developed LGRPv2 (https://fabaceae.cgrpoee.top), an updated version of the Legume Genomics Research Platform. LGRPv2 integrates 413 genomes, covering all published legume genomes and containing our latest deciphered Tamarindus indica genome from early-diverging legumes and three outgroup genomes (Euscaphis pleiosperma, Vitis vinifera, and Platycodon tenuifolia). It features user-friendly interactive interfaces for studying functional annotations, gene duplications, regulatory proteins, N[6]-methyladenosine modifications, and transposable elements. For easily exploring genome evolution associated with polyploidizations, we incorporated DotView, SynView, and DecoBrowse with genome synteny (GenS) to establish a central GenS database for legumes. Specialized web services for ancestral legume genomes enable scientists to analyse the role of paleogenome reshuffling in shaping genomic diversity. The platform offers 184 511 synteny-based orthogroups and 1 086 836 genes from 139 families, and tools to explore agronomic trait origins. LGRPv2 integrates 40 550 transcriptomes, 5091 pan-genomes, 12 136 metabolomes, species encyclopaedias, ecological resources, and literature for exploring legume genomics comprehensively. Furthermore, LGRPv2 implemented 58 window-based operating tools (31 new) to efficiently support new mining, especially in advancing assembling pipelines for polyploidization identification, ancestral genome reconstruction, and gene family evolution. Finally, we provided detailed usage guides and community support to empower LGRPv2 with user-friendly and continuously updated features.},
}

@article {pmid40539515,
year = {2025},
author = {González Ojeda, I and Palace, SG and Martinez, PP and Azarian, T and Grant, LR and Hammitt, LL and Hanage, WP and Lipsitch, M},
title = {Linkage-based ortholog refinement in bacterial pangenomes with CLARC.},
journal = {Nucleic acids research},
volume = {53},
number = {12},
pages = {},
doi = {10.1093/nar/gkaf488},
pmid = {40539515},
issn = {1362-4962},
support = {T32GM008313/NH/NIH HHS/United States ; NSF 24-59.1//National Science Foundation Graduate Research Fellowship/ ; },
mesh = {*Genome, Bacterial ; *Software ; Streptococcus pneumoniae/genetics ; *Genomics/methods ; Molecular Sequence Annotation ; Evolution, Molecular ; Genetic Linkage ; Phylogeny ; *Bacteria/genetics/classification ; },
abstract = {Bacterial genomes exhibit significant variation in gene content and sequence identity. Pangenome analyses explore this diversity by classifying genes into core and accessory clusters of orthologous groups (COGs). However, strict sequence identity cutoffs can misclassify divergent alleles as different genes, inflating accessory gene counts. CLARC (Connected Linkage and Alignment Redefinition of COGs) (https://github.com/IndraGonz/CLARC) improves pangenome analyses by condensing accessory COGs using functional annotation and linkage information. Through this approach, orthologous groups are consolidated into more practical units of selection. Analyzing 8000+ Streptococcus pneumoniae genomes, CLARC reduced accessory gene estimates by >30% and improved evolutionary predictions based on accessory gene frequencies. CLARC is effective across different bacterial species, making it a broadly applicable tool for comparative genomics. By refining COG definitions, CLARC offers critical insights into bacterial evolution, aiding genetic studies across diverse populations.},
}

*Genome, Bacterial
*Software
Streptococcus pneumoniae/genetics
*Genomics/methods
Molecular Sequence Annotation
Evolution, Molecular
Genetic Linkage
Phylogeny
*Bacteria/genetics/classification

@article {pmid40534107,
year = {2025},
author = {Garg, V and Barmukh, R and Huang, Y and Chitikineni, A and Hobson, K and Yang, B and Jia, Y and Bi, S and Kaur, S and Asif, MA and Hayden, M and Norton, S and Sharma, DL and Siddique, KHM and Liu, X and Li, C and Varshney, RK},
title = {An Australian chickpea pan-genome provides insights into genome organization and offers opportunities for enhancing drought adaptation for crop improvement.},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/pbi.70192},
pmid = {40534107},
issn = {1467-7652},
support = {UMU2303-003RTX//Grains Research and Development Corporation/ ; UMU2403-009RTX//Grains Research and Development Corporation/ ; },
abstract = {Chickpea (Cicer arietinum L.) is an important legume crop that has been subjected to intensive breeding, resulting in limited genetic diversity. Australia is the world's second largest producer and the leading exporter of chickpea; the genomic architecture of its cultivars remains largely unexplored. This knowledge gap hinders efforts to enhance their genetic potential for production, protection, and stress adaptation. To address this, we generated high-quality genome assemblies and annotations for 15 leading Australian chickpea cultivars using single-tube long-fragment read technology. The pan-genome analysis identified 34 345 gene families, including 13 986 dispensable families enriched for genes associated with key agronomic traits. Comparative genomic analysis revealed ~2.5 million single-nucleotide polymorphisms, nearly 200 000 insertions/deletions, and over 280 000 structural variations. These variations were found in key flowering time genes, seed weight-related genes, and disease resistance genes, providing insights into the genetic diversity underlying these critical traits. Haplotype analysis of key genes within the 'QTL-hotspot' region revealed the absence of superior haplotypes in Australian cultivars. Validation using Kompetitive allele-specific PCR markers confirmed these findings, highlighting the need to introduce beneficial haplotypes from diverse accessions to enhance drought tolerance in Australian chickpea cultivars. The genomic resources generated in this study provide valuable insights into chickpea genetic diversity and offer potential avenues for crop improvement.},
}

@article {pmid40529231,
year = {2025},
author = {Shi, X and Patil, S and Yi, Q and Liu, Z and Wang, H and Zhu, C and Chen, Y and Zheng, Y and Dong, S and Bao, Y},
title = {Pan-Genome-Wide Association Study Identifies Genetic Factors Associated with the Pathogenicity of Invasive Serotype 19F Streptococcus Pneumoniae.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {2963-2975},
pmid = {40529231},
issn = {1178-6973},
abstract = {BACKGROUND: Streptococcus pneumoniae is a common respiratory pathogen that poses significant health concerns in children, particularly serotype 19F strains that demonstrate high level of invasiveness in China. To investigate the genetic variations associated with high invasiveness of serotype 19F S. pneumoniae strains isolated from children in Shenzhen.

METHODS: We compared the genomic profiles of 42 invasive and 162 noninvasive strains from children's respiratory tracts and employed pan-genome-wide association methods to elucidate the origins of genetic variation.

RESULTS: Significant gene presence variability was observed between invasive and noninvasive strains, suggesting a genetic basis for their pathogenicity differences. Invasive 19F strains demonstrated enhanced adhesion in co-culture experiments with human epithelial cells, with adhesion abilities correlating with the presence of specific genes. Despite high non-susceptibility to common antibiotics across all strains, no significant differences in antimicrobial susceptibility patterns were found between invasive and noninvasive groups.

CONCLUSION: Although genomic differences within serotype 19F were relatively minor, invasive and noninvasive strains exhibited significant differences in adherence and invasiveness in the host microenvironment. While the underlying regulatory mechanisms remain uncertain, genetic differences play a crucial role in determining the invasiveness of S. pneumoniae serotype 19F strains in children.},
}

@article {pmid40528225,
year = {2025},
author = {Shivakumar, VS and Langmead, B},
title = {Mumemto: efficient maximal matching across pangenomes.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {169},
pmid = {40528225},
issn = {1474-760X},
support = {DGE2139757//National Science Foundation, United States/ ; IIBR 2029552//National Science Foundation, United States/ ; R01HG011392/HG/NHGRI NIH HHS/United States ; R01HG011392/HG/NHGRI NIH HHS/United States ; },
mesh = {Humans ; *Software ; *Genomics/methods ; *Sequence Alignment/methods ; *Genome, Human ; },
abstract = {Aligning genomes into common coordinates is central to pangenome construction, though computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) help to frame and solve the multiple alignment problem. We introduce Mumemto, a tool that computes multi-MUMs and other match types across large pangenomes. Mumemto allows for visualization of synteny, reveals aberrant assemblies and scaffolds, and highlights pangenome conservation and structural variation. Mumemto computes multi-MUMs across 320 human assemblies (960GB) in 25.7 h with 800 GB of memory and hundreds of fungal assemblies in minutes. Mumemto is implemented in C++ and Python and available open-source at https://github.com/vikshiv/mumemto (v1.1.1 at doi.org/10.5281/zenodo.15053447).},
}

Humans
*Software
*Genomics/methods
*Sequence Alignment/methods
*Genome, Human

@article {pmid40527417,
year = {2025},
author = {Yaikhan, T and Singkhamanan, K and Suwannasin, S and Dechathai, T and Yingkajorn, M and Chusri, S and Surachat, K},
title = {Genomic insights into Metapseudomonas otitidis PA-NS83: The first clinical isolate from Thailand and its comparative genomic analysis.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105786},
doi = {10.1016/j.meegid.2025.105786},
pmid = {40527417},
issn = {1567-7257},
abstract = {Metapseudomonas otitidis was first isolated from human middle ear fluid and has since been detected in both environmental and clinical samples, emerging as an opportunistic pathogen linked to chronic otitis media and other infections. This study reports the first clinical isolate of M. otitidis from Thailand, PA-NS83, and presents a comprehensive genomic characterization. Whole-genome sequencing and comparative analysis with 37 publicly available M. otitidis genomes revealed a diverse antimicrobial resistance (AMR) profile, with PA-NS83 carrying AMR genes commonly found in environmental isolates. Virulence gene analysis identified key determinants associated with biofilm formation, motility, secretion systems, and iron acquisition, highlighting its potential pathogenicity. Pan-genome analysis demonstrated substantial genomic diversity, with PA-NS83 clustering closely with M. otitidis CSMC7, an environmental isolate from polystyrene waste. However, PA-NS83 harbored 419 unique genes, including virulence-associated genes and a CRISPR-Cas system, suggesting adaptation to clinical settings. These findings underscore the genetic plasticity of M. otitidis and its potential role in human infections. Continued genomic surveillance and functional studies are essential to further assess its clinical significance and antimicrobial resistance mechanisms.},
}

@article {pmid40526067,
year = {2025},
author = {Chan, DTC and Agarwal, V and Baltrus, DA and Dillon, MM},
title = {Unified Classification of the Type III Secreted Effectors of Bacterial Plant Pathogens to Advance Phytopathology Research.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-02-25-0055-FI},
pmid = {40526067},
issn = {0031-949X},
abstract = {Many diverse bacterial phytopathogens deploy type III secreted effectors (T3SEs) to promote virulence by interrupting host immunity and other critical plant processes. However, the virulence of T3SEs has been countered on the host side through the evolution of a multitude of resistance genes (R-genes) capable of recognizing the presence of T3SEs and eliciting a response termed effector triggered immunity (ETI). This dynamic sets up an evolutionary arms race that has led to enormous diversification of both bacterial T3SEs and plant R-genes. Over the past decade, efforts to document and characterize the pangenome T3SE profiles of individual pathogens have generated indispensable resources that have facilitated collaborative research progress on these focal pathogens. However, despite the deeply integrated evolutionary history of T3SEs, the lack of concerted effort to synthesize T3SE conventions across diverse pathosystems has resulted in a lack of connectivity across the literature. Here, we catalogue the distribution of T3SEs across six of the most globally significant genera of bacterial phytopathogens. We show that the number of T3SEs per genome varies dramatically within and between genera, and that many T3SE families are present in multiple genera despite their sparse distributions across closely related strains. We also document all inter-genera evolutionary relationships for each T3SE family and propose integrated nomenclature conventions for all phytopathogen T3SEs. Ultimately, our expanded T3SE collection includes thousands of newly classified alleles, catalogues several previously unestablished homologies between distinct genera, and will enable more comprehensive studies on the implications of T3SE diversification for virulence and immunity.},
}

@article {pmid40525812,
year = {2025},
author = {Gelgie, AE and Gelalcha, BD and Christensen, D and Freeman, T and Beever, JE and Dego, OK},
title = {Prevalence and Whole Genome Sequence Analysis of Mycoplasma bovis Isolates From Bulk Tank Milk of Dairy Farms in Tennessee, USA.},
journal = {Journal of veterinary internal medicine},
volume = {39},
number = {4},
pages = {e70164},
pmid = {40525812},
issn = {1939-1676},
support = {//The 10× Genomics Single Cell Grant Program/ ; //UTIA Genomics Center for the Advancement of Agriculture/ ; },
mesh = {Animals ; Cattle ; *Mycoplasma bovis/genetics/isolation & purification ; Tennessee/epidemiology ; *Milk/microbiology ; Female ; *Mycoplasma Infections/veterinary/epidemiology/microbiology ; Prevalence ; *Mastitis, Bovine/microbiology/epidemiology ; Dairying ; Whole Genome Sequencing/veterinary ; },
abstract = {BACKGROUND: Mycoplasma bovis mastitis is an important disease of dairy cows that causes substantial economic losses. However, its prevalence in different states in the United States (US), including Tennessee, is not well known. Furthermore, recent studies showed a high prevalence of bovine hemotropic mycoplasmas in US dairy farms.

OBJECTIVES: Determine the prevalence of M. bovis in bulk tank milk (BTM) of dairy farms in Tennessee and evaluate the genetic diversity, virulence factors, and antimicrobial resistance genes of the identified isolates. In addition, the prevalence of Mycoplasma wenyonii and Candidatus Mycoplasma haemobos in the bulk tank milk was determined.

METHODS: Seventy-five BTM samples were collected from 59 dairy farms. Of the 59 farms, 56 are in Tennessee and the remaining 3 farms are in the neighboring states, Georgia (n = 2) and Alabama (n = 1). Milk samples were tested using bacterial culture, PCR, and qPCR. M. bovis isolates were genetically characterized by pangenome analysis.

RESULTS: Of the 56 farms, 3 (5.3%) were positive for M. bovis by bacterial culture and 43 (76.7%) were positive by PCR. Pangenome analysis showed clustering of current isolates with mastitis isolates from the US, Israel, and Europe. Of 75 BTM samples tested by qPCR, 42 (56%) and 51 (68%) were positive for M. wenyonii and C. M. haemobos, respectively.

CONCLUSIONS: M. bovis intramammary infection is prevalent in Tennessee dairy farms.},
}

Animals
Cattle
*Mycoplasma bovis/genetics/isolation & purification
Tennessee/epidemiology
*Milk/microbiology
Female
*Mycoplasma Infections/veterinary/epidemiology/microbiology
Prevalence
*Mastitis, Bovine/microbiology/epidemiology
Dairying
Whole Genome Sequencing/veterinary

@article {pmid40523568,
year = {2025},
author = {Zhao, Y and Zhao, Y and Shen, Q and Hu, X and Zhou, S and Huang, J},
title = {Evolution and epidemiology of pks[+]Klebsiella pneumoniae: Global and local insights.},
journal = {Microbial pathogenesis},
volume = {206},
number = {},
pages = {107812},
doi = {10.1016/j.micpath.2025.107812},
pmid = {40523568},
issn = {1096-1208},
abstract = {OBJECTIVE: This study aimed to investigate the epidemiological characteristics and genomic evolutionary mechanisms of pks-positive Klebsiella pneumoniae (pks [+] KPN), providing theoretical insights for infection prevention and control strategies.

METHODS: A total of 873 non-duplicate K. pneumoniae isolates collected between 2016 and 2022 at the Fifth Affiliated Hospital of Wenzhou Medical University were screened for pks [+] strains via PCR targeting clbA, clbB, clbN, and clbQ. Clonal structures of pks[+] and pks[-] strains were determined by MLST and KL typing, and virulence gene profiles (peg344, iucA, rmpA, rmpA2, iroB) were analyzed to compare the two populations. Global distribution patterns of pks [+] KPN were analyzed using data from the Bacterial and Viral Bioinformatics Resource Center (BV-BRC). Pan-genomic analysis via the IPGA platform and a phylogenetic tree was constructed. Core-genome comparative analysis identified lineage-specific genes in dominant pks[+] strains, and KEGG enrichment revealed their putative biological functions. Statistical analyses were performed using SPSS 26.0, with p < 0.05 considered statistically significant.

RESULTS: Among 873 clinical isolates, 105 (12.03 %) were pks [+] KPN, predominantly isolated from infectious disease and surgical departments. The pks island prevalence was significantly higher in non-carbapenem-resistant strains (25.45 %) than in carbapenem-resistant strains (1.04 %) (χ[2] = 125.57, p < 0.001). pks [+] strains exhibited higher virulence gene carriage rates (p < 0.05) and infected younger patients (57.97 ± 14.90 vs. 64.18 ± 17.29 years, t = 3.46, p = 0.001). pks [+] isolates showed a conserved clonal structure dominated by ST23-KL1 (66.7 %), while pks[-] strains displayed greater heterogeneity with 37 distinct ST-KL types. Analysis of 706 global pks [+] KPN revealed that ST23 (45.18 %), ST11 (15.72 %), and ST258 (15.16 %) are the predominant clonal lineages. Phylogenetic construction delineated five evolutionarily distinct clades among pks[+] strains. Comparative core genome analysis identified 245 lineage-associated genes, of which 96 were shared among dominant strains. Functional enrichment (KEGG) demonstrated that these conserved genes are significantly enriched in the galactose metabolism.

CONCLUSION: This study systematically elucidates the clinical epidemiology, clonal dissemination patterns, and genomic evolution of pks [+] KPN, identifying ST23-KL1 as the dominant clone. The findings reveal that galactose metabolism may enhance the adaptability of dominant strains, thereby driving their global spread.},
}

@article {pmid40522106,
year = {2025},
author = {Garzon, A and Miramontes, C and Weimer, BC and Profeta, R and Hoyos-Jaramillo, A and Fritz, HM and Pereira, RV},
title = {Comparison of virulence and resistance genes in Mannheimia haemolytica and Pasteurella multocida from dairy cattle with and without bovine respiratory disease.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0120025},
doi = {10.1128/spectrum.01200-25},
pmid = {40522106},
issn = {2165-0497},
abstract = {UNLABELLED: Mannheimia haemolytica and Pasteurella multocida are two of the main bacterial pathogens associated with bovine respiratory disease (BRD). BRD represents one of the most significant health challenges in the cattle industry, causing substantial economic losses through animal morbidity and mortality while raising serious welfare concerns. The objectives of this project were to (i) characterize virulence factor (VF) and antimicrobial resistance (AMR) genes in M. haemolytica and P. multocida isolates from dairy cattle of different ages with and without BRD using whole-genome sequencing (WGS); (ii) evaluate associations between microbial genetic elements and animal disease status; and (iii) assess the accuracy of genome-based predictions for the antimicrobial resistance phenotype. Using a case-control study, AMR and VF genes were characterized from 149 P. multocida and 68 M. haemolytica isolates from preweaned calves, weaned heifers, and cows with and without BRD. The large genetic diversity observed in both bacterial species prevented the identification of unique genetic markers associated with disease status or age group. AMR genes (22 genes) from 12 antimicrobial classes were identified in P. multocida isolates, while 11 AMR genes for seven antimicrobial classes were identified in M. haemolytica isolates. Additionally, 28 and 15 virulence genes were identified in P. multocida and M. haemolytica, respectively. The ability of WGS-based predictions to predict phenotypic antimicrobial resistance showed variable accuracy across different antimicrobials, achieving moderate levels of agreement overall. Findings from this project demonstrate that identifying genomic markers based on gene presence/absence lacks discriminatory power within this population for identifying unique genotypes associated with disease status in these genomically diverse organisms.

IMPORTANCE: This case-control study provides key microbial ecological advances by elucidating the role of bacteria in the bovine respiratory disease complex in dairy cattle. Previous research has identified specific virulence factors in both bacterial genomes that resulted in disease. Our results challenge this perception and are of high impact, revealing that the pan-genome of both bacteria did not differentiate among the clinical cases or age groups, and a specific pathogenic pathotype was not evident in the isolates from this study, and it did not emerge when including additional public whole-genome sequences to increase the analytical power of the analysis (the first study to use this approach to evaluate bovine respiratory disease in cattle). In addition to these novel discoveries, this study describes the first population-scale genomic comparison of both Mannheimia haemolytica and Pasteurella multocida genomes collected from affected and healthy dairy cattle from different age groups and from multiple farms.},
}

@article {pmid40518659,
year = {2025},
author = {Gurung, S and Lee, CM and Weon, HY and Han, SR and Oh, TJ},
title = {Comparative Genome Analysis of Three Halobacillus Strains Isolated From Saline Environments Reveal Potential Salt Tolerance and Algicidal Mechanisms.},
journal = {Environmental microbiology reports},
volume = {17},
number = {3},
pages = {e70121},
pmid = {40518659},
issn = {1758-2229},
support = {RS-2024-00441423//The Bio & Medical Technology Development Program of the National Research Foundation (NRF) funded by the Korean government (MSIT)/ ; },
mesh = {*Salt Tolerance/genetics ; *Genome, Bacterial ; Harmful Algal Bloom ; Phylogeny ; *Bacillaceae/genetics/isolation & purification/physiology/classification ; Computational Biology ; Genomics ; },
abstract = {Harmful algal blooms (HABs) pose a significant global threat to water ecosystems, prompting extensive research into their inhibition and control strategies. This study presents genomic and bioinformatic analyses to investigate the algicidal potential and elucidate the survival mechanisms in harsh conditions of newly identified Halobacillus species three strains (SSTM10-2[T], SSBR10-3[T], and SSHM10-5[T]) isolated from saline environments. Moreover, genomic and bioinformatic analyses were conducted to elucidate their survival mechanisms in harsh conditions. Moreover, comparative genomic analysis revealed a diverse set of orthologous genes, with a core genome primarily associated with metabolism and information processing. Pangenome analysis highlighted accessory and unique genes potentially involved in environmental adaptation and stress response. Functional annotation using KEGG pathways identified genes linked to xenobiotic compound degradation, stress tolerance, and salt adaptation. Additionally, the study elucidated potential mechanisms underlying algicidal activity, implicating Carbohydrate-Active enZYmes (CAZymes), cytochrome P450 oxidases (CYP), and quorum sensing (QS) systems. Finally, analysis of KEGG pathways related to microcystin degradation suggested the strains' capacity to mitigate HABs. Thus, this research enhances understanding of the genomic diversity, phylogeny, and functional characteristics of Halobacillus species, offering insights into their ecological roles and potential applications in biotechnology and environmental management.},
}

*Salt Tolerance/genetics
*Genome, Bacterial
Harmful Algal Bloom
Phylogeny
*Bacillaceae/genetics/isolation & purification/physiology/classification
Computational Biology
Genomics

@article {pmid40517404,
year = {2025},
author = {Yu, J and Chen, Q and Yuan, L and Feng, S and Huang, M and Zheng, P and Chen, G and Tao, X and Edwards, D and Chen, ZH and Xu, S},
title = {Phylogenomic and super-pangenome analyses unveil the genetic landscape of tomato evolution and domestication.},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/pbi.70199},
pmid = {40517404},
issn = {1467-7652},
support = {2023C1S01002//Project of Xianghu Laboratory/ ; 2024SSYS0099//Key Research and Development Program of Zhejiang Province/ ; },
abstract = {The tomato (Solanum lycopersicum L.), a principal fruit crop, exhibits significant genetic diversity shaped by domestication and breeding. Analysis of the gene-based super-pangenome, a catalogue of all genes across diverse genome-sequenced tomatoes, has not yet been fully explored. Here, we present a comprehensive analysis of the gene-based super-pangenome across 61 genetically diverse tomato varieties, revealing 59 066 orthologous groups, thereby providing a detailed genetic framework for understanding the evolution of tomatoes. Our phylogenetic analysis recalibrates the position of S. galapagense, challenging existing paradigms of tomato evolution. Identification of genes linked to key agronomic traits such as fruit size, ripening and stress tolerance, along with their presence/absence variation among accessions, offers a rich source of genetic markers for breeding programs. The study also highlights the impact of whole-genome triplication (WGT) and tandem gene duplication (TD) events on gene family expansion, particularly in distant wild relatives. The analysis of the LRR-RLK gene family, important for plant development and defence, reveals substantial sequence diversity and conservation. Rapidly evolving genes and those under positive selection, such as HAI3, CYP711A1/MAX1, WRKY9 and CNGC15, are implicated in stress tolerance and defence mechanisms. The identification of these genes, along with specific pathogenesis-related genes in distant wild relatives, suggests potential strategies to improve fruit shelf life, fruit set and stress tolerance in elite tomato cultivar breeding. Additionally, we have developed the tomatoPangenome platform, integrating genomic and pangenomic data, gene families and tools, to support sustainable production of high-quality, climate-resilient tomatoes and advance selective breeding for future food security.},
}

@article {pmid40517149,
year = {2025},
author = {Gonzalez-Garcia, LN and Rodriguez, MP and Parra-Muñoz, M and Clavijo, AM and Levy, L and Ovalle-Bracho, C and Colorado, C and Camargo, C and Quiceno, E and Moncada, MJ and Muskus, C and Urrea, DA and Baez-Aguirre, F and Restrepo, S and Echeverry, MC and Duitama, J},
title = {Genetic diversity and comparative genomics across Leishmania (Viannia) species.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {925},
pmid = {40517149},
issn = {2399-3642},
mesh = {*Leishmania/genetics/classification ; *Genetic Variation ; Phylogeny ; *Genomics/methods ; *Genome, Protozoan ; Humans ; Leishmaniasis/parasitology ; DNA Copy Number Variations ; },
abstract = {Leishmaniasis is an important public health problem worldwide, with a broad spectrum of clinical and epidemiological features partly associated with the diversity and complex life cycle of the Leishmania parasites. This study analyzes genomic data from 205 Leishmania (Viannia) samples, including 65 newly sequenced clinical isolates. It also provides chromosome-level genome assemblies for 10 isolates representing different species and populations. The observed distribution of Leishmania genomic diversity across the sampling locations suggests rapid adaptation to different ecosystems. The phylogenomic analysis provides new hypotheses challenging the current delimitation of species. Pangenomic analysis of high-quality assemblies shows consistent copy number variation between species for different gene families. Larger and more diverse amastin gene families were observed in the assembled genomes compared to previous reports based on the analysis of short-read data. This work provides genomic resources and helpful information regarding central problems in the biology of Leishmania spp, including species diversification, transmission dynamics, and the evolution of virulence mechanisms.},
}

*Leishmania/genetics/classification
*Genetic Variation
Phylogeny
*Genomics/methods
*Genome, Protozoan
Humans
Leishmaniasis/parasitology
DNA Copy Number Variations

@article {pmid40516885,
year = {2025},
author = {Cunha da Silva, G and Rossi, CC},
title = {Defense systems and mobile elements in Staphylococcus haemolyticus: a genomic view of resistance dissemination.},
journal = {Microbial pathogenesis},
volume = {206},
number = {},
pages = {107808},
doi = {10.1016/j.micpath.2025.107808},
pmid = {40516885},
issn = {1096-1208},
abstract = {Staphylococcus haemolyticus is a multidrug-resistant opportunistic pathogen and a major reservoir of antimicrobial resistance (AMR) genes within the Staphylococcaceae family. Its high genomic plasticity, frequent association with mobile genetic elements (MGEs), and prevalence in clinical settings underscore its relevance as both a threat and a conduit for resistance dissemination. In this study, we performed a comprehensive pan-genomic analysis of the S. haemolyticus defensome - including restriction-modification (RM), abortive infection (Abi), and CRISPR-Cas systems - across 692 high-quality genomes. Our results reveal a highly diverse and modular repertoire of immune systems, often organized in physical clusters and frequently associated with MGEs. We identified evidence of antagonistic interactions, with both defense and anti-defense elements encoded on plasmids and prophages. CRISPR spacer analysis showed a predominant targeting of phages, and genomes encoding CRISPR-Cas systems exhibited a lower abundance of MGEs and AMR genes, suggesting a trade-off between defense and gene acquisition. RNA-seq data from one reference strain indicate that only a fraction of the defensome is actively transcribed under standard conditions, hinting at environment-responsive regulation. Together, these findings provide new insights into the genomic strategies sustaining the persistence and adaptability of S. haemolyticus in clinical environments. The interplay between its immune systems and mobilome likely contributes not only to its evolutionary trajectory, but also to its role in the horizontal transfer of resistance determinants among pathogenic staphylococci. A deeper understanding of this immune-mobilome interface may help inform future strategies to limit the spread of resistance.},
}

@article {pmid40513520,
year = {2025},
author = {Wu, K and Yang, J and Zhang, T and Zuo, J and Lin, H and Wang, J and Zhang, A and Lei, C and Wang, H},
title = {Emergence and traceability of Salmonella enterica serotype Mbandaka harboring blaOXA-10 from chickens in China.},
journal = {Veterinary microbiology},
volume = {307},
number = {},
pages = {110593},
doi = {10.1016/j.vetmic.2025.110593},
pmid = {40513520},
issn = {1873-2542},
abstract = {Salmonella enterica serotype Mbandaka (S. Mbandaka), a multi-host adapted non-typhoidal Salmonella, has emerged as a significant public health concern in recent years. In this study, we isolated S. Mbandaka strains carrying a multidrug-resistant IncHI2A/IncHI2 plasmid from deceased chickens in China and performed whole-genome sequencing and comparative genomic analyses to investigate their global dissemination and evolutionary adaptation. The multidrug-resistant IncHI2A/IncHI2 plasmid in isolate YK35 harbored multiple antibiotic resistance genes (ARGs) including blaOXA-10, which was firstly observed in S. Mbandaka in China. It exhibited high sequence identity with IncHI2A/IncHI2 plasmids identified in other bacterial species, including S. Typhimurium, Klebsiella aerogenes, and E. coli, which suggested the cross-species dissemination of IncHI2A/IncHI2 plasmids and ARGs. Global genomic epidemiology classified S. Mbandaka strains into seven distinct clades, with the majority originating from the USA and the UK. The pan-genomic analysis indicated an open pan-genome structure, with continuous expansion of accessory genes, particularly those associated with replication, recombination, repair, and defense mechanisms, underscoring the evolutionary adaptation of S. Mbandaka to external environments. Evolutionary analysis further traced the international transmission routes of S. Mbandaka, revealing potential cross-regional spread, particularly from the USA and the UK to other countries, including China. The findings emphasize the global spread and evolutionary adaptation of S. Mbandaka, likely driven by international trade and horizontal gene transfer, including the acquisition of ARGs, which have contributed to its increasing public health risks. This study underscores the urgent need for enhanced surveillance and control measures to mitigate the spread of S. Mbandaka and its antibiotic resistance, particularly in the context of global food supply chains and international trade.},
}

@article {pmid40512587,
year = {2025},
author = {He, Y and Zhou, X and Zhang, L and Cui, Y and He, Y and Gehring, A and Deng, X and Shi, X},
title = {Prediction of Antibiotic Resistance Phenotypes and Minimum Inhibitory Concentrations in Salmonella Using Machine Learning Analysis of Its Pan-Genome and Pan-Resistome Features.},
journal = {Foodborne pathogens and disease},
volume = {},
number = {},
pages = {},
doi = {10.1089/fpd.2024.0170},
pmid = {40512587},
issn = {1556-7125},
abstract = {Traditional experimental methods for determining antibiotic resistance phenotypes (ARPs) and minimum inhibitory concentrations (MICs) in bacteria are laborious and time consuming. This study aims to explore the potential of whole-genome sequencing data combined with machine learning models for robustly predicting ARPs and MICs in Salmonella. Using a training set of 6394 Salmonella genomes alongside antimicrobial susceptibility testing results, we built two machine learning (ML) predictive models based on the pan-genome and pan-resistome. Each model was implemented using three algorithms: random forest, extreme gradient boosting (XGB), and convolutional neural network. Among them, XGB achieved the highest overall accuracy, with the pan-genome and pan-resistome models accurately predicting ARPs (98.51% and 97.77%) and MICs (81.42% and 78.99%) for 15 commonly used antibiotics. Feature extraction from pan-genome and pan-resistome data effectively reduced computational complexity and significantly decreased computation time. Notably, fewer than 10 key genomic features, often linked to known resistance or mobile genes, were sufficient for robust predictions for each antibiotic. This study also identified challenges, including imbalanced resistance classes and imprecise MIC measurements, which impacted prediction accuracy. These findings highlight the importance of using multiple evaluation metrics to assess model performance comprehensively. Overall, our findings demonstrated that ML, utilizing pan-genome or pan-resistome features, was highly effective in predicting antibiotic resistance and identifying correlated genetic features in Salmonella. This approach holds great potential to supplement conventional culture-based methods for routine surveillance of antibiotic-resistant bacteria.},
}

@article {pmid40512264,
year = {2025},
author = {Admas, T and Jiao, S and Pan, R and Zhang, W},
title = {Pan-omics insights into abiotic stress responses: bridging functional genomics and precision crop breeding.},
journal = {Functional & integrative genomics},
volume = {25},
number = {1},
pages = {128},
pmid = {40512264},
issn = {1438-7948},
support = {32372052//National Natural Science Foundation of China/ ; 32372052//National Natural Science Foundation of China/ ; 32372052//National Natural Science Foundation of China/ ; 32372052//National Natural Science Foundation of China/ ; },
mesh = {*Crops, Agricultural/genetics/growth & development/metabolism ; *Stress, Physiological/genetics ; *Plant Breeding ; *Genomics/methods ; Metabolomics/methods ; Proteomics/methods ; Multiomics ; },
abstract = {Crop production has been regarded as the major goal of agricultural activities, but the rapidly growing population and climate change have become more complex in the agricultural systems. Abiotic stress greatly affects crop productivity globally; developing more resilient crop varieties has become imperative. However, we can understand how plants tolerate abiotic stress better by using new methods that combine different scientific approaches like pan-genomics, pan-transcriptomics, pan-proteomics, pan-metabolomics, and pan-phenomics. Investigations using a pan-omics approach are necessary to consider the variation resulting from complex interactions among genes, proteins, metabolites, and regulatory networks within a species. A comparative study of core, dispensable, and unique components across different accessions assists in identifying novel genes, proteins, and metabolites responsible for stress tolerance. Moreover, databases and online repositories now enable the storage, analysis, and retrieval of data generated by high-throughput technologies. The combination provides guidelines for researchers to harness the potential of pan-omics in promoting sustainable agricultural practices. Therefore, the review focuses on recent trends in pan-omics for studying abiotic stress responses and their applications in crop improvement. It also highlights the application of artificial intelligence (AI) in data integration and monitoring crop environments.},
}

*Crops, Agricultural/genetics/growth & development/metabolism
*Stress, Physiological/genetics
*Plant Breeding
*Genomics/methods
Metabolomics/methods
Proteomics/methods
Multiomics

@article {pmid40511850,
year = {2025},
author = {Coelho, JT and Teubner, L and Henson, MW and Lanclos, VC and Kojima, CY and Thrash, JC},
title = {Culture-supported ecophysiology of the SAR116 clade demonstrates metabolic and spatial niche partitioning.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf124},
pmid = {40511850},
issn = {1751-7370},
abstract = {Marine SAR116 bacterioplankton are ubiquitous in surface waters across global oceans and form their own order, Puniceispirillales, within the Alphaproteobacteria. To date no comparative physiology among diverse SAR116 isolates has been performed to capture the functional diversity within the clade, and further, diversity through the lens of metabolic potential and environmental preferences via clade-wide pangenomics continues to evolve with the addition of new genomes. Using high-throughput dilution-to-extinction cultivation, we isolated and genome sequenced five new and diverse SAR116 isolates from the northern Gulf of Mexico. Here we present a comparative physiological analysis of these SAR116 isolates, along with a pangenomic investigation of the SAR116 clade using a combination of metagenome-assembled genomes (MAGs, n = 258), single-amplified genomes (SAGs, n = 84), previously existing (n = 2), and new isolate genomes (n = 5), totaling 349 SAR116 genomes. Phylogenomic investigation supported the division of SAR116 into three distinct subclades, each with additional structure totaling 15 monophyletic groups. Our SAR116 isolates belonged to three groups within subclade I representing distinct genera with different morphologies and varied phenotypic responses to salinity and temperature. Overall, SAR116 genomes encoded differences in vitamin and amino acid synthesis, trace metal transport, and osmolyte synthesis and transport. They also had genetic potential for diverse sulfur oxidation metabolisms, placing SAR116 at the confluence of the organic and inorganic sulfur pools. SAR116 subclades showed distinct patterns in habitat preferences across open ocean, coastal, and estuarine environments, and three of our isolates represented the most abundant coastal and estuarine subclade. This investigation provides the most comprehensive exploration of SAR116 to date anchored by new culture genomes and physiology.},
}

@article {pmid40511294,
year = {2025},
author = {Wang, H and Zhang, C and Chen, Y and Guo, Y and Ding, L and Zhang, S and Du, G and Zhang, W and He, S},
title = {Gracilimonas qinghaiensis sp. nov., a halophilic bacterium from a high-altitude saline lake exhibiting diverse metabolic potential and ecological adaptation.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100413},
pmid = {40511294},
issn = {2666-5174},
abstract = {Saline lakes are extreme habitats that host unique microbial communities with high biotechnological potential. In this study, a novel strain, designated Q87[T], was isolated from Gaxiukule Lake, a high-altitude magnesium sulfate-type saline lake in the Qaidam Basin, China. A polyphasic taxonomic approach, including morphological, physiological, chemotaxonomic, phylogenetic, and genomic analyses, was applied to characterize the isolate. Strain Q87[T] is a Gram-stain-negative, non-motile, rod-shaped bacterium showing high tolerance to salinity (0-15.0 %, w/v; optimum 5.0 %) and alkalinity (pH 6.0-10.5; optimum pH 7.0), with a temperature range for growth of 10-40 °C (optimum 32 °C). Phylogenetic and genomic analyses confirmed its affiliation with the genus Gracilimonas and revealed it as a distinct species. The genome of strain Q87[T] (3.3 Mb, G + C 41.5 %) encodes diverse functional genes associated with nitrogen and sulfur metabolism, stress adaptation, and biosynthesis of secondary metabolites, including terpenoids and polyketides. Comparative analyses with reference Gracilimonas strains demonstrated its unique genomic features and ecological adaptability. Structural modeling confirmed functional conservation of key enzymes involved in nitrogen detoxification and sulfide oxidation. Pangenome analysis highlighted the genetic diversity and open nature of the species of the genus Gracilimonas. Biogeographic assessments suggest a wide distribution of the genus in saline environments, especially in sediments. This study expands our understanding of the genus Gracilimonas taxonomy, physiology, and ecological potential, and underscores the importance of extremophilic bacteria as promising resources for environmental and industrial biotechnology.},
}

@article {pmid40508367,
year = {2025},
author = {Zhao, F and Li, X and Chen, Z and Guo, C},
title = {Pan-Genome-Wide Investigation and Expression Analysis of GATA Gene Family in Maize.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
pmid = {40508367},
issn = {2223-7747},
support = {20220101330JC;CXGC2024ZD001//Ziqi Chen/ ; },
abstract = {GATA is a crucial transcription factor involved in plant growth, development, and responses to abiotic stress. Therefore, identifying and exploring GATA transcription factors in maize is of significant importance. In this study, we identified 75 ZmGATA genes based on the pan-genome of maize, which includes 26 high-quality maize genomes. These consist of 58 core genes (present in all 26 lines), 12 non-essential genes (present in 2 to 23 lines), 2 near-core genes (present in 24 to 25 lines), and 3 private genes (present in only 1 line). By evaluating the Ka/Ks ratio of the ZmGATA genes in 26 maize varieties, we found that the Ka/Ks ratios of ZmGATA31, ZmGATA32, ZmGATA36, and ZmGATA9 were greater than 1, which may indicate that these four genes are under positive selection. In contrast, the Ka/Ks ratios of other ZmGATA genes were less than 1, suggesting that these genes may be under purifying selection. In the 26 maize genomes, we observed a significant difference in the expression of ZmGATA8 between varieties affected by structural variations (SVs) and those not affected. In certain varieties, SVs altered conserved structures. Additionally, we analyzed the expression levels of ZmGATA genes in different maize tissues and under abiotic stress. ZmGATA38 and ZmGATA39 were highly expressed in the endosperm, thereby influencing starch synthesis, while ZmGATA7, ZmGATA10, ZmGATA19, ZmGATA28, and ZmGATA40 were found to be associated with abiotic stress responses. These findings provide valuable new resources for functional research on ZmGATA.},
}

@article {pmid40506254,
year = {2025},
author = {Varki, R and Rossi, M and Ferro, E and Oliva, M and Garrison, E and Langmead, B and Boucher, C},
title = {Accurate short-read alignment through r-index-based pangenome indexing.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279858.124},
pmid = {40506254},
issn = {1549-5469},
abstract = {Aligning to a linear reference genome can result in a higher percentage of reads going unmapped or being incorrectly mapped owing to variations not captured by the reference, otherwise known as reference bias. Recently, in efforts to mitigate reference bias, there has been a movement to switch to using pangenomes, a collection of genomes, as the reference. In this paper, we introduce Moni-align, the first short-read pangenome aligner built on the r-index, a variation of the classical FM-index that can index collections of genomes in O(r)-space, where r is the number of runs in the Burrows-Wheeler transform. Moni-align uses a seed-and-extend strategy for aligning reads, utilizing maximal exact matches as seeds, which can be efficiently obtained with the r-index. Using both simulated and real short-read data sets, we demonstrate that Moni-align achieves alignment accuracy comparable to vg map and vg giraffe, the leading pangenome aligners. Although currently best suited for aligning to localized pangenomes owing to computational constraints, Moni-align offers a robust foundation for future optimizations that could further broaden its applicability.},
}

@article {pmid40502105,
year = {2025},
author = {Tan, S and Majidian, S and Langmead, B and Zakeri, M},
title = {Movi Color: fast and accurate long-read classification with the move structure.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.22.655637},
pmid = {40502105},
issn = {2692-8205},
abstract = {The number of reference genomes is rapidly increasing, thanks to advances in long-read sequencing and assembly. While these collections can improve the sensitivity and specificity of classification methods, this requires highly efficient compressed indexes. K-mer-based approaches like Kraken 2 are efficient but limit the analysis to a fixed k-mer length. This is hard for the user to set ahead of time, and suboptimal settings can harm sensitivity and specificity. Methods that use compressed full-text indexes like SPUMONI2 and Cliffy lift this constraint, but are less efficient than k-mer-based tools. Further, these methods either cannot report a full listing of genomes where a match occurs, or cannot scale to large reference databases. We propose new methods and algorithms that use compressed full-text indexes to enable multi-class and taxonomic classification. Unlike past compressed-indexing methods for classification, ours uses the move structure, which is extremely fast thanks to its locality of reference. Our method, called Movi Color, augments the main table of the Movi index. Specifically, Movi Color assigns a "color" to each run of the Burrows-Wheeler Transform according to the subset of genomes from which the run suffixes originated. When the reference is highly repetitive - as is typical when indexing pangenomes or reference databases - only certain colors occur, creating opportunities to compress the index. For species-level classification, Movi Color achieves over 1.6 × higher precision and 2 × higher recall than Kraken 2 and Metabuli. At the genus level, it achieves 70% higher precision and 80% higher recall. Movi Color's read processing time is 7-20× faster than Metabuli and is a comparable to Kraken 2. Although Movi Color uses more memory than both Kraken 2 and Metabuli, its speed-accuracy trade-off makes it well-suited for real-time or high-throughput scenarios.},
}

@article {pmid40501862,
year = {2025},
author = {Asri, M and Chang, PC and Mier, JC and Sirén, J and Eskandar, P and Kolesnikov, A and Cook, DE and Brambrink, L and Hickey, G and Novak, AM and Dorfman, L and Webster, DR and Carroll, A and Paten, B and Shafin, K},
title = {Pangenome-aware DeepVariant.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.05.657102},
pmid = {40501862},
issn = {2692-8205},
abstract = {Population-scale genomics information provides valuable prior knowledge for various genomic analyses, especially variant calling. A notable example of such application is the human pangenome reference released by the Human Pangenome Reference Consortium, which has been shown to improve read mapping and structural variant genotyping. In this work, we introduce pangenome-aware DeepVariant, a variant caller that uses a pangenome reference alongside sample-specific read alignments. It generates pileup images of both reads and pangenome haplotypes near potential variants and uses a Convolutional Neural Network to infer genotypes. This approach allows directly using a pangenome for distinguishing true variant signals from sequencing or alignment noise. We assessed its performance on various short-read sequencing platforms and read mappers. Across all settings, pangenome-aware DeepVariant outperformed the linear-reference-based DeepVariant, reducing errors by up to 25.5%. We also show that Element reads with pangenome-aware DeepVariant can achieve 23.6% more accurate variant calling performance compared to existing methods.},
}

@article {pmid40498527,
year = {2025},
author = {Onetto, CA and Ward, C and Varela, C and Hale, L and Schmidt, SA and Borneman, A},
title = {Genetic and phenotypic diversity of wine-associated Hanseniaspora species.},
journal = {FEMS yeast research},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsyr/foaf031},
pmid = {40498527},
issn = {1567-1364},
abstract = {The genus Hanseniaspora includes apiculate yeasts commonly found in fruit- and fermentation-associated environments. Their genetic diversity and evolutionary adaptations remain largely unexplored despite their ecological and oenological significance. This study investigated the phylogenetic relationships, genome structure, selection patterns, and phenotypic diversity of Hanseniaspora species isolated primarily from Australian wine environments, focusing on Hanseniaspora uvarum, the most abundant non-Saccharomyces yeast in wine fermentation. A total of 151 isolates were sequenced, including long-read genomes for representatives of the main phylogenetic clades. Comparative genomics revealed ancestral chromosomal rearrangements between the slow- (SEL) and fast-evolving lineages (FEL) that could have contributed to their evolutionary split, as well as significant loss of genes associated with mRNA splicing, chromatid segregation and signal recognition particle protein targeting in the FEL. Pangenome analysis within H. uvarum identified extensive copy number variation, particularly in genes related to xenobiotic tolerance and nutrient transport. Investigation into the selective landscape following the FEL/SEL divergence identified diversifying selection in 229 genes in the FEL, with significant enrichment in genes within the lysine biosynthetic pathway. Furthermore, phenotypic screening of 113 isolates revealed substantial intraspecific diversity, with specific species exhibiting enhanced ethanol, osmotic, copper, SO2, and cold tolerance.},
}

@article {pmid40495924,
year = {2025},
author = {Kamath B, V and Mallya, S and Mallikarjuna, SV and Kolathur, KK},
title = {The complete genome sequences of Bacillus velezensis B26: a promising biocontrol agent and biofertilizer.},
journal = {F1000Research},
volume = {14},
number = {},
pages = {170},
pmid = {40495924},
issn = {2046-1402},
mesh = {*Bacillus/genetics ; *Genome, Bacterial ; *Biological Control Agents ; *Whole Genome Sequencing ; *Fertilizers/microbiology ; Soil Microbiology ; Base Composition ; Animals ; },
abstract = {Bacillus velezensis is a bacterium widely recognized for its biocontrol properties and ability to promote plant growth. This study presents the whole-genome sequence of B. velezensis B26, a newly identified strain isolated from chicken carcass soil in Udupi, India. The bacterium showed strong activity against fungal pathogens and exhibited diverse enzymatic activities. The whole-genome sequencing was executed using Illumina technologies. Assembly revealed that strain B26 possesses a genome of 3,946,698-bp with a G+C content of 46.3%. Genome annotation identified 3776 protein-coding genes, 1 rRNA gene, 50 tRNA genes, 5 ncRNA genes, and 59 pseudogenes. Functional analysis of the B. velezensis B26 genome revealed 216 genes involved in carbohydrate metabolism, 3 genes in potassium metabolism, 148 genes linked for cofactors, vitamins, prosthetic groups and pigments, 10 genes involved in phosphorus metabolism, 24 genes associated with iron acquisition and metabolism, 20 genes for nitrogen metabolism, 6 genes involved in sulfur metabolism, 6 genes in secondary metabolism, 12 genes associated with metabolism of aromatic compounds, 43 genes involved in stress response and 36 genes associated with virulence, disease and defence. The raw sequence data generated in this work have been deposited in the NCBI database and the genome sequence is available under the accession number JAYKOV000000000. These genomic data provide insight into the biocontrol ability and plant-growth promoting capabilities of B. velezensis B26.},
}

*Bacillus/genetics
*Genome, Bacterial
*Biological Control Agents
*Whole Genome Sequencing
*Fertilizers/microbiology
Soil Microbiology
Base Composition
Animals

@article {pmid40487211,
year = {2025},
author = {Fan, H and Li, J and Huang, W and Liang, A and Jing, L and Li, J and Yang, QY and Liu, K and Yang, Z},
title = {Pan-genome analysis of the R2R3-MYB genes family in Brassica napus unveils phylogenetic divergence and expression profiles under hormone and abiotic stress treatments.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1588362},
pmid = {40487211},
issn = {1664-462X},
abstract = {INTRODUCTION: The R2R3-MYB transcription factors (TFs) are pivotal regulators of plant growth, development, and stress responses. However, their genetic diversity and functional roles in Brassica napus remain underexplored at a pan-genome scale.

METHODS: We identified R2R3-MYB genes in 18 published rapeseed genomes and analyzed their genomic distribution patterns, gene duplication, selective pressure, gene structure, conserved motifs, and phylogenetic relationships using a pan-genome approach. Additionally, transcriptomic datasets from hormone treatments and drought/heat stress experiments were analyzed to identify hormone-responsive and stress-responsive genes.

RESULTS: We systematically identified 7,552 R2R3-MYB genes from 18 B. napus genomes, which were grouped into 353 gene clusters based on the pan-genome approach, including 139 core, 121 softcore, 68 dispensable, and 25 private gene clusters. Similar to Arabidopsis, the B. napus R2R3-MYB genes can be clustered into 29 subgroups based on the phylogenetic tree, suggesting conserved functional roles in B. napus and A. thaliana. Cis-element profiling highlighted enrichment in hormone-responsive and stress-related elements in the promoter regions of the R2R3-MYB genes. Transcriptomic analyses identified 283 hormone-responsive and 266 stress-responsive R2R3-MYB genes, and 30 co-regulated genes under drought and heat stress implicate their roles in combined stress adaptation.

DISCUSSION: These findings provide the first pan-genome resource for R2R3-MYB genes in B. napus, which can serve as pivotal targets for enhancing stress resilience in rapeseed breeding programs.},
}

@article {pmid40484528,
year = {2025},
author = {Jeong, E and Seo, JA},
title = {Comparative genome analyses of Aspergillus oryzae and Aspergillus flavus originated from a Korean fermentation starter, nuruk.},
journal = {Food microbiology},
volume = {131},
number = {},
pages = {104807},
doi = {10.1016/j.fm.2025.104807},
pmid = {40484528},
issn = {1095-9998},
mesh = {*Aspergillus oryzae/genetics/isolation & purification/classification/metabolism ; *Aspergillus flavus/genetics/isolation & purification/classification/metabolism ; Phylogeny ; *Genome, Fungal ; Fermentation ; *Fermented Foods/microbiology ; Republic of Korea ; Food Microbiology ; Whole Genome Sequencing ; Polymorphism, Single Nucleotide ; Fungal Proteins/genetics ; },
abstract = {Aspergillus oryzae is an industrially important fungus used to produce traditional fermented foods and beverages in Korea and other East Asian countries. Conversely, A. flavus, which exhibits approximately 99.5 % of genomic similarity to A. oryzae, is a species that endangers food safety due to aflatoxin production. This study involved the genome sequences of A. oryzae KBP3 and KSS2 isolated from nuruk, a traditional Korean fermentation starter, assembled at the chromosomal level. To investigate differences among closely related species concerning food safety, compartive genome analysis was conducted on 30 strains of Aspergillus section Flavi, including nuruk strains and 28 genome sequences sourced from additional sequencing and the GenBank database. A detailed interspecific diversity was compared by examining the composition and chromosomal locations of annotated genes across 30 strains. A phylogenetic tree based on whole genome sequences, orthologous genes, and single nucleotide polymorphisms of core genes across 30 strains divided A. oryzae and A. flavus into two separate clades with some exceptions. This study presents two high-quality whole genome sequences of A. oryzae, providing significant genetic insights for this species and its closely related species. Our study confirmed the wide range of enzyme-related genes in A. oryzae isolated from nuruk, and its intraspecific genomic diversity. Our findings also systematically organize the pangenome analysis data of closely related species within Aspergillus section Flavi at the chromosomal level, enhancing the understanding of the genetic information relevant to food safety-related species.},
}

*Aspergillus oryzae/genetics/isolation & purification/classification/metabolism
*Aspergillus flavus/genetics/isolation & purification/classification/metabolism
Phylogeny
*Genome, Fungal
Fermentation
*Fermented Foods/microbiology
Republic of Korea
Food Microbiology
Whole Genome Sequencing
Polymorphism, Single Nucleotide
Fungal Proteins/genetics

@article {pmid40479512,
year = {2025},
author = {Strader, LC and Chen, T and Dong, X and Edwards, D and Sureshkumar, S and Balasubramanian, S and Antunes, MS and Zebluim, L and Chaisupa, P and Wright, RC},
title = {Core biological principles and tools stemming from basic Arabidopsis research.},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koaf141},
pmid = {40479512},
issn = {1532-298X},
abstract = {The model plant Arabidopsis thaliana has been a cornerstone of research in plant biology, contributing transformative insights into fundamental biological processes across eukaryotes. In this vignette, we explore the role of Arabidopsis in elucidating immune mechanisms, where plant studies have informed mammalian immunity and translational regulation. We discuss how Arabidopsis-driven advancements in pangenomics and repeat expansions have reshaped our understanding of genomic variability and its implications for diseases like Friedreich's ataxia. Breakthroughs in synthetic biology and bioproduction underscore Arabidopsis' role as a testbed for engineering specialized metabolites and advancing biotechnological applications. Finally, we examine how the development of tools like Auxin-Inducible Degradation (AID) has extended beyond plant research, providing critical methodologies to study protein function and develop novel therapeutics.},
}

@article {pmid40478766,
year = {2025},
author = {Ross, TA and Janice, J and Arredondo-Alonso, S and Löhr, IH and Holsbø, E and Corander, J and Pöntinen, AK and Kampffmeyer, M and Hegstad, K},
title = {Enterococcus lactis is ecologically and genetically distinct from the major opportunistic pathogen Enterococcus faecium.},
journal = {Microbial genomics},
volume = {11},
number = {6},
pages = {},
pmid = {40478766},
issn = {2057-5858},
mesh = {*Enterococcus faecium/genetics/classification/pathogenicity ; Genome, Bacterial ; Humans ; Phylogeny ; Animals ; Whole Genome Sequencing ; *Enterococcus/genetics/classification ; Evolution, Molecular ; Genetic Variation ; },
abstract = {Enterococcus faecium is a major human opportunistic bacterial pathogen and a close relative of the recently established species Enterococcus lactis. As a species, commensal E. lactis remains relatively understudied, and its genetic connectivity with E. faecium is not thoroughly understood. Here, we introduce a large collection of whole-genome sequenced isolates comprising 894 E. faecium and 392 E. lactis genomes. Using these genomes to complement publicly available data, we studied the genome content and the evolutionary relationship between these species. A wider range of host species was observed in E. faecium; in particular, there is a radiation of E. faecium clades specialized to domesticated and pet animals among which E. lactis is uncommon. Of note, pangenome analyses reveal that E. lactis has significantly more allelic variation and lower recombination rates in core genes compared with E. faecium. These observations suggest that E. lactis represents a population that has occupied its ecological niche longer than E. faecium has. This study enhances understanding of the evolutionary histories of these species and highlights the importance of sampling and studying closely related commensal bacteria in addition to clinically relevant opportunistic pathogens.},
}

*Enterococcus faecium/genetics/classification/pathogenicity
Genome, Bacterial
Humans
Phylogeny
Animals
Whole Genome Sequencing
*Enterococcus/genetics/classification
Evolution, Molecular
Genetic Variation

@article {pmid40475428,
year = {2025},
author = {Shivakumar, VS and Langmead, B},
title = {Partitioned Multi-MUM finding for scalable pangenomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.20.654611},
pmid = {40475428},
issn = {2692-8205},
abstract = {Pangenome collections are growing to hundreds of high-quality genomes. This necessitates scalable methods for constructing pangenome alignments that can incorporate newly-sequenced assemblies. We previously developed Mumemto, which computes maximal unique matches (multi-MUMs) across pangenomes using compressed indexing. In this work, we extend Mumemto by introducing two new partitioning and merging strategies. Both strategies enable highly parallel, memory efficient, and updateable computation of multi-MUMs. One of the strategies, called string-based merging, is also capable of conducting the merges in a way that follows the shape of a phylogenetic tree, naturally yielding the multi-MUM for the tree's internal nodes as well as the root. With these strategies, Mumemto now scales to 474 human haplo-types, the only multi-MUM method able to do so. It also introduces a time-memory tradeoff that allows Mumemto to be tailored to more scenarios, including in resource-limited settings.},
}

@article {pmid40472804,
year = {2025},
author = {Stanley, S and Silva-Costa, C and Gomes-Silva, J and Melo-Cristino, J and Malley, R and Ramirez, M},
title = {CC180 clade dynamics do not universally explain Streptococcus pneumoniae serotype 3 persistence post-vaccine: a global comparative population genomics study.},
journal = {EBioMedicine},
volume = {117},
number = {},
pages = {105781},
doi = {10.1016/j.ebiom.2025.105781},
pmid = {40472804},
issn = {2352-3964},
abstract = {BACKGROUND: Clonal complex 180 (CC180) is currently the major clone of serotype 3 Streptococcus pneumoniae (Spn) causing disease among children and adults worldwide. The 13-valent pneumococcal conjugate vaccine (PCV13) does not have significant efficacy against serotype 3 despite polysaccharide inclusion in the vaccine. It was hypothesized that PCV13 may effectively control Clade I of CC180 but that Clades III and IV are resistant, provoking a population shift that enables serotype 3 persistence. This has been observed in the United States, England, and Wales but not Spain. We tested this hypothesis further utilizing a dataset from Portugal to conduct our population genomics and molecular epidemiology comparative study.

METHODS: We performed whole-genome sequencing (WGS) of 501 serotype 3 strains from Portugal isolated from patients with pneumococcal infections between 1999 and 2020. The draft genomes underwent phylogenetic analyses, pangenome profiling, and a genome-wide association study (GWAS). We also completed antibiotic susceptibility testing and compiled over 2600 serotype 3 multilocus sequence type 180 (MLST180) WGSs to perform global comparative genomics.

FINDINGS: Relative to strains from all other lineages, CC180 Clades I, II, III, IV, and VI strains trend towards a decreased association with invasive disease cases compared to non-invasive pneumonia cases (binomial logistic regression, odds ratio or OR = 0.59, 95% confidence interval or CI = [0.34, 0.98], P = 0.046) and adult patients compared to paediatric patients (binomial logistic regression, OR = 0.34, 95% CI = [0.098, 0.92], P = 0.054). The serotype 3 CCs shifted post-PCV13 such that Clades I-VI comprise the majority of post-PCV13 lineages (binomial logistic regression, OR = 7.33, 95% CI = 4.36, 12.80, P < 0.0001), with Clade I representing 54% (220/404) of all post-PCV13 strains. As observed elsewhere, Clade I strains from Portugal are largely antibiotic-sensitive and carry the ΦOXC141 prophage. However, strains from Portugal and Spain, where Clade I remains dominant post-PCV13, have larger pangenomes and are associated with the presence of two genes encoding hypothetical proteins.

INTERPRETATION: Clade I became dominant in Portugal post-PCV13, despite the burden of the prophage and antibiotic sensitivity. The additional accessory genome content may mitigate these fitness costs. Regional differences in Clade I prevalence and pangenome heterogeneity suggest that clade dynamics is not a generalizable approach to understanding serotype 3 vaccine escape.

FUNDING: National Institute of Child Health and Human Development, Pfizer, and Merck Sharp & Dohme.},
}

@article {pmid40467258,
year = {2025},
author = {Li, Y and Liu, Y and Zheng, B and Zhang, C and Cai, Y and Cheng, Y and Wang, J},
title = {Multicellular behavior and genomic characterization of Salmonella Typhimurium in animal-derived food chains in Xinjiang, China: Phenotypic resistance, biofilm formation, and sequence types.},
journal = {Food research international (Ottawa, Ont.)},
volume = {214},
number = {},
pages = {116698},
doi = {10.1016/j.foodres.2025.116698},
pmid = {40467258},
issn = {1873-7145},
mesh = {*Biofilms/growth & development ; Animals ; China ; *Salmonella typhimurium/genetics/drug effects/isolation & purification/physiology/classification ; *Food Microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Phenotype ; Anti-Bacterial Agents/pharmacology ; Sheep ; Cattle ; Whole Genome Sequencing ; Genome, Bacterial ; },
abstract = {Salmonella Typhimurium Is a globally significant foodborne pathogen that causes diseases in livestock and poultry, which can lead to human infections and fatalities through contaminated food. In this study, we investigated the prevalence of Salmonella Typhimurium in the animal-derived food chain in Xinjiang, China. Among 5075 samples, the detection rate of Salmonella was 8.26 % (419/5075). Of these isolates, 27.21 % (114/419) were identified as Salmonella Typhimurium. Phenotypic analysis revealed significant antibiotic resistance: 82.46 % (94/114) of the strains exhibited multidrug resistance (MDR), with high resistance rates to amoxicillin / clavulanic acid, ampicillin, and tetracycline. Congo red plate assays demonstrated that 62.28 % (71/114) of the strains exhibited multicellular behavior (RDAR morphotype). Biofilm formation assays indicated that 96.49 % (110/114) of the strains possessed biofilm-forming capabilities, with 18.18 % (20/110) showing strong biofilm formation. Notably, strains displaying multicellular behavior exhibited enhanced biofilm formation, and biofilm capability was positively correlated with antibiotic resistance phenotypes. Whole-genome sequencing of 40 representative strains identified four sequence types (ST19, ST34, ST99, ST128), with ST34 being the most predominant. Distinct host preferences were observed: ST34 strains originated exclusively from cattle and sheep, while ST19, ST99, and ST128 strains were isolated from geese and pigeons. Resistance gene profiling revealed that strains harboring resistance genes exhibited stronger resistance phenotypes, while ST99 and ST128 strains lacked detectable resistance genes. Plasmids R64, R478, and pKPC_CAV1321 were identified in cattle- and sheep-derived strains, whereas pSLT-BT and pSPCV plasmids were predicted in strains from geese and pigeons. Pan-genome analysis and phylogenetic reconstruction demonstrated distinct genetic clustering among ST types, with ST19 and ST128 showing closer evolutionary relationships. This study provides comprehensive insights into the prevalence, phenotypic characteristics, and genomic diversity of Salmonella Typhimurium in the animal-derived food chain in Xinjiang. Our findings contribute to region-specific pathogen control strategies, enhancing public health safety and consumer protection.},
}

*Biofilms/growth & development
Animals
China
*Salmonella typhimurium/genetics/drug effects/isolation & purification/physiology/classification
*Food Microbiology
Drug Resistance, Multiple, Bacterial/genetics
Phenotype
Anti-Bacterial Agents/pharmacology
Sheep
Cattle
Whole Genome Sequencing
Genome, Bacterial

@article {pmid40463162,
year = {2025},
author = {Das, A and Biddanda, A and McCoy, RC and Schatz, MC},
title = {Assembling unmapped reads reveals hidden variation in South Asian genomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.14.653340},
pmid = {40463162},
issn = {2692-8205},
abstract = {Conventional genome mapping-based approaches systematically miss genetic variation, particularly in regions that substantially differ from the reference. To explore this hidden variation, we examined unmapped and poorly mapped reads from the genomes of 640 human individuals from South Asian (SAS) populations in the 1000 Genomes Project and the Simons Genome Diversity Project. We assembled tens of megabases of non-redundant sequence in tens of thousands of large contigs, much of which is present in both SAS and non-SAS populations. We demonstrated that much of this sequence is not discovered by traditional variant discovery approaches even when using complete genomes and pangenomes. Across 20,000 placed contigs, we found 8,215 intersections with 106 protein coding genes and >15,000 placements within 1 kbp of a known GWAS hit. We used long read data from a subset of samples to validate the majority of their assembled sequences, aligned RNA-seq data to identify hundreds of unplaced contigs with transcriptional potential, and queried existing nucleotide databases to evaluate the origins of the remaining unplaced sequences. Our results highlight the limitations of even the most complete reference genomes and provide a model for understanding the distribution of hidden variation in any human population.},
}

@article {pmid40463112,
year = {2025},
author = {Eskandar, P and Paten, B and Sirén, J},
title = {Lossless Pangenome Indexing Using Tag Arrays.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.12.653561},
pmid = {40463112},
issn = {2692-8205},
abstract = {Pangenome graphs represent the genomic variation by encoding multiple haplotypes within a unified graph structure. However, efficient and lossless indexing of such structures remains challenging due to the scale and complexity of pangenomic data. We present a practical and scalable indexing framework based on tag arrays, which annotate positions in the Burrows-Wheeler transform (BWT) with graph coordinates. Our method extends the FM-index with a run-length compressed tag structure that enables efficient retrieval of all unique graph locations where a query pattern appears. We introduce a novel construction algorithm that combines unique k -mers, graph-based extensions, and haplotype traversal to compute the tag array in a memory-efficient manner. To support large genomes, we process each chromosome independently and then merge the results into a unified index using properties of the multi-string BWT and r-index. Our evaluation on the HPRC graphs demonstrates that the tag array structure compresses effectively, scales well with added haplotypes, and preserves accurate mapping information across diverse regions of the genome. This indexing method enables lossless and haplotype-aware querying in complex pangenomes and offers a practical indexing layer to develop scalable aligners and downstream graph-based analysis tools.},
}

@article {pmid40463106,
year = {2025},
author = {Hamilton, W and Massey, J and Hardy, E and López-Madrigal, S and Phelps, M and Martin, M and Newton, I},
title = {Wolbachia uses ankyrin repeats to target specific fly proteins.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40463106},
issn = {2692-8205},
abstract = {UNLABELLED: Arthropods, the most diverse phylum on Earth, are hosts to a plethora of bacterial parasites that secrete various effectors of unknown function during infection. The most prevalent of these is the intracellular bacterium Wolbachia pipientis . The microbe infects between 40-60% of insect species, causes important reproductive manipulations, and limits virus replication in arthropod vectors, becoming a promising biocontrol agent. Understanding the molecular basis of Wolbachia infection and Wolbachia- induced phenotypes is critical to the use of Wolbachia in vector control. These Wolbachia ankyrin repeat proteins (WARPs) represent a highly dynamic and diverse part of the Wolbachia pangenome and remain thus far, largely uncharacterized. Here, we perform molecular and genetic screens to identify interactions between Wolbachia w Mel WARPs and their target host proteins in Drosophila melanogaster . Our results identify strong interactions of two Wolbachia proteins, WARP434 and WARP754, with two host targets (CG11327 and Ptp61F, respectively). Heterologous expression of these two WARPs is extremely toxic in Drosophila tissues and the toxicity is dependent on the ankyrin repeat domain of each WARP. Importantly, knockdown of the host targets alleviates toxicity, confirming WARP/target interactions. Finally, antibodies targeting both WARPs show expression by Wolbachia during infection of Drosophila cells. Understanding how Wolbachia manipulates its host biology and which host pathways it targets during infection will help us divine how the most prevalent intracellular bacterial parasite on Earth interacts with its insect hosts at the molecular level. Our screen is the first step towards that goal.

IMPORTANCE: Molecular interactions drive co-evolutionary arms races between hosts and pathogens. These interactions shape the structure and function of both host and parasite proteins, enabling immunity or virulence during infection. Understanding the molecular details that unfold during these events illustrates not only how hosts and parasites co-evolve at the molecular level but also may help characterize the function of poorly understood proteins. The most prevalent intracellular infection on earth is Wolbachia pipientis, with between 40-60% of insects harboring the bacterial symbiont. Understanding how Wolbachia infects host cells and the molecular tools it uses to alter cell biology is critical to the use of the microbe in vector control. Here, we identify Wolbachia proteins used by the symbiont to interface with specific host proteins. Understanding the molecular mechanisms underlying this host-microbe interaction will shed light on how an important symbiont, used in the control of vector populations and disease transmission, uses WARPs to interact with host targets and how targeting this host protein contributes to infection.},
}

@article {pmid40462382,
year = {2025},
author = {Yacoub, MN and Stajich, JE},
title = {Comparative genomics reveals intra and inter species variation in the pathogenic fungus Batrachochytrium dendrobatidis.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf114},
pmid = {40462382},
issn = {1759-6653},
abstract = {The Global Panzootic Lineage (GPL) of Batrachochytrium dendrobatidis (Bd) has been described as a main driver of amphibian extinctions. Pathogen studies have benefited from three Bd-GPL strain genomes, but identifying the genetic and molecular features that distinguish the B. dendrobatidis lineages requires additional high quality genomes from diverse lineages. We sequenced and assembled genomes with Oxford Nanopore Technologies to produce assemblies of three Bd-BRAZIL isolates and one non-pathogen outgroup species Polyrhizophydium stewartii. The Bd-BRAZIL assembly sizes ranged between 22.0-26.1 Mb with 8,495 - 8,620 predicted protein-coding genes. We sought to categorize the pangenome of the species by identifying homologous genes across the sampled genomes as either being core and present in all strains, or accessory and shared among strains in a lineage, an analysis that has not yet been conducted on B. dendrobatidis and its lineages. We identified a core genome consisting of 6,278 gene families, and an accessory genome of 202 Bd-BRAZIL and 172 Bd-GPL specific gene families. We discovered copy number differences in pathogenicity gene families: M36 Peptidases, Crinkler Necrosis genes, Aspartyl Peptidases, Carbohydrate-Binding Module-18 genes, and S41 Proteases, between Bd-BRAZIL and Bd-GPL strains. Comparison of B. dendrobatidis and two closely related saprophytic species identified differences in protein sequence and domain counts for M36 and CBM18 families respectively. Our pangenome analysis of lineage-specific gene content led us to explore how the selection of the reference genome affects recovery of RNAseq transcripts when comparing different strains. We tested the hypothesis that genomic variation among Bd-GPL and Bd-BRAZIL lineages can impact transcript count data by comparing results with our new Bd-BRAZIL genomes as the reference genomes. Our analysis examines the genomic variation between strains in Bd-BRAZIL and Bd-GPL and offers insights into the application of these high quality reference genomes resources for future studies.},
}

@article {pmid40453788,
year = {2025},
author = {Golletz, P and Jensen, SD and Collignon, M and Hall, C and Khamas, AB and Møllebjerg, A and Schlafer, S and Meyer, RL and Tykwinska, K},
title = {Coaggregation of oral pathogens by postbiotic lactobacilli.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2508483},
pmid = {40453788},
issn = {2000-2297},
abstract = {INTRODUCTION: Coaggregation may reduce the abundance of bacteria in physiological fluids, such as saliva, as aggregated bacteria are cleared more easily than planktonic cells. This study aimed to identify Lactobacillus strains that coaggregate with oral pathogens with the perspective of using this approach to improve oral health.

MATERIAL AND METHODS: Coaggregation of 719 postbiotic Lactobacillus strains with target pathogens Fusobacterium nucleatum, Porphyromonas gingivalis, and Prevotella intermedia was quantified by absorbance. Coaggregation efficacy of selected strains with clinical isolates and in the presence of other salivary bacteria was determined by flow cytometry. Brightfield and confocal microscopy were applied to characterize the size and structure of coaggregates. Pangenome analysis was used to identify genomic regions potentially involved in the coaggregation activity.

RESULTS: Two strains, Lacticaseibacillus rhamnosus 1B06 and Lacticaseibacillus paracasei 8A12, coaggregated efficiently with all three target pathogens and clinical isolates of the same species even in the presence of other salivary bacteria. The coaggregation capability of the selected Lactobacillus strains was unique and could not be reproduced with other genetically similar lactic acid bacteria of the same species.

CONCLUSION: Lactobacillus strains capable of coaggregating oral pathogens were identified as promising candidates for the development of new postbiotic ingredients for oral hygiene products.},
}

@article {pmid40445831,
year = {2025},
author = {Dong, Z and Whitehead, J and Fu, M and MacIsaac, JL and Rehkopf, DH and Rosero-Bixby, L and Kobor, MS and Korthauer, K},
title = {Complete reference genome and pangenome improve genome-wide detection and interpretation of DNA methylation using sequencing and array data.},
journal = {Cell reports},
volume = {44},
number = {6},
pages = {115755},
doi = {10.1016/j.celrep.2025.115755},
pmid = {40445831},
issn = {2211-1247},
abstract = {The complete telomere-to-telomere human genome assembly (T2T-CHM13) and the draft human pangenome reference provide unique opportunities to refine DNA methylation (DNAm) studies. Here, we find that T2T-CHM13 calls 7.4% more CpGs genome wide compared to GRCh38 across four widely used short-read DNAm profiling methods and improves the evaluation of probe cross-reactivity and mismatch for Illumina DNAm arrays, yielding new and more reproducible sets of unambiguous probes. The pangenome reference further expands CpG calling by 4.5% in short-read sequencing data and identifies cross-population and population-specific unambiguous probes in DNAm arrays, owing to its improved representation of genetic diversity. These benefits facilitate the discovery of biologically relevant DNAm alterations in epigenome-wide association studies (EWASs). For instance, additional DNAm alterations enriched in cancer-related genes and pathways are identified in cancer EWASs. Together, this study highlights the practical applications of T2T-CHM13 and pangenome for genome biology and provides a basis for expansion of DNAm investigations.},
}

@article {pmid40444387,
year = {2025},
author = {Lötter, A and Bruna, T and Duong, TA and Barry, K and Lipzen, A and Daum, C and Yoshinaga, Y and Grimwood, J and Jenkins, JW and Talag, J and Borevitz, J and Lovell, JT and Schmutz, J and Wegrzyn, JL and Myburg, AA},
title = {A haplotype-resolved reference genome for Eucalyptus grandis.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf112},
pmid = {40444387},
issn = {2160-1836},
abstract = {E. grandis is a hardwood tree used worldwide as pure species or hybrid partner to breed fast-growing plantation forestry crops that serve as feedstocks of timber and lignocellulosic biomass for pulp, paper, biomaterials and biorefinery products. The current v2.0 genome reference for the species (Bartholome et al. 2015; Myburg et al. 2014) served as the first reference for the genus and has helped drive the development of molecular breeding tools for eucalypts. Using PacBio HiFi long reads and Omni-C proximity ligation sequencing, we produced an improved, haplotype-phased assembly (v4.0) for TAG0014, an early-generation selection of E. grandis. The two haplotypes are 571 Mbp (HAP1) and 552 Mbp (HAP2) in size and consist of 37 and 46 contigs scaffolded onto 11 chromosomes (contig N50 of 28.9 and 16.7 Mbp), respectively. These haplotype assemblies are 70 to 90 Mbp smaller than the diploid v2.0 assembly but capture all except one of the 22 telomeres, suggesting that substantial redundant sequence was included in the previous assembly. A total of 35,929 (HAP1) and 35,583 (HAP2) gene models were annotated, of which 438 and 472 contain long introns (>10 kbp) in gene models previously (v2.0) identified as multiple smaller genes. These and other improvements have increased gene annotation completeness levels from 93.8% to 99.4% in the v4.0 assembly. We found that 6,493 and 6,346 genes are within tandem duplicate arrays (HAP1 and HAP2, respectively, 18.4% and 17.8% of the total) and >43.8% of the haplotype assemblies consists of repeat elements. Analysis of synteny between the haplotypes and the E. grandis v2.0 reference genome revealed extensive regions of collinearity, but also some major rearrangements, and provided a preview of population and pan-genome variation in the species.},
}

@article {pmid40442592,
year = {2025},
author = {Wang, H and Liu, J and Guo, Y and Chen, Y and Zhang, C and He, S and Zhang, W and Ding, L},
title = {Taxonomic, genomic, and ecological insights into a novel Flavobacteriaceae strain from coastal tidal flats.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {344},
pmid = {40442592},
issn = {1471-2180},
support = {42176101//National Natural Science Foundation of China/ ; 2021Z046//Ningbo Key Science and Technology Development Program/ ; IF2021087//Scientific Research Foundation of Graduate School of Ningbo University/ ; D16013//National 111 Project of China/ ; },
mesh = {Phylogeny ; *Flavobacteriaceae/classification/genetics/isolation & purification/physiology ; China ; *Genome, Bacterial ; *Seawater/microbiology ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Genomics ; *Geologic Sediments/microbiology ; Ecosystem ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Tidal flats are vital coastal ecosystems that play a significant role in organic carbon accumulation and biogeochemical cycles. Members of the family Flavobacteriaceae is known for its ability to degrade complex organic matter, including polysaccharides. However, the ecological roles and metabolic capabilities of Flavobacteriaceae in tidal flat environments remain underexplored.

RESULTS: In this study, we isolated and characterized a novel bacterium, strain NBU2967[T], from the tidal flats of Meishan Island in the East China Sea. Phylogenetic and genomic analyses identified this strain as a new genus and species within the family Flavobacteriaceae, for which we propose the name Meishania litoralis gen. nov., sp. nov. Comprehensive polyphasic characterization, including morphological, physiological, chemotaxonomic, and genomic analyses, confirmed its distinct taxonomic status. Genomic analysis revealed a diverse set of carbohydrate-active enzymes (CAZymes), along with multiple metabolic pathways associated with carbon and sulfur cycling, highlighting the strain's potential adaptation to organic-rich marine environments. Comparative genomic and pangenome analyses further demonstrated significant genetic divergence from related taxa. Environmental distribution data revealed that the newly proposed genus Meishania is widely distributed across global marine ecosystems.

CONCLUSIONS: We isolated and characterized a novel bacterium, designated NBU2967[T] (= KCTC 82912[ T] = MCCC 1K06391[T]), for which we propose the name Meishania litoralis gen. nov., sp. nov. This strain is classified as a new genus within the family Flavobacteriaceae. The strain's ability to process both carbon and sulfur compounds underscores its ecological significance in marine ecosystems. These findings provide novel insights into the ecological functions of the family Flavobacteriaceae in coastal tidal flats environments and enhance our understanding of microbial-mediated degradation and transformation of chemical compounds in dynamic coastal ecosystems.},
}

Phylogeny
*Flavobacteriaceae/classification/genetics/isolation & purification/physiology
China
*Genome, Bacterial
*Seawater/microbiology
RNA, Ribosomal, 16S/genetics
DNA, Bacterial/genetics
Genomics
*Geologic Sediments/microbiology
Ecosystem
Sequence Analysis, DNA

@article {pmid40442154,
year = {2025},
author = {Seong, HJ and Park, YM and Kim, BS and Yoo, HJ and Kim, T and Yoon, SM and Kim, JH and Lee, SY and Lee, YK and Lee, DW and Nam, MH and Hong, SJ},
title = {Integrated multi-omics reveals different host crosstalk of atopic dermatitis-enriched Bifidobacterium longum Strains.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {91},
pmid = {40442154},
issn = {2055-5008},
mesh = {Humans ; *Dermatitis, Atopic/microbiology ; *Gastrointestinal Microbiome ; Infant ; *Bifidobacterium longum/genetics/isolation & purification/classification/metabolism ; Female ; Male ; Metabolomics ; Metagenomics/methods ; Feces/microbiology ; *Host Microbial Interactions ; Clostridium/genetics/isolation & purification ; Transcriptome ; Multiomics ; },
abstract = {The infant gut microbiome is essential for long-term health and is linked to atopic dermatitis (AD), although the underlying mechanisms are not fully understood. This study investigated gut microbiome-host interactions in 31 infants with AD and 29 healthy controls using multi-omics approaches, including metagenomic, host transcriptomic, and metabolomic analyses. Microbial diversity was significantly altered in AD, with Bifidobacterium longum and Clostridium innocuum associated with these changes. At the strain-level, only B. longum differed significantly between groups, with pangenome analyses identifying genetic variations potentially affecting amino acid and lipid metabolites. Notably, B. longum subclade I, which was more prevalent in healthy controls, correlated with host transcriptomic pathways involved in phosphatidylinositol 3-kinase-AKT signaling and neuroactive ligand-receptor pathways, as well as specific metabolites, including tetrahydrocortisol and ornithine. These findings highlight the role of B. longum strain-level variation in infants, offering new insights into microbiome-host interactions related to AD.},
}

Humans
*Dermatitis, Atopic/microbiology
*Gastrointestinal Microbiome
Infant
*Bifidobacterium longum/genetics/isolation & purification/classification/metabolism
Female
Male
Metabolomics
Metagenomics/methods
Feces/microbiology
*Host Microbial Interactions
Clostridium/genetics/isolation & purification
Transcriptome
Multiomics

@article {pmid40442108,
year = {2025},
author = {Meng, Q and Xie, P and Xu, Z and Tang, J and Hui, L and Gu, J and Gu, X and Jiang, S and Rong, Y and Zhang, J and Udall, JA and Grover, CE and Zheng, K and Chen, Q and Kong, J and Wang, M and Nie, X and Lin, Z and Jin, S and Wendel, JF and Zhang, X and Yuan, D},
title = {Pangenome analysis reveals yield- and fiber-related diversity and interspecific gene flow in Gossypium barbadense L.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4995},
pmid = {40442108},
issn = {2041-1723},
mesh = {*Gossypium/genetics ; *Cotton Fiber ; *Genome, Plant/genetics ; Genome-Wide Association Study ; *Gene Flow ; Genetic Variation ; Quantitative Trait Loci ; },
abstract = {Gossypium barbadense is renowned for its superior fiber quality, particularly its extra-long fibers, although its fiber yield is lower compared to G. hirsutum. Here, to further reveal fiber-related genomic variants of G. barbadense, we de novo assemble 12 genomes of G. barbadense that span the wild-to-domesticated continuum, and construct a graph-based pangenome by integrating these assemblies and 17 publicly available tetraploid cotton genome assemblies. We uncover the divergent evolutionary trajectories and subsequent exchanges between G. barbadense and G. hirsutum through investigation of structural variants (SVs). We perform the SV-based GWAS analysis in G. barbadense and identify four, three, and seven candidate SVs for fiber length, fiber strength, and lint percentage, respectively. Furthermore, we detect the underlying candidate genes and uncover the origin and distribution of favorable alleles, and reveal the tradeoff between lint percentage and fiber quality. These pangenome and trait-associated SVs provide insights into and resources for improving cotton fiber.},
}

*Gossypium/genetics
*Cotton Fiber
*Genome, Plant/genetics
Genome-Wide Association Study
*Gene Flow
Genetic Variation
Quantitative Trait Loci

@article {pmid40438217,
year = {2025},
author = {Zhou, G and Yu, Y and Ge, T and Tang, C and Zhang, H and He, M},
title = {Whole-genome probe capture sequencing reveals genomic diversity and characteristics of Mycoplasma pneumoniae in Nanjing, China.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1589971},
pmid = {40438217},
issn = {1664-302X},
abstract = {Mycoplasma pneumoniae (M. pneumoniae), a slow-growing, fastidious Gram-negative bacterium and a leading cause of community-acquired pneumonia globally, remains understudied and underreported across numerous geographical areas in China despite its worldwide significance. This study employed probe capture sequencing for targeted enrichment and direct sequencing of M. pneumoniae from clinical samples, combined with comparative genomic analyses of contemporary and historical global genomes. Core genome and pan-genome revealed that the M. pneumoniae genomes were classified into two distinct clades, P1-I and P1-II, each associated with a specific sequence type (ST). Most of the genomes sequenced in this study were identified as P1-I (86.96%, 20/23), contrasting with the previously reported predominance of P1-II in the area. A limited number of single-nucleotide variations were identified in the virulence-associated genes between P1-I and P1-II, leading to amino acid substitutions. The A2063G point mutation in the 23S rRNA gene was detected in all sequenced genomes (23/23), demonstrating a 100% mutation rate. This study provides the first reported application of probe capture methodology for M. pneumoniae, highlighting the critical importance of sustained surveillance efforts to monitor the evolution and epidemiology of this pathogen.},
}

@article {pmid40437759,
year = {2025},
author = {Xia, Z and Du, Z and Zhou, X and Jiang, S and Zhu, T and Wang, L and Chen, F and Carvalho, L and Zou, M and Becerra López-Lavalle, LA and Zhang, X and Xu, L and Wang, Z and Chen, M and Guo, X and Wang, S and Li, M and Li, Y and Wang, H and Liu, S and Bao, Y and Zhao, L and Zhang, C and Xiao, J and Guo, F and Shen, X and Li, H and Lu, C and Qiao, F and Ceballos, H and Yan, H and Qin, X and Ma, L and Zhang, H and He, S and Zhao, W and Wan, Y and Chen, Y and Huang, D and Li, K and Liu, B and Peng, M and Zhang, W and Møller, BL and Chen, X and Luo, MC and Xiao, J and Wang, W},
title = {Pan-genome and Haplotype Map of Cassava Cultivars and Wild Ancestors Provide Insights into its Adaptive Evolution and Domestication.},
journal = {Molecular plant},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molp.2025.05.014},
pmid = {40437759},
issn = {1752-9867},
abstract = {Cassava is an important, resilient tropical crop that produces large starchy storage roots and high biomass. But how did cassava´s remarkable environmental adaptability and key economic traits evolve from its wild species? We constructed nearly T2T genomes and their haplotype forms for the cultivar AM560, wild ancestors FLA4047 and W14, a graphic pan-genome of 30 representatives with 1.15 Gb, and built a clarified evolutionary tree of 486 accessions. A comparison of structural variations (SVs) and single-nucleotide variations (SNVs) between the ancestors and cultivated cassavas reveals predominant expansions and contractions of genes and gene families, which are mainly driven by transposons. Significant selective sweeping occurred in 122 footprints of genomes and affects 1,519 domesticated genes. We identify selective mutations in MeCSK and MeFNR2 that could promote photoreactions associated with MeNADP-ME in C4 photosynthesis in modern cassava. Co-evolution of retard floral primordia and initiation of storage roots may arise from MeCOL5 variants with altered bindings to MeFT1, MeFT2, and MeTFL2. Mutations of MeMATE1 and MeGTR occur in sweet cassava, and MeAHL19 has evolved to regulate the biosynthesis, transport, and endogenous remobilization of cyanogenic glucosides in cassava. These extensive genomic and gene resources provided here and the findings of the evolutionary mechanisms responsible for beneficial traits in modern cultivars represent a stepping-stone in future breeding of cassava.},
}

@article {pmid40437706,
year = {2025},
author = {Kim, J and Zhang, J and Kinch, L and Shen, J and Field, S and Khan, S and Klapproth, JM and Forsberg, KJ and Harris-Tryon, T and Orth, K and Cong, Q and Ni, J},
title = {Genetic and Microbial Analysis of Invasiveness for Escherichia coli Strains Associated With Inflammatory Bowel Disease.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {19},
number = {4},
pages = {101451},
doi = {10.1016/j.jcmgh.2024.101451},
pmid = {40437706},
issn = {2352-345X},
mesh = {Humans ; *Escherichia coli/genetics/pathogenicity/isolation & purification/drug effects ; *Inflammatory Bowel Diseases/microbiology ; *Escherichia coli Infections/microbiology ; Phenotype ; Epithelial Cells/microbiology ; Genotype ; Whole Genome Sequencing ; Virulence/genetics ; Drug Resistance, Bacterial/genetics ; Virulence Factors/genetics ; },
abstract = {BACKGROUND & AIMS: The adherent-invasive Escherichia coli (AIEC) pathotype is implicated in inflammatory bowel disease (IBD) pathogenesis. AIEC strains are currently defined by phenotypic measurement of their pathogenicity, including invasion of epithelial cells. This broad definition, combined with the genetic diversity of AIEC across patients with IBD, has complicated the identification of virulence determinants. We sought to quantify the invasion phenotype of clinical isolates from patients with IBD and identify the genetic basis for their invasion into epithelial cells.

METHODS: A pangenome with core and accessory genes (genotype) was assembled using whole genome sequencing of 168 E coli samples isolated from 13 patients with IBD. A modified assay for invasion of epithelial cells (phenotype) was established with consideration of antibiotic resistance phenotypes. Isolate genotype was correlated to invasiveness phenotype to identify genetic factors that cosegregate with invasion.

RESULTS: Pangenome-wide comparisons of E coli clinical isolates identified accessory genes that can cosegregate with invasion phenotype. These correlations found the acquisition of antibiotic resistance genes in clinical isolates compromised the traditional gentamicin protection assays used to quantify invasion. Therefore, an alternate assay, based on amikacin resistance, identified genes cosegregating with invasion. These genes encode an arylsulfatase, a glycoside hydrolase, and genetic islands carrying propanediol utilization and sulfoquinovose metabolism pathways.

CONCLUSIONS: This study highlights the importance of incorporating antibiotic resistance screening for invasion assays used in AIEC identification. Accurately screened invasion phenotypes identified accessory genome elements among E coli IBD isolates that correlate with their ability to invade epithelial cells. These results help explain why single genetic markers for the AIEC phylotype are challenging to identify.},
}

Humans
*Escherichia coli/genetics/pathogenicity/isolation & purification/drug effects
*Inflammatory Bowel Diseases/microbiology
*Escherichia coli Infections/microbiology
Phenotype
Epithelial Cells/microbiology
Genotype
Whole Genome Sequencing
Virulence/genetics
Drug Resistance, Bacterial/genetics
Virulence Factors/genetics

@article {pmid40437092,
year = {2025},
author = {Lynch, RC and Padgitt-Cobb, LK and Garfinkel, AR and Knaus, BJ and Hartwick, NT and Allsing, N and Aylward, A and Bentz, PC and Carey, SB and Mamerto, A and Kitony, JK and Colt, K and Murray, ER and Duong, T and Chen, HI and Trippe, A and Harkess, A and Crawford, S and Vining, K and Michael, TP},
title = {Domesticated cannabinoid synthases amid a wild mosaic cannabis pangenome.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40437092},
issn = {1476-4687},
abstract = {Cannabis sativa is a globally important seed oil, fibre and drug-producing plant species. However, a century of prohibition has severely restricted development of breeding and germplasm resources, leaving potential hemp-based nutritional and fibre applications unrealized. Here we present a cannabis pangenome, constructed with 181 new and 12 previously released genomes from a total of 144 biological samples including both male (XY) and female (XX) plants. We identified widespread regions of the cannabis pangenome that are surprisingly diverse for a single species, with high levels of genetic and structural variation, and propose a novel population structure and hybridization history. Across the ancient heteromorphic X and Y sex chromosomes, we observed a variable boundary at the sex-determining and pseudoautosomal regions as well as genes that exhibit male-biased expression, including genes encoding several key flowering regulators. Conversely, the cannabinoid synthase genes, which are responsible for producing cannabidiol acid and delta-9-tetrahydrocannabinolic acid, contained very low levels of diversity, despite being embedded within a variable region with multiple pseudogenized paralogues, structural variation and distinct transposable element arrangements. Additionally, we identified variants of acyl-lipid thioesterase genes that were associated with fatty acid chain length variation and the production of the rare cannabinoids, tetrahydrocannabivarin and cannabidivarin. We conclude that the C. sativa gene pool remains only partially characterized, the existence of wild relatives in Asia is likely and its potential as a crop species remains largely unrealized.},
}

@article {pmid40436163,
year = {2025},
author = {Gagneja, S and Capalash, N and Sharma, P},
title = {Whole genome sequence analysis of an environmental isolate Bacillus subtilis K3C: Genome plasticity and acquisition of hyaluronic acid capsule traits through horizontal multigene transfer.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {144696},
doi = {10.1016/j.ijbiomac.2025.144696},
pmid = {40436163},
issn = {1879-0003},
abstract = {B. subtilis K3C was isolated from an environmental sample. Genomic analysis revealed that the GRAS strain harbors a circular chromosome of 4,120,051 bp composed of 4361 protein coding sequences with a GC content of 43.4 %, 80 tRNA, and 3 rRNA genes. Two regions containing complete assembly of prophages encoded by 83 prophage genes were present suggesting the role of bacteriophage infection in evolutionary accumulation of strain-specific genes contributing towards strain diversification. Strong recombination, repair, transfer and competence systems were identified, suggesting their role in strain fitness and evolutionary process. Pan-genomic analysis revealed 3824 protein homologs as the bacterial core genome shared among different strains and 390 singletons in the pan-genome orthologous groups. The hyaluronic acid capsule trait in the isolate seems to be acquired through selective pressure to adapt in environmentally stressed niches. Phyloproteomic analysis showed that the acquired genes responsible for HA production were phylogenetically closer to Streptococcal clade, evidencing the role of horizontal gene transfer. The bacterial genome showed the presence of multiple HA genes translating HasB and HasC proteins suggesting gene dosage in the strain. However, no gene rearrangement events seem to have taken course as the HA genes were integrated in different contigs of the genome.},
}

@article {pmid40431301,
year = {2025},
author = {Wang, K and Zhang, C and Munang'andu, HM and Xu, C and Cai, W and Yan, X and Tao, Z},
title = {Comparative Genomic Analysis of Two Vibrio harveyi Strains from Larimichthys crocea with Divergent Virulence Profiles.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
pmid = {40431301},
issn = {2076-2607},
support = {42376108//National Natural Science Foundation of China/ ; },
abstract = {Vibrio harveyi is a significant pathogen in marine aquaculture, causing vibriosis in various marine species. This study presents a comparative genomic analysis of two V. harveyi strains, N8T11 and 45T2, which exhibit differing virulence profiles. Virulence assays revealed that N8T11 caused 92% mortality in infected fish, while 45T2 resulted in 0% mortality. Whole-genome sequencing revealed that strain N8T11 harbors five plasmids (pN8T11a, pN8T11b, pN8T11c, pN8T11d and pN8T11e) absent in 45T2, encoding genes potentially linked to virulence, such as siderophore-mediated iron acquisition and stress response mechanisms. Pan-genome analysis highlighted substantial genomic plasticity within V. harveyi, with mobile genetic elements, including plasmids and prophages, contributing to horizontal gene transfer. Conjugation experiments demonstrated that all five N8T11 plasmids can transfer to 45T2 with efficiencies up to 87%, with pN8T11b remaining stable across multiple subcultures, enabling the dissemination of virulence-associated genes. These findings suggest that plasmid-mediated gene transfer plays a role in the virulence variability observed between V. harveyi strains. This study contributes to understanding the genomic factors underlying pathogenicity in V. harveyi and provides insights for future research aimed at controlling vibriosis in aquaculture.},
}

@article {pmid40431107,
year = {2025},
author = {Shi, F and Li, L and Chen, M and Chang, J and Tu, M and He, G and Li, Y and Yang, G},
title = {Genus-Wide Pan-Genome Analysis of Oryza Calcium-Dependent Protein Kinase Genes and Their Related Kinases Highlights the Complexity of Protein Domain Architectures and Expression Dynamics.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
pmid = {40431107},
issn = {2223-7747},
support = {31570261//National Natural Science Foundation of China/ ; 2016CFB549//National Natural Science Foundation of Hubei China/ ; 5001170128//the Research Support Programs for the HUST Research Facilities and Bases/ ; 2024EHA056//the International Science and Technology Collaboration Project of Hubei Province/ ; 2021XXJS070, 3004170157//the Fundamental Research Funds for Central Universities, HUST/ ; 2024AFB955//Natural Science Foundation of Hubei Province of China/ ; 2021RZ100, 53210052172//Start-Up Research Funding of Wuhan Polytechnic University/ ; },
abstract = {The Oryza genus serves not only as a gene pool for rice improvement but also as a model system for plant evolutionary research. Calcium-dependent protein kinases (CPKs) function as both effectors and sensors in calcium signaling and play versatile roles in plant development and stress responses. Four kinase families, namely CPK-related kinases (CRKs), phosphoenolpyruvate carboxylase kinases (PPCKs), PPCK-related kinases (PEPRKs), and calcium- and calmodulin-dependent kinases (CCaMKs), are frequently called CPK-related kinases. This study utilized evolutionary genomics approaches and provided the pan-genome repertoires of CPKs and their related kinases in 34 Oryza genomes by leveraging the rich genomics resources of the Orzya genus. Gene duplication analysis revealed that distinct duplication types contributed to expanding CPKs and their related kinases in wild rice. We depicted the protein domain architectures of CPKs and their related kinases, highlighting the complexity of EF-hand motifs in CPKs and CCaMKs. Transcriptome analysis determined that alternative splicing was a mechanism contributing to the diversity in the domain architectures of CPKs and CCaMKs. We also generated the expression atlas of CPKs and their related kinases in multiple species of Oryza genus, emphasizing divergent homoeolog expression patterns across tissues and species in allotetraploid wild rice. Collectively, our Oryza-wide analysis of CPKs and their related kinases revealed their evolutionary trajectories and highlighted their diversified domain architectures and expression dynamics, providing gene resources of wild relatives for rice improvement.},
}

@article {pmid40430797,
year = {2025},
author = {Kuufire, E and Bentum, KE and Nyarku, R and Osei, V and Elrefaey, A and James, T and Woube, Y and Folitse, R and Samuel, T and Abebe, W},
title = {Identification of Novel Gene-Specific Markers for Differentiating Various Pathogenic Campylobacter Species Using a Pangenome Analysis Approach.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
pmid = {40430797},
issn = {2076-0817},
mesh = {*Campylobacter/genetics/classification/isolation & purification ; Genetic Markers ; *Genome, Bacterial ; *Campylobacter Infections/microbiology/diagnosis ; Humans ; Phylogeny ; Animals ; Genomics/methods ; },
abstract = {Campylobacter spp. are the causative agents of campylobacteriosis, a major foodborne illness globally, with millions of cases reported annually. These pathogens pose significant risks to both human and animal health. Conventional culture-based diagnostic methods are labor-intensive and time-consuming, underscoring the need for more efficient molecular detection strategies. This study employed a pangenomic analysis to identify novel gene-specific markers for pathogenic Campylobacter species and subspecies, laying the groundwork for their application in diverse diagnostic assays. A curated dataset of 105 high-quality genomes, representing 33 species and 9 subspecies, was analyzed using the Roary ILP Bacterial Annotation Pipeline. The results revealed substantial genomic diversity within the genus, with core gene counts varying across different nucleotide identity thresholds. Ribosomal genes such as rpsL, rpsJ, rpsS, rpmA, rpsK, rpsU, rpsG, rpmH, and rpsZ were consistently identified in the core genome, whereas accessory genes exhibited marked variability. This study uncovered novel and highly specific genetic markers for various Campylobacter species, including petB, clpX, and carB for C. coli; hypothetical proteins for C. jejuni and C. fetus; porA2 for C. lari; and mdtJ for C. upsaliensis. These markers demonstrated a specificity of at least 90% with minimal cross-reactivity with non-target organisms. The findings underscore the genomic heterogeneity within Campylobacter and provide essential genetic targets for the enhanced molecular detection of its pathogenic species, subspecies, and biovars.},
}

*Campylobacter/genetics/classification/isolation & purification
Genetic Markers
*Genome, Bacterial
*Campylobacter Infections/microbiology/diagnosis
Humans
Phylogeny
Animals
Genomics/methods

@article {pmid40425278,
year = {2025},
author = {Nakashima, T and Miyauchi, T and Takeuchi, R and Sugihara, Y and Funakoshi, Y and Ohka, F and Maeda, S and Hirato, J and Yoshioka, T and Okita, H and Narita, Y and Kanemura, Y and Kojima, Y and Watanabe, Y and Saito, R and Suzuki, H},
title = {Diversity of U1 Small Nuclear RNAs and Diagnostic Methods for Their Mutations.},
journal = {Cancer science},
volume = {},
number = {},
pages = {},
doi = {10.1111/cas.70110},
pmid = {40425278},
issn = {1349-7006},
support = {//Astellas Foundation for Research on Metabolic Disorders/ ; 2024-D-01//Japan Health Research Promotion Bureau/ ; //MSD Life Science Foundation, Public Interest Incorporated Foundation/ ; //National Cancer Center Japan/ ; JST FOREST Program JPMJFR210Q//Japan Science and Technology Agency/ ; //Takeda Science Foundation/ ; //Uehara Memorial Foundation/ ; 21K21001//Japan Society for the Promotion of Science/ ; 22H03190//Japan Society for the Promotion of Science/ ; 22K19591//Japan Society for the Promotion of Science/ ; //Cell Science Research Foundation/ ; //Kobayashi Foundation for Cancer Research/ ; 22ck0106693h0002//Japan Agency for Medical Research and Development/ ; 23ck0106877h0001//Japan Agency for Medical Research and Development/ ; 23ama221525h00//Japan Agency for Medical Research and Development/ ; //Authorized NPO (Non Profit Organization) Gold Ribbon Network/ ; },
abstract = {U1 small nuclear RNA (snRNA) mutations are recurrent non-coding alterations found in various malignancies, yet their identification has proven challenging due to their repetitive nature. We characterized the complex interindividual diversity and genomic architecture of U1 snRNA loci using sequencing data and a pangenome reference. Our analysis uncovered copy number variations and the diversity of single-nucleotide variants in regions not predicted to have significant functional impact. Compared to traditional linear reference-based analyses for mutations, the pangenome graph demonstrated the best accuracy, successfully identifying previously undetectable mutations. This underscores the utility of pangenome graph references for cancer genome research, particularly in repetitive and highly diverse genomic regions. Additionally, we developed mutation detection methods employing targeted capture sequencing, rapid quantitative polymerase chain reaction, and a machine learning approach based on splicing patterns, all exhibiting high precision in identifying U1 snRNA mutations. Our findings elucidate the structural complexity of U1 snRNA loci and establish robust methodologies for precise mutation detection in these regions.},
}

@article {pmid40422680,
year = {2025},
author = {Bai, R and Wang, Q and Bao, H},
title = {Whole-Genome Characterization of Inonotus hispidus from Ulmus macrocarpa and Its Comparative Genomics with Strains from Morus alba and Acer truncatum.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {5},
pages = {},
pmid = {40422680},
issn = {2309-608X},
support = {No.20240180//the research and development of authentic medicinal materials and high-quality new varieties of Sanghuang in the old course of the Yellow River/ ; No.32070021//the national natural science foundation of China/ ; },
abstract = {Inonotus hispidus growing on Morus alba is traditionally regarded as the authentic source of the medicinal fungus. However, this species is also found on other host trees, such as Ulmus macrocarpa and Acer truncatum; yet, whether these strains share comparable genomic and functional traits with Morus-derived strains remains unknown. Here, we performed whole-genome sequencing of a strain isolated from U. macrocarpa (UMI) using Illumina and PacBio platforms and conducted comparative genomic analysis with strains from M. alba (MAI) and A. truncatum (AMI). Antagonistic interactions were also evaluated via dual-culture confrontation assays. The UMI genome was 36.44 Mb in size, comprising 9097 predicted genes, of which 6991 and 1672 were annotated in the KEGG and COG databases, respectively. SNP analysis revealed 623,498 and 335,343 variants in AMI and MAI, with AMI showing greater genomic variation. Core-pan genome analysis identified 2651 core genes and 1046, 1424, and 1217 strain-specific genes in UMI, AMI, and MAI, respectively. Phenotypic assays demonstrated distinct mycelial growth dynamics and antagonistic behaviors, which likely reflect host-related environmental adaptation. Overall, I. hispidus strains from non-Morus hosts exhibit unique genomic and phenotypic features, providing a valuable basis for resource evaluation, artificial domestication, and the medicinal development of wild Sanghuang strains beyond traditional sources.},
}

@article {pmid40421466,
year = {2025},
author = {Catalano Gonzaga, O and McKenna, S and O'Neill, I and Cotter, PD and McAuliffe, FM and Coffey, A and van Sinderen, D and Bottacini, F},
title = {Gene-trait matching among Bifidobacterium dentium strains reveals various glycan metabolism loci including a strain-specific fucosyllactose utilization cluster.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1584694},
pmid = {40421466},
issn = {1664-302X},
abstract = {In contrast to other human-associated bifidobacteria, Bifidobacterium dentium is commonly classified as an opportunistic pathogen as its presence in the oral cavity has been associated with the development of dental caries. While B. dentium is frequently isolated from the oral cavity of children with caries, recent microbiome investigations and preliminary genomic analyses have suggested that this species is also adapted to colonize the gastrointestinal tract. Understanding the genetic and metabolic adaptations that enable this flexible colonization ability is crucial to clarify its role in human health and disease. To assess B. dentium genomic diversity and metabolic potential, the current study presents analysis and characterization of 10 complete genome sequences from recently isolated B. dentium strains obtained from human fecal samples together with 48 publicly available genome sequences. We investigated genetic loci predicted to be involved in host interaction and carbohydrate utilization in this species by means of comparative genomics, pan-genome analysis, and gene-trait matching. These analyses identified gene clusters involved in the utilization of plant-derived glycans and, for the first time, revealed B. dentium strains capable of utilizing human milk oligosaccharides (HMOs) through a fucosyllactose utilization cluster homologous to the one found in several infant-derived bifidobacterial species. Moreover, additional investigations of strain-specific genetic features highlighted a taxon that is evolved to colonize multiple niches and to compete with other colonizers. These findings challenge the narrow classification of B. dentium as an opportunist and underscore its ecological versatility.},
}

@article {pmid40417475,
year = {2024},
author = {Marini, S and Barquero, A and Wadhwani, AA and Bian, J and Ruiz, J and Boucher, C and Prosperi, M},
title = {OCTOPUS: Disk-based, Multiplatform, Mobile-friendly Metagenomics Classifier.},
journal = {AMIA ... Annual Symposium proceedings. AMIA Symposium},
volume = {2024},
number = {},
pages = {798-807},
pmid = {40417475},
issn = {1942-597X},
mesh = {*Metagenomics/methods ; *Software ; *Mobile Applications ; },
abstract = {Portable genomic sequencers such as Oxford Nanopore's MinION enable real-time applications in clinical and environmental health. However, there is a bottleneck in the downstream analytics when bioinformatics pipelines are unavailable, e.g., when cloud processing is unreachable due to absence of Internet connection, or only low-end computing devices can be carried on site. Here we present a platform-friendly software for portable metagenomic analysis of Nanopore data, the Oligomer-based Classifier of Taxonomic Operational and Pan-genome Units via Singletons (OCTOPUS). OCTOPUS is written in Java, reimplements several features of the popular Kraken2 and KrakenUniq software, with original components for improving metagenomics classification on incomplete/sampled reference databases, making it ideal for running on smartphones or tablets. OCTOPUS obtains sensitivity and precision comparable to Kraken2, while dramatically decreasing (4- to 16-fold) the false positive rate, and yielding high correlation on real-word data. OCTOPUS is available along with customized databases at https://github.com/DataIntellSystLab/OCTOPUS and https://github.com/Ruiz-HCI-Lab/OctopusMobile.},
}

*Metagenomics/methods
*Software
*Mobile Applications

@article {pmid40414962,
year = {2025},
author = {Pearl, S and Anbarasu, A},
title = {Genomic landscape of nosocomial Acinetobacter baumannii: A comprehensive analysis of the resistome, virulome, and mobilome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {18203},
pmid = {40414962},
issn = {2045-2322},
mesh = {*Acinetobacter baumannii/genetics/pathogenicity/drug effects ; *Genome, Bacterial ; Humans ; *Cross Infection/microbiology ; *Acinetobacter Infections/microbiology ; *Drug Resistance, Multiple, Bacterial/genetics ; Multilocus Sequence Typing ; Virulence Factors/genetics ; Genomics/methods ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; },
abstract = {Acinetobacter baumannii (A. baumannii) is a major multidrug-resistant pathogen, posing serious threats in the healthcare settings. This study provides a comprehensive genomic analysis of nosocomial A. baumannii whole-genome sequences retrieved from NCBI Genome database. Multilocus sequence typing and capsule typing were performed to investigate the clonal diversity. The genomes were characterized to identify antimicrobial resistance genes (ARGs), virulence factors, and mobile genetic elements. Further, pangenome analysis was conducted to examine the core and accessory genomes of A. baumannii. Our dataset comprised of 609 genomes deposited from diverse geographic regions worldwide between 2004 and 2024. The genomes showed high clonal heterogeneity, with sequence type ST2 being the predominant sequence type. A total of 185 unique ARGs were identified, with majority of them associated with efflux pump and β-lactamase coding genes. Over 25,000 IS elements were detected, with IS4 family being the prevalent type. High abundance of integron-mediated resistance determinants, especially for aminoglycosides and β-lactams, were identified. The open pangenome window due to its larger accessory genome suggested substantial genome plasticity. Our findings highlight A. baumannii's rapid evolution and resistance potential, emphasizing need for alternative therapeutic strategies. Enhanced surveillance, infection control measures, and antimicrobial stewardship are crucial to combat this persistent threat.},
}

*Acinetobacter baumannii/genetics/pathogenicity/drug effects
*Genome, Bacterial
Humans
*Cross Infection/microbiology
*Acinetobacter Infections/microbiology
*Drug Resistance, Multiple, Bacterial/genetics
Multilocus Sequence Typing
Virulence Factors/genetics
Genomics/methods
Anti-Bacterial Agents/pharmacology
Whole Genome Sequencing

@article {pmid40407329,
year = {2025},
author = {Eripogu, KK and Yu, C-P and Tsai, A and Lin, J-J and Lin, H-C and Li, W-H},
title = {Nocardia genomes are a large reservoir of diverse gene content, biosynthetic gene clusters, and species-specific genes.},
journal = {mBio},
volume = {},
number = {},
pages = {e0094725},
doi = {10.1128/mbio.00947-25},
pmid = {40407329},
issn = {2150-7511},
abstract = {UNLABELLED: The Nocardia genus represents a largely untapped source of valuable secondary metabolites, yet its biosynthetic potential, gene content, and evolutionary history remain underexplored. By analyzing 263 genomes across 88 species, we found that Nocardia varies greatly in genome size and gene content. It exhibits an open pangenome with a small core genome (<900 genes) and high genomic fluidity (0.76), indicating high gene turnover. A large proportion (75%) of its genes are species-specific, indicating high genomic plasticity. Average nucleotide identity (ANI) analysis confirmed taxonomic relationships, with most species showing ANI values (80-85%). N. globerula showed an ANI of ~84% with Rhodococcus erythropolis, supporting its reclassification under Rhodococcus. The biosynthetic capabilities of the Nocardia genus are striking, with the presence of >8,000 biosynthetic gene clusters (BGCs), dominated by type 1 polyketide synthase, terpenes, and non-ribosomal polypeptide synthetases, establishing Nocardia as the Actinomycetota genus that has the largest biosynthetic repertoire. Around 35% of BGCs remain uncharacterized, suggesting Nocardia's high potential for novel natural product discoveries. Our study is the first to identify a prodigiosin BGC in Nocardia. Network analysis revealed complex evolutionary connections between Nocardia's gene cluster families (GCFs) and MIBiG reference BGCs, suggesting evolutionary changes, including gene gains and losses, that may have influenced the genus's BGC diversity and composition. Synteny analysis uncovered conserved and unique gene arrangements across Nocardia and related genera, mostly with core genes conserved in Actinomycetota. Our study addressed unmet clinical and biotechnological challenges while revealing evolutionary mechanisms that shape microbial diversity and adaptability.

IMPORTANCE: Understanding the genomic diversity and biosynthetic potential of microorganisms is instrumental for addressing issues in microbial evolution, natural product discovery, and host-microbe interactions. Nocardia, a bacterial genus known for its opportunistic pathogenicity, represents an underexplored group of immense genomic diversity and biosynthetic capabilities. This study employed genome mining to reveal the open pangenome of Nocardia and identified an extensive repertoire of BGCs, including novel clusters with the potential to produce therapeutically significant compounds such as prodigiosin-related compounds. By integrating genome mining, phylogenetics, and synteny analysis, this study provides insights into how genomic plasticity, species-specific genes, and evolutionary changes such as gene gains and losses that contribute to Nocardia's biosynthetic diversity and evolution. These findings contribute to advancing microbial genomics, evolution, and biotechnology by uncovering the potential of Nocardia to address challenges in infectious diseases and natural product discovery. This study exemplifies how genome mining can illuminate the ecological and clinical significance of microbial diversity.},
}