@article {pmid38698240,
year = {2024},
author = {Mertz, P and Costedoat-Chalumeau, N and Ferrada, MA and Moulis, G and Mekinian, A and Grayson, PC and Arnaud, L},
title = {Relapsing polychondritis: clinical updates and new differential diagnoses.},
journal = {Nature reviews. Rheumatology},
volume = {},
number = {},
pages = {},
pmid = {38698240},
issn = {1759-4804},
abstract = {Relapsing polychondritis is a rare inflammatory disease characterized by recurrent inflammation of cartilaginous structures, mainly of the ears, nose and respiratory tract, with a broad spectrum of accompanying systemic features. Despite its rarity, prompt recognition and accurate diagnosis of relapsing polychondritis is crucial for appropriate management and optimal outcomes. Our understanding of relapsing polychondritis has changed markedly in the past couple of years with the identification of three distinct patient clusters that have different clinical manifestations and prognostic outcomes. With the progress of pangenomic sequencing and the discovery of new somatic and monogenic autoinflammatory diseases, new differential diagnoses have emerged, notably the vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic (VEXAS) syndrome, autoinflammatory diseases and immune checkpoint inhibitor-related adverse events. In this Review, we present a detailed update of the newly identified clusters and highlight red flags that should raise suspicion of these alternative diagnoses. The identification of these different clusters and mimickers has a direct impact on the management, follow-up and prognosis of patients with relapsing polychondritis and autoinflammatory syndromes.},
}

@article {pmid38698002,
year = {2024},
author = {Da Silva Morais, E and Grimaud, GM and Warda, A and Stanton, C and Ross, P},
title = {Genome plasticity shapes the ecology and evolution of Phocaeicola dorei and Phocaeicola vulgatus.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {10109},
pmid = {38698002},
issn = {2045-2322},
support = {BACtheWINNER, Project No. 101054719/ERC_/European Research Council/International ; },
mesh = {*Phylogeny ; *Genome, Bacterial ; Humans ; Gastrointestinal Microbiome/genetics ; Gene Transfer, Horizontal ; Evolution, Molecular ; Genomics/methods ; Bacteroidetes/genetics ; },
abstract = {Phocaeicola dorei and Phocaeicola vulgatus are very common and abundant members of the human gut microbiome and play an important role in the infant gut microbiome. These species are closely related and often confused for one another; yet, their genome comparison, interspecific diversity, and evolutionary relationships have not been studied in detail so far. Here, we perform phylogenetic analysis and comparative genomic analyses of these two Phocaeicola species. We report that P. dorei has a larger genome yet a smaller pan-genome than P. vulgatus. We found that this is likely because P. vulgatus is more plastic than P. dorei, with a larger repertoire of genetic mobile elements and fewer anti-phage defense systems. We also found that P. dorei directly descends from a clade of P. vulgatus¸ and experienced genome expansion through genetic drift and horizontal gene transfer. Overall, P. dorei and P. vulgatus have very different functional and carbohydrate utilisation profiles, hinting at different ecological strategies, yet they present similar antimicrobial resistance profiles.},
}

*Phylogeny
*Genome, Bacterial
Humans
Gastrointestinal Microbiome/genetics
Gene Transfer, Horizontal
Evolution, Molecular
Genomics/methods
Bacteroidetes/genetics

@article {pmid38695578,
year = {2024},
author = {Samanta, D and Rauniyar, S and Saxena, P and Sani, RK},
title = {From genome to evolution: investigating type II methylotrophs using a pangenomic analysis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0024824},
doi = {10.1128/msystems.00248-24},
pmid = {38695578},
issn = {2379-5077},
abstract = {UNLABELLED: A comprehensive pangenomic approach was employed to analyze the genomes of 75 type II methylotrophs spanning various genera. Our investigation revealed 256 exact core gene families shared by all 75 organisms, emphasizing their crucial role in the survival and adaptability of these organisms. Additionally, we predicted the functionality of 12 hypothetical proteins. The analysis unveiled a diverse array of genes associated with key metabolic pathways, including methane, serine, glyoxylate, and ethylmalonyl-CoA (EMC) metabolic pathways. While all selected organisms possessed essential genes for the serine pathway, Methylooceanibacter marginalis lacked serine hydroxymethyltransferase (SHMT), and Methylobacterium variabile exhibited both isozymes of SHMT, suggesting its potential to utilize a broader range of carbon sources. Notably, Methylobrevis sp. displayed a unique serine-glyoxylate transaminase isozyme not found in other organisms. Only nine organisms featured anaplerotic enzymes (isocitrate lyase and malate synthase) for the glyoxylate pathway, with the rest following the EMC pathway. Methylovirgula sp. 4MZ18 stood out by acquiring genes from both glyoxylate and EMC pathways, and Methylocapsa sp. S129 featured an A-form malate synthase, unlike the G-form found in the remaining organisms. Our findings also revealed distinct phylogenetic relationships and clustering patterns among type II methylotrophs, leading to the proposal of a separate genus for Methylovirgula sp. 4M-Z18 and Methylocapsa sp. S129. This pangenomic study unveils remarkable metabolic diversity, unique gene characteristics, and distinct clustering patterns of type II methylotrophs, providing valuable insights for future carbon sequestration and biotechnological applications.

IMPORTANCE: Methylotrophs have played a significant role in methane-based product production for many years. However, a comprehensive investigation into the diverse genetic architectures across different genera of methylotrophs has been lacking. This study fills this knowledge gap by enhancing our understanding of core hypothetical proteins and unique enzymes involved in methane oxidation, serine, glyoxylate, and ethylmalonyl-CoA pathways. These findings provide a valuable reference for researchers working with other methylotrophic species. Furthermore, this study not only unveils distinctive gene characteristics and phylogenetic relationships but also suggests a reclassification for Methylovirgula sp. 4M-Z18 and Methylocapsa sp. S129 into separate genera due to their unique attributes within their respective genus. Leveraging the synergies among various methylotrophic organisms, the scientific community can potentially optimize metabolite production, increasing the yield of desired end products and overall productivity.},
}

@article {pmid38693490,
year = {2024},
author = {Lu, Y and Liu, D and Kong, X and Song, Y and Jing, L},
title = {Pangenome characterization and analysis of the NAC gene family reveals genes for Sclerotinia sclerotiorum resistance in sunflower (Helianthus annuus).},
journal = {BMC genomic data},
volume = {25},
number = {1},
pages = {39},
pmid = {38693490},
issn = {2730-6844},
support = {32160642 and 32060598//National Natural Science Foundation of China/ ; 32160642 and 32060598//National Natural Science Foundation of China/ ; 32160642 and 32060598//National Natural Science Foundation of China/ ; 32160642 and 32060598//National Natural Science Foundation of China/ ; 32160642 and 32060598//National Natural Science Foundation of China/ ; NMGIRT2320//Program for Innovative Research Team in Universities of Inner Mongolia Autonomous Region/ ; NMGIRT2320//Program for Innovative Research Team in Universities of Inner Mongolia Autonomous Region/ ; NMGIRT2320//Program for Innovative Research Team in Universities of Inner Mongolia Autonomous Region/ ; NMGIRT2320//Program for Innovative Research Team in Universities of Inner Mongolia Autonomous Region/ ; NMGIRT2320//Program for Innovative Research Team in Universities of Inner Mongolia Autonomous Region/ ; },
abstract = {BACKGROUND: Sunflower (Helianthus annuus) is one of the most important economic crops in oilseed production worldwide. The different cultivars exhibit variability in their resistance genes. The NAC transcription factor (TF) family plays diverse roles in plant development and stress responses. With the completion of the H. annuus genome sequence, the entire complement of genes coding for NACs has been identified. However, the reference genome of a single individual cannot cover all the genetic information of the species.

RESULTS: Considering only a single reference genome to study gene families will miss many meaningful genes. A pangenome-wide survey and characterization of the NAC genes in sunflower species were conducted. In total, 139 HaNAC genes are identified, of which 114 are core and 25 are variable. Phylogenetic analysis of sunflower NAC proteins categorizes these proteins into 16 subgroups. 138 HaNACs are randomly distributed on 17 chromosomes. SNP-based haplotype analysis shows haplotype diversity of the HaNAC genes in wild accessions is richer than in landraces and modern cultivars. Ten HaNAC genes in the basal stalk rot (BSR) resistance quantitative trait loci (QTL) are found. A total of 26 HaNAC genes are differentially expressed in response to Sclerotinia head rot (SHR). A total of 137 HaNAC genes are annotated in Gene Ontology (GO) and are classified into 24 functional groups. GO functional enrichment analysis reveals that HaNAC genes are involved in various functions of the biological process.

CONCLUSIONS: We identified NAC genes in H. annuus (HaNAC) on a pangenome-wide scale and analyzed S. sclerotiorum resistance-related NACs. This study provided a theoretical basis for further genomic improvement targeting resistance-related NAC genes in sunflowers.},
}

@article {pmid38693487,
year = {2024},
author = {Gangurde, SS and Korani, W and Bajaj, P and Wang, H and Fountain, JC and Agarwal, G and Pandey, MK and Abbas, HK and Chang, PK and Holbrook, CC and Kemerait, RC and Varshney, RK and Dutta, B and Clevenger, JP and Guo, B},
title = {Aspergillus flavus pangenome (AflaPan) uncovers novel aflatoxin and secondary metabolite associated gene clusters.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {354},
pmid = {38693487},
issn = {1471-2229},
abstract = {BACKGROUND: Aspergillus flavus is an important agricultural and food safety threat due to its production of carcinogenic aflatoxins. It has high level of genetic diversity that is adapted to various environments. Recently, we reported two reference genomes of A. flavus isolates, AF13 (MAT1-2 and highly aflatoxigenic isolate) and NRRL3357 (MAT1-1 and moderate aflatoxin producer). Where, an insertion of 310 kb in AF13 included an aflatoxin producing gene bZIP transcription factor, named atfC. Observations of significant genomic variants between these isolates of contrasting phenotypes prompted an investigation into variation among other agricultural isolates of A. flavus with the goal of discovering novel genes potentially associated with aflatoxin production regulation. Present study was designed with three main objectives: (1) collection of large number of A. flavus isolates from diverse sources including maize plants and field soils; (2) whole genome sequencing of collected isolates and development of a pangenome; and (3) pangenome-wide association study (Pan-GWAS) to identify novel secondary metabolite cluster genes.

RESULTS: Pangenome analysis of 346 A. flavus isolates identified a total of 17,855 unique orthologous gene clusters, with mere 41% (7,315) core genes and 59% (10,540) accessory genes indicating accumulation of high genomic diversity during domestication. 5,994 orthologous gene clusters in accessory genome not annotated in either the A. flavus AF13 or NRRL3357 reference genomes. Pan-genome wide association analysis of the genomic variations identified 391 significant associated pan-genes associated with aflatoxin production. Interestingly, most of the significantly associated pan-genes (94%; 369 associations) belonged to accessory genome indicating that genome expansion has resulted in the incorporation of new genes associated with aflatoxin and other secondary metabolites.

CONCLUSION: In summary, this study provides complete pangenome framework for the species of Aspergillus flavus along with associated genes for pathogen survival and aflatoxin production. The large accessory genome indicated large genome diversity in the species A. flavus, however AflaPan is a closed pangenome represents optimum diversity of species A. flavus. Most importantly, the newly identified aflatoxin producing gene clusters will be a new source for seeking aflatoxin mitigation strategies and needs new attention in research.},
}

@article {pmid38689698,
year = {2024},
author = {Tan, W and Zhou, P and Huang, X and Liao, R and Wang, X and Wu, Y and Ni, Z and Shi, T and Yu, X and Zhang, H and Ma, C and Gao, F and Ma, Y and Bai, Y and Hayat, F and Omondi, OK and Coulibaly, D and Gao, Z},
title = {Haplotype-resolved genome of Prunus zhengheensis provides insight into its evolution and low temperature adaptation in apricot.},
journal = {Horticulture research},
volume = {11},
number = {4},
pages = {uhae103},
doi = {10.1093/hr/uhae103},
pmid = {38689698},
issn = {2662-6810},
abstract = {Prunus zhengheensis, an extremely rare population of apricots, originated in warm South-East China and is an excellent material for genetic breeding. However, most apricots and two related species (P. sibirica, P. mandshurica) are found in the cold northern regions in China and the mechanism of their distribution is still unclear. In addition, the classification status of P. zhengheensis is controversial. Thus, we generated a high-quality haplotype-resolved genome for P. zhengheensis, exploring key genetic variations in its adaptation and the causes of phylogenetic incongruence. We found extensive phylogenetic discordances between the nuclear and organelle phylogenies of P. zhengheensis, which could be explained by incomplete lineage sorting. A 242.22-Mb pan-genome of the Armeniaca section was developed with 13 chromosomal genomes. Importantly, we identified a 566-bp insertion in the promoter of the HSFA1d gene in apricot and showed that the activity of the HSFA1d promoter increased under low temperatures. In addition, HSFA1d overexpression in Arabidopsis thaliana indicated that HSFA1d positively regulated plant growth under chilling. Therefore, we hypothesized that the insertion in the promoter of HSFA1d in apricot improved its low-temperature adaptation, allowing it to thrive in relatively cold locations. The findings help explain the weather adaptability of Armeniaca plants.},
}

@article {pmid38689648,
year = {2024},
author = {Ma, Y and Sun, J and Zhang, X and Sadaqat, M and Tahir Ul Qamar, M and Liu, T},
title = {Comparative genomics analysis of pheophorbide a oxygenase (PAO) genes in eight pyrus genomes and their regulatory role in multiple stress responses in Chinese pear (Pyrus bretschneideri).},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1396744},
doi = {10.3389/fgene.2024.1396744},
pmid = {38689648},
issn = {1664-8021},
abstract = {Pyrus (pear) is among the most nutritious fruits and contains fibers that have great health benefits to humans. It is mostly cultivated in temperate regions globally and is highly subjected to biotic and abiotic stresses which affect its yield. Pheophorbide a oxygenase (PAO) is an essential component of the chlorophyll degradation system and contributes to the senescence of leaves. It is responsible for opening the pheophorbide a porphyrin macrocycle and forming the main fluorescent chlorophyll catabolite However, this gene family and its members have not been explored in Pyrus genomes. Here we report a pangenome-wide investigation has been conducted on eight Pyrus genomes: Cuiguan, Shanxi Duli, Zhongai 1, Nijisseiki, Yunhong No.1, d'Anjou, Bartlett v2.0, and Dangshansuli v.1.1. The phylogenetic history, their gene structure, conservation patterns of motifs, their distribution on chromosomes, and gene duplication are studied in detail which shows the intraspecific structural conservation as well as evolutionary patterns of Pyrus PAOs. Cis-elements, protein-protein interactions (PPI), and the Gene Ontology (GO) enrichment analyses show their potential biological functions. Furthermore, their expression in various tissues, fruit hardening conditions, and drought stress conditions is also studied. Based on phylogenetics, the identified PAOs were divided into four groups. The expansion of this gene family in Pyrus is caused by both tandem and segmental duplication. Moreover, positive and negative selection pressure equally directed the gene's duplication process. The Pyrus PAO genes were enriched in hormones-related, light, development, and stress-related elements. RNA-seq data analysis showed that PAOs have varied levels of expression under diseased and abiotic stress conditions. The 3D structures of PAOs are also predicted to get more insights into functional conservation. Our research can be used further to get a deeper knowledge of the PAO gene family in Pyrus and to guide future research on improving the genetic composition of Pyrus to enhance stress tolerance.},
}

@article {pmid38686794,
year = {2024},
author = {Nuhamunada, M and Mohite, OS and Phaneuf, PV and Palsson, BO and Weber, T},
title = {BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae314},
pmid = {38686794},
issn = {1362-4962},
support = {NNF20CC0035580//Novo Nordisk Foundation/ ; CeMiSt//Danish National Research Foundation/ ; NNF20SA0035588//Novo Nordisk Foundation Copenhagen Bioscience PhD program/ ; },
abstract = {Genome mining is revolutionizing natural products discovery efforts. The rapid increase in available genomes demands comprehensive computational platforms to effectively extract biosynthetic knowledge encoded across bacterial pangenomes. Here, we present BGCFlow, a novel systematic workflow integrating analytics for large-scale genome mining of bacterial pangenomes. BGCFlow incorporates several genome analytics and mining tools grouped into five common stages of analysis such as: (i) data selection, (ii) functional annotation, (iii) phylogenetic analysis, (iv) genome mining, and (v) comparative analysis. Furthermore, BGCFlow provides easy configuration of different projects, parallel distribution, scheduled job monitoring, an interactive database to visualize tables, exploratory Jupyter Notebooks, and customized reports. Here, we demonstrate the application of BGCFlow by investigating the phylogenetic distribution of various biosynthetic gene clusters detected across 42 genomes of the Saccharopolyspora genus, known to produce industrially important secondary/specialized metabolites. The BGCFlow-guided analysis predicted more accurate dereplication of BGCs and guided the targeted comparative analysis of selected RiPPs. The scalable, interoperable, adaptable, re-entrant, and reproducible nature of the BGCFlow will provide an effective novel way to extract the biosynthetic knowledge from the ever-growing genomic datasets of biotechnologically relevant bacterial species.},
}

@article {pmid38682181,
year = {2024},
author = {Aziz, T and Naveed, M and Shabbir, MA and Sarwar, A and Khan, AA and Hasnain, A and Haq, TU and Yang, Z and Zinedine, A and Rocha, JM and Alharbi, M},
title = {Whole Genome Analysis of Tibetan Kefir-Derived Lactiplantibacillus Plantarum 12-3 Elucidates Its Genomic Architecture, Antimicrobial and Drug Resistance, Potential Probiotic Functionality and Safety.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {29},
number = {4},
pages = {147},
doi = {10.31083/j.fbl2904147},
pmid = {38682181},
issn = {2768-6698},
support = {32272296//National Natural Science Foundation of China/ ; IFKSUOR3- 619-3//Deputyship for Research and Innovation/ ; },
mesh = {*Probiotics ; Tibet ; *Genome, Bacterial ; *Phylogeny ; *Kefir/microbiology ; Drug Resistance, Bacterial/genetics ; Lactobacillus plantarum/genetics ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; CRISPR-Cas Systems ; },
abstract = {BACKGROUND: Lactiplantibacillus plantarum 12-3 holds great promise as a probiotic bacterial strain, yet its full potential remains untapped. This study aimed to better understand this potential therapeutic strain by exploring its genomic landscape, genetic diversity, CRISPR-Cas mechanism, genotype, and mechanistic perspectives for probiotic functionality and safety applications.

METHODS: L. plantarum 12-3 was isolated from Tibetan kefir grains and, subsequently, Illumina and Single Molecule Real-Time (SMRT) technologies were used to extract and sequence genomic DNA from this organism. After performing pan-genomic and phylogenetic analysis, Average Nucleotide Identity (ANI) was used to confirm the taxonomic identity of the strain. Antibiotic resistance gene analysis was conducted using the Comprehensive Antibiotic Resistance Database (CARD). Antimicrobial susceptibility testing, and virulence gene identification were also included in our genomic analysis to evaluate food safety. Prophage, genomic islands, insertion sequences, and CRISPR-Cas sequence analyses were also carried out to gain insight into genetic components and defensive mechanisms within the bacterial genome.

RESULTS: The 3.4 Mb genome of L. plantarum 12-3, was assembled with 99.1% completeness and low contamination. A total of 3234 genes with normal length and intergenic spacing were found using gene prediction tools. Pan-genomic studies demonstrated gene diversity and provided functional annotation, whereas phylogenetic analysis verified taxonomic identity. Our food safety study revealed a profile of antibiotic resistance that is favorable for use as a probiotic. Analysis of insertional sequences, genomic islands, and prophage within the genome provided information regarding genetic components and their possible effects on evolution.

CONCLUSIONS: Pivotal genetic elements uncovered in this study play a crucial role in bacterial defense mechanisms and offer intriguing prospects for future genome engineering efforts. Moreover, our findings suggest further in vitro and in vivo studies are warranted to validate the functional attributes and probiotic potential of L. plantarum 12-3. Expanding the scope of the research to encompass a broader range of L. plantarum 12-3 strains and comparative analyses with other probiotic species would enhance our understanding of this organism's genetic diversity and functional properties.},
}

*Probiotics
Tibet
*Genome, Bacterial
*Phylogeny
*Kefir/microbiology
Drug Resistance, Bacterial/genetics
Lactobacillus plantarum/genetics
Anti-Bacterial Agents/pharmacology
Whole Genome Sequencing
CRISPR-Cas Systems

@article {pmid38676570,
year = {2024},
author = {Avila Cartes, J and Bonizzoni, P and Ciccolella, S and Della Vedova, G and Denti, L and Didelot, X and Monti, D and Pirola, Y},
title = {RecGraph: recombination-aware alignment of sequences to variation graphs.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btae292},
pmid = {38676570},
issn = {1367-4811},
abstract = {MOTIVATION: Bacterial genomes present more variability than human genomes, which requires important adjustments in computational tools that are developed for human data. In particular, bacteria exhibit a mosaic structure due to homologous recombinations, but this fact is not sufficiently captured by standard read mappers that align against linear reference genomes. The recent introduction of pangenomics provides some insights in that context, as a pangenome graph can represent the variability within a species. However, the concept of sequence-to-graph alignment that captures the presence of recombinations has not been previously investigated.

RESULTS: In this paper, we present the extension of the notion of sequence-to-graph alignment to a variation graph that incorporates a recombination, so that the latter are explicitly represented and evaluated in an alignment. Moreover, we present a dynamic programming approach for the special case where there is at most a recombination-we implement this case as RecGraph. From a modeling point of view, a recombination corresponds to identifying a new path of the variation graph, where the new arc is composed of two halves, each extracted from an original path, possibly joined by a new arc. Our experiments show that RecGraph accurately aligns simulated recombinant bacterial sequences that have at most a recombination, providing evidence for the presence of recombination events.

AVAILABILITY: Our implementation is open source and available at https://github.com/AlgoLab/RecGraph.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid38674443,
year = {2024},
author = {Du, X and Sun, Y and Fu, T and Gao, T and Zhang, T},
title = {Research Progress and Applications of Bovine Genome in the Tribe Bovini.},
journal = {Genes},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/genes15040509},
pmid = {38674443},
issn = {2073-4425},
support = {CARS-36//the National Dairy Industry Technology System of China/ ; 2023ZW04048//The Science and Technology Innovation 2030/ ; },
mesh = {Animals ; Cattle/genetics ; *Genome/genetics ; *Genomics/methods ; Buffaloes/genetics ; Phenotype ; High-Throughput Nucleotide Sequencing ; Breeding ; },
abstract = {Various bovine species have been domesticated and bred for thousands of years, and they provide adequate animal-derived products, including meat, milk, and leather, to meet human requirements. Despite the review studies on economic traits in cattle, the genetic basis of traits has only been partially explained by phenotype and pedigree breeding methods, due to the complexity of genomic regulation during animal development and growth. With the advent of next-generation sequencing technology, genomics projects, such as the 1000 Bull Genomes Project, Functional Annotation of Animal Genomes project, and Bovine Pangenome Consortium, have advanced bovine genomic research. These large-scale genomics projects gave us a comprehensive concept, technology, and public resources. In this review, we summarize the genomics research progress of the main bovine species during the past decade, including cattle (Bos taurus), yak (Bos grunniens), water buffalo (Bubalus bubalis), zebu (Bos indicus), and gayal (Bos frontalis). We mainly discuss the development of genome sequencing and functional annotation, focusing on how genomic analysis reveals genetic variation and its impact on phenotypes in several bovine species.},
}

Animals
Cattle/genetics
*Genome/genetics
*Genomics/methods
Buffaloes/genetics
Phenotype
High-Throughput Nucleotide Sequencing
Breeding

@article {pmid38674043,
year = {2024},
author = {Sáez, LP and Rodríguez-Caballero, G and Olaya-Abril, A and Cabello, P and Moreno-Vivián, C and Roldán, MD and Luque-Almagro, VM},
title = {Genomic Insights into Cyanide Biodegradation in the Pseudomonas Genus.},
journal = {International journal of molecular sciences},
volume = {25},
number = {8},
pages = {},
doi = {10.3390/ijms25084456},
pmid = {38674043},
issn = {1422-0067},
support = {P18-RT-3048//Junta de Andalucía/ ; PPIT_2022E_025814//University of Córdoba/ ; Program Frontiers in Science//Fundación Torres Gutiérrez/ ; },
mesh = {*Cyanides/metabolism ; *Biodegradation, Environmental ; *Pseudomonas/genetics/metabolism ; *Phylogeny ; *Genome, Bacterial ; Genomics/methods ; Bacterial Proteins/genetics/metabolism ; Aminohydrolases/genetics/metabolism ; Pseudomonas pseudoalcaligenes/metabolism/genetics ; },
abstract = {Molecular studies about cyanide biodegradation have been mainly focused on the hydrolytic pathways catalyzed by the cyanide dihydratase CynD or the nitrilase NitC. In some Pseudomonas strains, the assimilation of cyanide has been linked to NitC, such as the cyanotrophic model strain Pseudomonas pseudoalcaligenes CECT 5344, which has been recently reclassified as Pseudomonas oleovorans CECT 5344. In this work, a phylogenomic approach established a more precise taxonomic position of the strain CECT 5344 within the species P. oleovorans. Furthermore, a pan-genomic analysis of P. oleovorans and other species with cyanotrophic strains, such as P. fluorescens and P. monteilii, allowed for the comparison and identification of the cioAB and mqoAB genes involved in cyanide resistance, and the nitC and cynS genes required for the assimilation of cyanide or cyanate, respectively. While cyanide resistance genes presented a high frequency among the analyzed genomes, genes responsible for cyanide or cyanate assimilation were identified in a considerably lower proportion. According to the results obtained in this work, an in silico approach based on a comparative genomic approach can be considered as an agile strategy for the bioprospection of putative cyanotrophic bacteria and for the identification of new genes putatively involved in cyanide biodegradation.},
}

*Cyanides/metabolism
*Biodegradation, Environmental
*Pseudomonas/genetics/metabolism
*Phylogeny
*Genome, Bacterial
Genomics/methods
Bacterial Proteins/genetics/metabolism
Aminohydrolases/genetics/metabolism
Pseudomonas pseudoalcaligenes/metabolism/genetics

@article {pmid38671539,
year = {2024},
author = {Goff, JL and Szink, EG and Durrence, KL and Lui, LM and Nielsen, TN and Kuehl, JV and Hunt, KA and Chandonia, JM and Huang, J and Thorgersen, MP and Poole, FL and Stahl, DA and Chakraborty, R and Deutschbauer, AM and Arkin, AP and Adams, MWW},
title = {Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed subsurface.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {26},
pmid = {38671539},
issn = {2524-6372},
support = {DE-AC02-05CH11231//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; },
abstract = {Castellaniella species have been isolated from a variety of mixed-waste environments including the nitrate and multiple metal-contaminated subsurface at the Oak Ridge Reservation (ORR). Previous studies examining microbial community composition and nitrate removal at ORR during biostimulation efforts reported increased abundances of members of the Castellaniella genus concurrent with increased denitrification rates. Thus, we asked how genomic and abiotic factors control the Castellaniella biogeography at the site to understand how these factors may influence nitrate transformation in an anthropogenically impacted setting. We report the isolation and characterization of several Castellaniella strains from the ORR subsurface. Five of these isolates match at 100% identity (at the 16S rRNA gene V4 region) to two Castellaniella amplicon sequence variants (ASVs), ASV1 and ASV2, that have persisted in the ORR subsurface for at least 2 decades. However, ASV2 has consistently higher relative abundance in samples taken from the site and was also the dominant blooming denitrifier population during a prior biostimulation effort. We found that the ASV2 representative strain has greater resistance to mixed metal stress than the ASV1 representative strains. We attribute this resistance, in part, to the large number of unique heavy metal resistance genes identified on a genomic island in the ASV2 representative genome. Additionally, we suggest that the relatively lower fitness of ASV1 may be connected to the loss of the nitrous oxide reductase (nos) operon (and associated nitrous oxide reductase activity) due to the insertion at this genomic locus of a mobile genetic element carrying copper resistance genes. This study demonstrates the value of integrating genomic, environmental, and phenotypic data to characterize the biogeography of key microorganisms in contaminated sites.},
}

@article {pmid38669452,
year = {2024},
author = {Hu, H and Li, R and Zhao, J and Batley, J and Edwards, D},
title = {Technological development and advances for constructing and analysing plant pangenomes.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae081},
pmid = {38669452},
issn = {1759-6653},
abstract = {A pangenome captures the genomic diversity for a species, derived from a collection of genetic sequences of diverse populations. Advances in sequencing technologies have given rise to three primary methods for pangenome construction and analysis: de novo assembly and comparison, reference genome-based iterative assembly and graph-based pangenome construction. Each method presents advantages and challenges in processing varying amounts and structures of DNA sequencing data. With the emergence of high-quality genome assemblies and advanced bioinformatics tools, the graph-based pangenome is emerging as an advanced reference for exploring the biological and functional implications of genetic variations.},
}

@article {pmid38669259,
year = {2024},
author = {Duchen, D and Clipman, SJ and Vergara, C and Thio, CL and Thomas, DL and Duggal, P and Wojcik, GL},
title = {A hepatitis B virus (HBV) sequence variation graph improves alignment and sample-specific consensus sequence construction.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0301069},
doi = {10.1371/journal.pone.0301069},
pmid = {38669259},
issn = {1932-6203},
mesh = {*Hepatitis B virus/genetics ; Humans ; *Genome, Viral ; *Consensus Sequence/genetics ; Phylogeny ; Sequence Alignment/methods ; Genetic Variation ; Hepatitis B, Chronic/virology ; DNA, Viral/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {Nearly 300 million individuals live with chronic hepatitis B virus (HBV) infection (CHB), for which no curative therapy is available. As viral diversity is associated with pathogenesis and immunological control of infection, improved methods to characterize this diversity could aid drug development efforts. Conventionally, viral sequencing data are mapped/aligned to a reference genome, and only the aligned sequences are retained for analysis. Thus, reference selection is critical, yet selecting the most representative reference a priori remains difficult. We investigate an alternative pangenome approach which can combine multiple reference sequences into a graph which can be used during alignment. Using simulated short-read sequencing data generated from publicly available HBV genomes and real sequencing data from an individual living with CHB, we demonstrate alignment to a phylogenetically representative 'genome graph' can improve alignment, avoid issues of reference ambiguity, and facilitate the construction of sample-specific consensus sequences more genetically similar to the individual's infection. Graph-based methods can, therefore, improve efforts to characterize the genetics of viral pathogens, including HBV, and have broader implications in host-pathogen research.},
}

*Hepatitis B virus/genetics
Humans
*Genome, Viral
*Consensus Sequence/genetics
Phylogeny
Sequence Alignment/methods
Genetic Variation
Hepatitis B, Chronic/virology
DNA, Viral/genetics
Sequence Analysis, DNA/methods

@article {pmid38667025,
year = {2024},
author = {Che, M and Fresno, AH and Calvo-Fernandez, C and Hasman, H and Kurittu, PE and Heikinheimo, A and Hansen, LT},
title = {Comparison of IncK-blaCMY-2 Plasmids in Extended-Spectrum Cephalosporin-Resistant Escherichia coli Isolated from Poultry and Humans in Denmark, Finland, and Germany.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/antibiotics13040349},
pmid = {38667025},
issn = {2079-6382},
support = {Fødevareforlig 3//Danish Veterinary and Food Administration/ ; Ph.D. stipend//Chinese Scholarship Council/ ; BG22/00150 - Beatriz Galindo program//Ministerio de Universidades, Spain/ ; },
abstract = {Escherichia coli carrying IncK-blaCMY-2 plasmids mediating resistance to extended-spectrum cephalosporins (ESC) has been frequently described in food-producing animals and in humans. This study aimed to characterize IncK-blaCMY-2-positive ESC-resistant E. coli isolates from poultry production systems in Denmark, Finland, and Germany, as well as from Danish human blood infections, and further compare their plasmids. Whole-genome sequencing (Illumina) of all isolates (n = 46) confirmed the presence of the blaCMY-2 gene. Minimum inhibitory concentration (MIC) testing revealed a resistant phenotype to cefotaxime as well as resistance to ≥3 antibiotic classes. Conjugative transfer of the blaCMY-2 gene confirmed the resistance being on mobile plasmids. Pangenome analysis showed only one-third of the genes being in the core with the remainder being in the large accessory gene pool. Single nucleotide polymorphism (SNP) analysis on sequence type (ST) 429 and 1286 isolates showed between 0-60 and 13-90 SNP differences, respectively, indicating vertical transmission of closely related clones in the poultry production, including among Danish, Finnish, and German ST429 isolates. A comparison of 22 ST429 isolates from this study with 80 ST429 isolates in Enterobase revealed the widespread geographical occurrence of related isolates associated with poultry production. Long-read sequencing of a representative subset of isolates (n = 28) allowed further characterization and comparison of the IncK-blaCMY-2 plasmids with publicly available plasmid sequences. This analysis revealed the presence of highly similar plasmids in ESC-resistant E. coli from Denmark, Finland, and Germany pointing to the existence of common sources. Moreover, the analysis presented evidence of global plasmid transmission and evolution. Lastly, our results indicate that IncK-blaCMY-2 plasmids and their carriers had been circulating in the Danish production chain with an associated risk of spreading to humans, as exemplified by the similarity of the clinical ST429 isolate to poultry isolates. Its persistence may be driven by co-selection since most IncK-blaCMY-2 plasmids harbor resistance factors to drugs used in veterinary medicine.},
}

@article {pmid38663087,
year = {2024},
author = {Taylor, DJ and Eizenga, JM and Li, Q and Das, A and Jenike, KM and Kenny, EE and Miga, KH and Monlong, J and McCoy, RC and Paten, B and Schatz, MC},
title = {Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References.},
journal = {Annual review of genomics and human genetics},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-genom-021623-081639},
pmid = {38663087},
issn = {1545-293X},
abstract = {The Human Genome Project was an enormous accomplishment, providing a foundation for countless explorations into the genetics and genomics of the human species. Yet for many years, the human genome reference sequence remained incomplete and lacked representation of human genetic diversity. Recently, two major advances have emerged to address these shortcomings: complete gap-free human genome sequences, such as the one developed by the Telomere-to-Telomere Consortium, and high-quality pangenomes, such as the one developed by the Human Pangenome Reference Consortium. Facilitated by advances in long-read DNA sequencing and genome assembly algorithms, complete human genome sequences resolve regions that have been historically difficult to sequence, including centromeres, telomeres, and segmental duplications. In parallel, pangenomes capture the extensive genetic diversity across populations worldwide. Together, these advances usher in a new era of genomics research, enhancing the accuracy of genomic analysis, paving the path for precision medicine, and contributing to deeper insights into human biology.},
}

@article {pmid38659906,
year = {2024},
author = {Schloissnig, S and Pani, S and Rodriguez-Martin, B and Ebler, J and Hain, C and Tsapalou, V and Söylev, A and Hüther, P and Ashraf, H and Prodanov, T and Asparuhova, M and Hunt, S and Rausch, T and Marschall, T and Korbel, JO},
title = {Long-read sequencing and structural variant characterization in 1,019 samples from the 1000 Genomes Project.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.18.590093},
pmid = {38659906},
abstract = {Structural variants (SVs) contribute significantly to human genetic diversity and disease [1-4] . Previously, SVs have remained incompletely resolved by population genomics, with short-read sequencing facing limitations in capturing the whole spectrum of SVs at nucleotide resolution [5-7] . Here we leveraged nanopore sequencing [8] to construct an intermediate coverage resource of 1,019 long-read genomes sampled within 26 human populations from the 1000 Genomes Project. By integrating linear and graph-based approaches for SV analysis via pangenome graph-augmentation, we uncover 167,291 sequence-resolved SVs in these samples, considerably advancing SV characterization compared to population-wide short-read sequencing studies [3,4] . Our analysis details diverse SV classes-deletions, duplications, insertions, and inversions-at population-scale. LINE-1 and SVA retrotransposition activities frequently mediate transductions [9,10] of unique sequences, with both mobile element classes transducing sequences at either the 3'- or 5'-end, depending on the source element locus. Furthermore, analyses of SV breakpoint junctions suggest a continuum of homology-mediated rearrangement processes are integral to SV formation, and highlight evidence for SV recurrence involving repeat sequences. Our open-access dataset underscores the transformative impact of long-read sequencing in advancing the characterisation of polymorphic genomic architectures, and provides a resource for guiding variant prioritisation in future long-read sequencing-based disease studies.},
}

@article {pmid38658835,
year = {2024},
author = {Liu, M and Zhang, F and Lu, H and Xue, H and Dong, X and Li, Z and Xu, J and Wang, W and Wei, C},
title = {PPanG: a precision pangenome browser enabling nucleotide-level analysis of genomic variations in individual genomes and their graph-based pangenome.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {405},
pmid = {38658835},
issn = {1471-2164},
support = {B23CJ0208//the Hainan Yazhou Bay Seed Lab Project/ ; B23CJ0208//the Hainan Yazhou Bay Seed Lab Project/ ; B23CJ0208//the Hainan Yazhou Bay Seed Lab Project/ ; YBXM//Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/ ; 2022ZD0401703//Scientific Innovation 2030 Program/ ; 2022ZD0401703//Scientific Innovation 2030 Program/ ; SQ2023YFF1000094//National Key Research and Development Program of China/ ; 32170643//National Natural Science Foundation of China/ ; 20ZR1428200//Natural Science Foundation of Shanghai Municipality/ ; },
abstract = {Graph-based pangenome is gaining more popularity than linear pangenome because it stores more comprehensive information of variations. However, traditional linear genome browser has its own advantages, especially the tremendous resources accumulated historically. With the fast-growing number of individual genomes and their annotations available, the demand for a genome browser to visualize genome annotation for many individuals together with a graph-based pangenome is getting higher and higher. Here we report a new pangenome browser PPanG, a precise pangenome browser enabling nucleotide-level comparison of individual genome annotations together with a graph-based pangenome. Nine rice genomes with annotations were provided by default as potential references, and any individual genome can be selected as the reference. Our pangenome browser provides unprecedented insights on genome variations at different levels from base to gene, and reveals how the structures of a gene could differ for individuals. PPanG can be applied to any species with multiple individual genomes available and it is available at https://cgm.sjtu.edu.cn/PPanG .},
}

@article {pmid38655077,
year = {2024},
author = {Chuang, SC and Dobhal, S and Alvarez, AM and Arif, M},
title = {Three new species, Xanthomonas hawaiiensis sp. nov., Stenotrophomonas aracearum sp. nov., and Stenotrophomonas oahuensis sp. nov., isolated from the Araceae family.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1356025},
pmid = {38655077},
issn = {1664-302X},
abstract = {Xanthomonas and Stenotrophomonas are closely related genera in the family Lysobacteraceae. In our previous study of aroid-associated bacterial strains, most strains isolated from anthurium and other aroids were reclassified as X. phaseoli and other Xanthomonas species. However, two strains isolated from Spathiphyllum and Colocasia were phylogenetically distant from other strains in the Xanthomonas clade and two strains isolated from Anthurium clustered within the Stenotrophomonas clade. Phylogenetic trees based on 16S rRNA and nine housekeeping genes placed the former strains with the type strain of X. sacchari from sugarcane and the latter strains with the type strain of S. bentonitica from bentonite. In pairwise comparisons with type strains, the overall genomic relatedness indices required delineation of new species; digital DNA-DNA hybridization and average nucleotide identity values were lower than 70 and 95%, respectively. Hence, three new species are proposed: S. aracearum sp. nov. and S. oahuensis sp. nov. for two strains from anthurium and X. hawaiiensis sp. nov. for the strains from spathiphyllum and colocasia, respectively. The genome size of X. hawaiiensis sp. nov. is ~4.88 Mbp and higher than S. aracearum sp. nov. (4.33 Mbp) and S. oahuensis sp. nov. (4.68 Mbp). Gene content analysis revealed 425 and 576 core genes present in 40 xanthomonads and 25 stenotrophomonads, respectively. The average number of unique genes in Stenotrophomonas spp. was higher than in Xanthomonas spp., implying higher genetic diversity in Stenotrophomonas.},
}

@article {pmid38654264,
year = {2024},
author = {He, X and Qi, Z and Liu, Z and Chang, X and Zhang, X and Li, J and Wang, M},
title = {Pangenome analysis reveals transposon-driven genome evolution in cotton.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {92},
pmid = {38654264},
issn = {1741-7007},
support = {32001595//National Natural Science Foundation of China/ ; 32170645//National Natural Science Foundation of China/ ; 31830062//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Transposable elements (TEs) have a profound influence on the trajectory of plant evolution, driving genome expansion and catalyzing phenotypic diversification. The pangenome, a comprehensive genetic pool encompassing all variations within a species, serves as an invaluable tool, unaffected by the confounding factors of intraspecific diversity. This allows for a more nuanced exploration of plant TE evolution.

RESULTS: Here, we constructed a pangenome for diploid A-genome cotton using 344 accessions from representative geographical regions, including 223 from China as the main component. We found 511 Mb of non-reference sequences (NRSs) and revealed the presence of 5479 previously undiscovered protein-coding genes. Our comprehensive approach enabled us to decipher the genetic underpinnings of the distinct geographic distributions of cotton. Notably, we identified 3301 presence-absence variations (PAVs) that are closely tied to gene expression patterns within the pangenome, among which 2342 novel expression quantitative trait loci (eQTLs) were found residing in NRSs. Our investigation also unveiled contrasting patterns of transposon proliferation between diploid and tetraploid cotton, with long terminal repeat (LTR) retrotransposons exhibiting a synchronized surge in polyploids. Furthermore, the invasion of LTR retrotransposons from the A subgenome to the D subgenome triggered a substantial expansion of the latter following polyploidization. In addition, we found that TE insertions were responsible for the loss of 36.2% of species-specific genes, as well as the generation of entirely new species-specific genes.

CONCLUSIONS: Our pangenome analyses provide new insights into cotton genomics and subgenome dynamics after polyploidization and demonstrate the power of pangenome approaches for elucidating transposon impacts and genome evolution.},
}

@article {pmid38652229,
year = {2024},
author = {Kavanova, K and Kostovova, I and Moravkova, M and Kubasova, T and Babak, V and Crhanova, M},
title = {Comparative Genome Analysis and Characterization of the Probiotic Properties of Lactic Acid Bacteria Isolated from the Gastrointestinal Tract of Wild Boars in the Czech Republic.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {38652229},
issn = {1867-1314},
support = {QK1910351, MZE-RO0523//Ministerstvo Zemědělství/ ; QK1910351, MZE-RO0523//Ministerstvo Zemědělství/ ; QK1910351, MZE-RO0523//Ministerstvo Zemědělství/ ; QK1910351, MZE-RO0523//Ministerstvo Zemědělství/ ; QK1910351, MZE-RO0523//Ministerstvo Zemědělství/ ; QK1910351, MZE-RO0523//Ministerstvo Zemědělství/ ; },
abstract = {Probiotics are crucial components for maintaining a healthy gut microbiota in pigs, especially during the weaning period. Lactic acid bacteria (LAB) derived from the gastrointestinal tract of wild boars can serve as an abundant source of beneficial probiotic strains with suitable properties for use in pig husbandry. In this study, we analyzed and characterized 15 strains of Limosilactobacillus mucosae obtained from the gut contents of wild boars to assess their safety and suitability as probiotic candidates. The strains were compared using pan-genomic analysis with 49 L. mucosae strains obtained from the NCBI database. All isolated strains demonstrated their safety by showing an absence of transferrable antimicrobial resistance genes and hemolysin activity. Based on the presence of beneficial genes, five candidates with probiotic properties were selected and subjected to phenotypic profiling. These five selected isolates exhibited the ability to survive conditions mimicking passage through the host's digestive tract, such as low pH and the presence of bile salts. Furthermore, five selected strains demonstrated the presence of corresponding carbohydrate-active enzymes and the ability to utilize various carbohydrate substrates. These strains can enhance the digestibility of oligosaccharide or polysaccharide substrates found in food or feed, specifically resistant starch, α-galactosides, cellobiose, gentiobiose, and arabinoxylans. Based on the results obtained, the L. mucosae isolates tested in this study appear to be promising candidates for use as probiotics in pigs.},
}

@article {pmid38651830,
year = {2024},
author = {Recuerda, M and Campagna, L},
title = {How structural variants shape avian phenotypes: Lessons from model systems.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17364},
doi = {10.1111/mec.17364},
pmid = {38651830},
issn = {1365-294X},
support = {NSF-DEB-2232929//Division of Environmental Biology/ ; },
abstract = {Despite receiving significant recent attention, the relevance of structural variation (SV) in driving phenotypic diversity remains understudied, although recent advances in long-read sequencing, bioinformatics and pangenomic approaches have enhanced SV detection. We review the role of SVs in shaping phenotypes in avian model systems, and identify some general patterns in SV type, length and their associated traits. We found that most of the avian SVs so far identified are short indels in chickens, which are frequently associated with changes in body weight and plumage colouration. Overall, we found that relatively short SVs are more frequently detected, likely due to a combination of their prevalence compared to large SVs, and a detection bias, stemming primarily from the widespread use of short-read sequencing and associated analytical methods. SVs most commonly involve non-coding regions, especially introns, and when patterns of inheritance were reported, SVs associated primarily with dominant discrete traits. We summarise several examples of phenotypic convergence across different species, mediated by different SVs in the same or different genes and different types of changes in the same gene that can lead to various phenotypes. Complex rearrangements and supergenes, which can simultaneously affect and link several genes, tend to have pleiotropic phenotypic effects. Additionally, SVs commonly co-occur with single-nucleotide polymorphisms, highlighting the need to consider all types of genetic changes to understand the basis of phenotypic traits. We end by summarising expectations for when long-read technologies become commonly implemented in non-model birds, likely leading to an increase in SV discovery and characterisation. The growing interest in this subject suggests an increase in our understanding of the phenotypic effects of SVs in upcoming years.},
}

@article {pmid38650915,
year = {2024},
author = {Pettersen, JS and Nielsen, FD and Andreassen, PR and Møller-Jensen, J and Jørgensen, MG},
title = {A comprehensive analysis of pneumococcal two-component system regulatory networks.},
journal = {NAR genomics and bioinformatics},
volume = {6},
number = {2},
pages = {lqae039},
pmid = {38650915},
issn = {2631-9268},
abstract = {Two-component systems are key signal-transduction systems that enable bacteria to respond to a wide variety of environmental stimuli. The human pathogen, Streptococcus pneumoniae (pneumococcus) encodes 13 two-component systems and a single orphan response regulator, most of which are significant for pneumococcal pathogenicity. Mapping the regulatory networks governed by these systems is key to understand pneumococcal host adaptation. Here we employ a novel bioinformatic approach to predict the regulons of each two-component system based on publicly available whole-genome sequencing data. By employing pangenome-wide association studies (panGWAS) to predict genotype-genotype associations for each two-component system, we predicted regulon genes of 11 of the pneumococcal two-component systems. Through validation via next-generation RNA-sequencing on response regulator overexpression mutants, several top candidate genes predicted by the panGWAS analysis were confirmed as regulon genes. The present study presents novel details on multiple pneumococcal two-component systems, including an expansion of regulons, identification of candidate response regulator binding motifs, and identification of candidate response regulator-regulated small non-coding RNAs. We also demonstrate a use for panGWAS as a complementary tool in target gene identification via identification of genotype-to-genotype links. Expanding our knowledge on two-component systems in pathogens is crucial to understanding how these bacteria sense and respond to their host environment, which could prove useful in future drug development.},
}

@article {pmid38650829,
year = {2024},
author = {Wei, H and Wang, X and Zhang, Z and Yang, L and Zhang, Q and Li, Y and He, H and Chen, D and Zhang, B and Zheng, C and Leng, Y and Cao, X and Cui, Y and Shi, C and Liu, Y and Lv, Y and Ma, J and He, W and Liu, X and Xu, Q and Yuan, Q and Yu, X and Wang, T and Qian, H and Li, X and Zhang, B and Zhang, H and Chen, W and Guo, M and Dai, X and Wang, Y and Zheng, X and Guo, L and Xie, X and Qian, Q and Shang, L},
title = {Uncovering key salt-tolerant regulators through a combined eQTL and GWAS analysis using the super pan-genome in rice.},
journal = {National science review},
volume = {11},
number = {4},
pages = {nwae043},
pmid = {38650829},
issn = {2053-714X},
abstract = {For sessile plants, gene expression plays a pivotal role in responding to salinity stress by activating or suppressing specific genes. However, our knowledge of genetic variations governing gene expression in response to salt stress remains limited in natural germplasm. Through transcriptome analysis of the Global Mini-Core Rice Collection consisting of a panel of 202 accessions, we identified 22 345 and 27 610 expression quantitative trait loci associated with the expression of 7787 and 9361 eGenes under normal and salt-stress conditions, respectively, leveraging the super pan-genome map. Notably, combined with genome-wide association studies, we swiftly pinpointed the potential candidate gene STG5-a major salt-tolerant locus known as qSTS5. Intriguingly, STG5 is required for maintaining Na[+]/K[+] homeostasis by directly regulating the transcription of multiple members of the OsHKT gene family. Our study sheds light on how genetic variants influence the dynamic changes in gene expression responding to salinity stress and provides a valuable resource for the mining of salt-tolerant genes in the future.},
}

@article {pmid38650702,
year = {2024},
author = {Shivute, FN and Zhong, Y and Wu, J and Bao, Y and Wang, W and Liu, X and Lu, Z and Yu, H},
title = {Genome-wide and pan-genomic analysis reveals rich variants of NBS-LRR genes in a newly developed wild rice line from Oryza alta Swallen.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1345708},
pmid = {38650702},
issn = {1664-462X},
abstract = {INTRODUCTION: Oryza alta Swallen is an allotetraploid perennial wild rice and contains CCDD genome, which may harbor favorable genes for the enrichment of genetic resource.

METHODS: A new wild rice line, Huaye 5, was developed from Oryza alta Swallen in our lab. Whole genome re-sequencing and pan-genomic analysis were employed to analyze its genomic variations and novel genes.

RESULTS AND DISCUSSION: More than ten million genomic variations were detected when compared with Asian cultivar. Among the variational genes, 724, 197 and 710 genes coded protein kinase, synthetase and transcription factor, respectively. A total of 353, 131 and 135 variational genes were associated with morphological trait, physiological trait, resistance or tolerance, respectively. A total of 62 were NBS-LRR genes were detected, in which 11 NBS-LRR genes expressed in sheath and mature stem, and 26 expressed in young and mature roots expressed. The pan-genome sequences of wild rice species with CCDD genome were constructed by integrating 8 Oryza alta (OA), 2 Oryza grandiglumis (OG) and 18 Oryza latifolia (OL) accessions. A total of 28 non-reference NBS-LRR genes were revealed, and 7 of which were mainly expressed in mature roots. This research demonstrated rich DNA variation in the Oryza alta Swallen that may provide a new germplasm for rice resistance breeding.},
}

@article {pmid38650588,
year = {2024},
author = {Lai, SK and Luo, AC and Chiu, IH and Chuang, HW and Chou, TH and Hung, TK and Hsu, JS and Chen, CY and Yang, WS and Yang, YC and Chen, PL},
title = {A novel framework for human leukocyte antigen (HLA) genotyping using probe capture-based targeted next-generation sequencing and computational analysis.},
journal = {Computational and structural biotechnology journal},
volume = {23},
number = {},
pages = {1562-1571},
pmid = {38650588},
issn = {2001-0370},
abstract = {Human leukocyte antigen (HLA) genes play pivotal roles in numerous immunological applications. Given the immense number of polymorphisms, achieving accurate high-throughput HLA typing remains challenging. This study aimed to harness the human pan-genome reference consortium (HPRC) resources as a potential benchmark for HLA reference materials. We meticulously annotated specific four field-resolution alleles for 11 HLA genes (HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1, -DRB3, -DRB4 and -DRB5) from 44 high-quality HPRC personal genome assemblies. For sequencing, we crafted HLA-specific probes and conducted capture-based targeted sequencing of the genomic DNA of the HPRC cohort, ensuring focused and comprehensive coverage of the HLA region of interest. We used publicly available short-read whole-genome sequencing (WGS) data from identical samples to offer a comparative perspective. To decipher the vast amount of sequencing data, we employed seven distinct software tools: OptiType, HLA-VBseq, HISAT genotype, SpecHLA, T1K, QzType, and DRAGEN. Each tool offers unique capabilities and algorithms for HLA genotyping, allowing comprehensive analysis and validation of the results. We then compared these results with benchmarks derived from personal genome assemblies. Our findings present a comprehensive four-field-resolution HLA allele annotation for 44 HPRC samples. Significantly, our innovative targeted next-generation sequencing (NGS) approach for HLA genes showed superior accuracy compared with conventional short-read WGS. An integrated analysis involving QzType, T1K, and DRAGEN was developed, achieving 100% accuracy for all 11 HLA genes. In conclusion, our study highlighted the combination of targeted short-read sequencing and astute computational analysis as a robust approach for HLA genotyping. Furthermore, the HPRC cohort has emerged as a valuable assembly-based reference in this realm.},
}

@article {pmid38643972,
year = {2024},
author = {Kogay, R and Wolf, YI and Koonin, EV},
title = {Defence systems and horizontal gene transfer in bacteria.},
journal = {Environmental microbiology},
volume = {26},
number = {4},
pages = {e16630},
doi = {10.1111/1462-2920.16630},
pmid = {38643972},
issn = {1462-2920},
support = {//Intramural Research Program of the National Institutes of Health (National Library of Medicine)/ ; },
abstract = {Horizontal gene transfer (HGT) is a fundamental process in prokaryotic evolution, contributing significantly to diversification and adaptation. HGT is typically facilitated by mobile genetic elements (MGEs), such as conjugative plasmids and phages, which often impose fitness costs on their hosts. However, a considerable number of bacterial genes are involved in defence mechanisms that limit the propagation of MGEs, suggesting they may actively restrict HGT. In our study, we investigated whether defence systems limit HGT by examining the relationship between the HGT rate and the presence of 73 defence systems across 12 bacterial species. We discovered that only six defence systems, three of which were different CRISPR-Cas subtypes, were associated with a reduced gene gain rate at the species evolution scale. Hosts of these defence systems tend to have a smaller pangenome size and fewer phage-related genes compared to genomes without these systems. This suggests that these defence mechanisms inhibit HGT by limiting prophage integration. We hypothesize that the restriction of HGT by defence systems is species-specific and depends on various ecological and genetic factors, including the burden of MGEs and the fitness effect of HGT in bacterial populations.},
}

@article {pmid38641647,
year = {2024},
author = {Lin, MJ and Iyer, S and Chen, NC and Langmead, B},
title = {Measuring, visualizing, and diagnosing reference bias with biastools.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {101},
pmid = {38641647},
issn = {1474-760X},
support = {R01HG011392/HG/NHGRI NIH HHS/United States ; },
abstract = {Many bioinformatics methods seek to reduce reference bias, but no methods exist to comprehensively measure it. Biastools analyzes and categorizes instances of reference bias. It works in various scenarios: when the donor's variants are known and reads are simulated; when donor variants are known and reads are real; and when variants are unknown and reads are real. Using biastools, we observe that more inclusive graph genomes result in fewer biased sites. We find that end-to-end alignment reduces bias at indels relative to local aligners. Finally, we use biastools to characterize how T2T references improve large-scale bias.},
}

@article {pmid38633703,
year = {2024},
author = {Arisan, D and Moya-Beltrán, A and Rojas-Villalobos, C and Issotta, F and Castro, M and Ulloa, R and Chiacchiarini, PA and Díez, B and Martín, AJM and Ñancucheo, I and Giaveno, A and Johnson, DB and Quatrini, R},
title = {Acidithiobacillia class members originating at sites within the Pacific Ring of Fire and other tectonically active locations and description of the novel genus 'Igneacidithiobacillus'.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1360268},
pmid = {38633703},
issn = {1664-302X},
abstract = {Recent studies have expanded the genomic contours of the Acidithiobacillia, highlighting important lacunae in our comprehension of the phylogenetic space occupied by certain lineages of the class. One such lineage is 'Igneacidithiobacillus', a novel genus-level taxon, represented by 'Igneacidithiobacillus copahuensis' VAN18-1[T] as its type species, along with two other uncultivated metagenome-assembled genomes (MAGs) originating from geothermally active sites across the Pacific Ring of Fire. In this study, we investigate the genetic and genomic diversity, and the distribution patterns of several uncharacterized Acidithiobacillia class strains and sequence clones, which are ascribed to the same 16S rRNA gene sequence clade. By digging deeper into this data and contributing to novel MAGs emerging from environmental studies in tectonically active locations, the description of this novel genus has been consolidated. Using state-of-the-art genomic taxonomy methods, we added to already recognized taxa, an additional four novel Candidate (Ca.) species, including 'Ca. Igneacidithiobacillus chanchocoensis' (mCHCt20-1[TS]), 'Igneacidithiobacillus siniensis' (S30A2[T]), 'Ca. Igneacidithiobacillus taupoensis' (TVZ-G3 [TS]), and 'Ca. Igneacidithiobacillus waiarikiensis' (TVZ-G4 [TS]). Analysis of published data on the isolation, enrichment, cultivation, and preliminary microbiological characterization of several of these unassigned or misassigned strains, along with the type species of the genus, plus the recoverable environmental data from metagenomic studies, allowed us to identify habitat preferences of these taxa. Commonalities and lineage-specific adaptations of the seven species of the genus were derived from pangenome analysis and comparative genomic metabolic reconstruction. The findings emerging from this study lay the groundwork for further research on the ecology, evolution, and biotechnological potential of the novel genus 'Igneacidithiobacillus'.},
}

@article {pmid38632127,
year = {2024},
author = {Jiménez-Edeza, M and Galván-Gordillo, SV and Pacheco-Arjona, R and Castañeda-Ruelas, GM},
title = {Genomic Approach of Listeria monocytogenes Strains Isolated from Deli-Meats in Mexico.},
journal = {Current microbiology},
volume = {81},
number = {6},
pages = {145},
pmid = {38632127},
issn = {1432-0991},
support = {PROFAPI2022/PRO_A7_069//Universidad Autónoma de Sinaloa/ ; },
abstract = {Listeria monocytogenes is a foodborne pathogen that causes listeriosis worldwide. In México, L. monocytogenes has been identified as a hazard of deli-meats. However, the genomic analysis that supports the transmission of L. monocytogenes strains via deli-meats and its role as a source for virulence and resistance genes is lacking. Here, we present four high-quality genome drafts of L. monocytogenes strains isolated from deli-meats in Mexico. In silico typing was used to determine the serotype, lineage, clonal complexes (CC), and multilocus sequence (ST). Also, comparative genomics were performed to explore the diversity, virulence, mobile elements, antimicrobial resistant and stress survival traits. The genome sequence size of these strains measured 3.05 ± 0.07 Mb with a mean value of 37.9%G+C. All strains belonged to linage I, which was divided into two groups: 4b, CC2, ST1 (n = 3) and 1/2b, CC5, ST5 (n = 1). The pangenome and core genome contained 3493 and 2625 genes, respectively. The strains harbor the L. monocytogenes pathogenicity island-1 (LIPI-1) and the same multidrug resistance pattern (fosX, norB, mprF, lin) via in silico analysis. Comparative analysis delineated the genomes as essentially syntenic, whose genomic differences were due to phage insertion. These results expand what is known about the biology of the L. monocytogenes strains isolated from deli-meats in Mexico and warns of the risk that these strains belong to epidemic linage and harbor virulence genes linked to human disease.},
}

@article {pmid38632370,
year = {2024},
author = {Sterzi, L and Nodari, R and Di Marco, F and Ferrando, ML and Saluzzo, F and Spitaleri, A and Allahverdi, H and Papaleo, S and Panelli, S and Rimoldi, SG and Batisti Biffignandi, G and Corbella, M and Cavallero, A and Prati, P and Farina, C and Cirillo, DM and Zuccotti, G and Bandi, C and Comandatore, F},
title = {Genetic barriers more than environmental associations explain Serratia marcescens population structure.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {468},
pmid = {38632370},
issn = {2399-3642},
abstract = {Bacterial species often comprise well-separated lineages, likely emerged and maintained by genetic isolation and/or ecological divergence. How these two evolutionary actors interact in the shaping of bacterial population structure is currently not fully understood. In this study, we investigate the genetic and ecological drivers underlying the evolution of Serratia marcescens, an opportunistic pathogen with high genomic flexibility and able to colonise diverse environments. Comparative genomic analyses reveal a population structure composed of five deeply-demarcated genetic clusters with open pan-genome but limited inter-cluster gene flow, partially explained by Restriction-Modification (R-M) systems incompatibility. Furthermore, a large-scale research on hundred-thousands metagenomic datasets reveals only a partial habitat separation of the clusters. Globally, two clusters only show a separate gene composition coherent with ecological adaptations. These results suggest that genetic isolation has preceded ecological adaptations in the shaping of the species diversity, an evolutionary scenario coherent with the Evolutionary Extended Synthesis.},
}

@article {pmid38632097,
year = {2024},
author = {Yu-Cheng, L and Yan-Ting, S and Zhi-Xi, T},
title = {Frontiers of soybean pan-genome studies.},
journal = {Yi chuan = Hereditas},
volume = {46},
number = {3},
pages = {183-198},
doi = {10.16288/j.yczz.23-321},
pmid = {38632097},
issn = {0253-9772},
abstract = {Artificial domestication provided the original motivation to the blooming of agriculture, following with the dramatic change of the genetic background of crops and livestock. According to theory and technology upgradation that contributing to the omics, we appreciate using the pan-genome instead of single reference genome for crop study. By comparison and integration of multiple genomes under the guidance of pan-genome theory, we can estimate the genomic information range of a species, leading to a global understanding of its genetic diversity. Combining pan-genome with large size chromosomal structural variations, high throughput population resequencing, and multi-omics data, we can profoundly study the genetic basis behind species traits we focus on. Soybean is one of the most important commercial crops over the world. It is also essential to our food security. Dissecting the formation of genetic diversity and the causal loci of key agricultural traits of soybean will make the modern soybean breeding more efficiently. In this review, we summarize the core idea of pan-genome and clarified the characteristics of construction strategies of pan-genome such as de novo/mapping assembly, iterative assembly and graph-based genome. Then we used the soybean pan-genome work as a case study to introduce the general way to study pan-genome. We highlighted the contribution of structural variation (SV) to the evolution/domestication of soybean and its value in understanding the genetic bases of agronomy traits. By those, we approved the value of graph-based pan-genome for data integration and SV calculation. Future research directions are also discussed for crop genomics and data science.},
}

@article {pmid38628868,
year = {2024},
author = {Narsing Rao, MP and Singh, RN and Sani, RK and Banerjee, A},
title = {Genome-based approach to evaluate the metabolic potentials and exopolysaccharides production of Bacillus paralicheniformis CamBx3 isolated from a Chilean hot spring.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1377965},
pmid = {38628868},
issn = {1664-302X},
abstract = {In the present study, a thermophilic strain designated CamBx3 was isolated from the Campanario hot spring, Chile. Based on 16S rRNA gene sequence, phylogenomic, and average nucleotide identity analysis the strain CamBx3 was identified as Bacillus paralicheniformis. Genome analysis of B. paralicheniformis CamBx3 revealed the presence of genes related to heat tolerance, exopolysaccharides (EPS), dissimilatory nitrate reduction, and assimilatory sulfate reduction. The pangenome analysis of strain CamBx3 with eight Bacillus spp. resulted in 26,562 gene clusters, 7,002 shell genes, and 19,484 cloud genes. The EPS produced by B. paralicheniformis CamBx3 was extracted, partially purified, and evaluated for its functional activities. B. paralicheniformis CamBx3 EPS with concentration 5 mg mL[-1] showed an optimum 92 mM ferrous equivalent FRAP activity, while the same concentration showed a maximum 91% of Fe[2+] chelating activity. B. paralicheniformis CamBx3 EPS (0.2 mg mL[-1]) demonstrated β-glucosidase inhibition. The EPS formed a viscoelastic gel at 45°C with a maximum instantaneous viscosity of 315 Pa.s at acidic pH 5. The present study suggests that B. paralicheniformis CamBx3 could be a valuable resource for biopolymers and bioactive molecules for industrial applications.},
}

@article {pmid38619241,
year = {2024},
author = {Feng, Y and Arsenault, D and Louyakis, AS and Altman-Price, N and Gophna, U and Papke, RT and Gogarten, JP},
title = {Using the pan-genomic framework for the discovery of genomic islands in the haloarchaeon Halorubrum ezzemoulense.},
journal = {mBio},
volume = {},
number = {},
pages = {e0040824},
doi = {10.1128/mbio.00408-24},
pmid = {38619241},
issn = {2150-7511},
abstract = {In this study, we use pan-genomics to characterize the genomic variability of the widely dispersed halophilic archaeal species Halorubrum ezzemoulense (Hez). We include a multi-regional sampling of newly sequenced, high-quality draft genomes. The pan-genome graph of the species reveals 50 genomic islands that represent rare accessory genetic capabilities available to members. Most notably, we observe rearrangements that have led to the insertion/recombination/replacement of mutually exclusive genomic islands in equivalent genome positions ("homeocassettes"). These conflicting islands encode for similar functions, but homologs from islands located between the same core genes exhibit high divergence on the amino acid level, while the neighboring core genes are nearly identical. Both islands of a homeocassette often coexist in the same geographic location, suggesting that either island may be beyond the reach of selective sweeps and that these loci of divergence between Hez members are maintained and persist long term. This implies that subsections of the population have different niche preferences and rare metabolic capabilities. After an evaluation of the gene content in the homeocassettes, we speculate that these islands may play a role in the speciation, niche adaptability, and group selection dynamics in Hez. Though homeocassettes are first described in this study, similar replacements and divergence of genes on genomic islands have been previously reported in other Haloarchaea and distantly related Archaea, suggesting that homeocassettes may be a feature in a wide range of organisms outside of Hez.IMPORTANCEThis study catalogs the rare genes discovered in strains of the species Halorubrum ezzemoulense (Hez), an obligate halophilic archaeon, through the perspective of its pan-genome. These rare genes are often found to be arranged on islands that confer metabolic and transport functions and contain genes that have eluded previous studies. The discovery of divergent, but homologous islands occupying equivalent genome positions ("homeocassettes") in different genomes, reveals significant new information on genome evolution in Hez. Homeocassette pairs encode for similar functions, but their dissimilarity and distribution imply high rates of recombination, different specializations, and niche preferences in Hez. The coexistence of both islands of a homeocassette pair in multiple environments demonstrates that both islands are beyond the reach of selective sweeps and that these genome content differences between strains persist long term. The switch between islands through recombination under different environmental conditions may lead to a greater range of niche adaptability in Hez.},
}

@article {pmid38613721,
year = {2024},
author = {Zhang, H and Su, X and Zheng, X and Liu, M and Zhao, C and Liu, X and Ma, Z and Zhang, S and Zhang, W},
title = {vB_EcoM-P896 coliphage isolated from duck sewage can lyse both intestinal pathogenic Escherichia coli and extraintestinal pathogenic E. coli.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {38613721},
issn = {1618-1905},
support = {2022AH052192//Natural Science Foundation of Anhui Province/ ; 2022AH052192//Natural Science Foundation of Anhui Province/ ; 2022AH052192//Natural Science Foundation of Anhui Province/ ; gxgnfx2022135//The Project of Cultivating Outstanding Talents in Colleges/ ; gxgnfx2022135//The Project of Cultivating Outstanding Talents in Colleges/ ; gxgnfx2022135//The Project of Cultivating Outstanding Talents in Colleges/ ; KJ2021ZD0153//The Natural Science Research Project of Anhui Province/ ; KJ2021ZD0153//The Natural Science Research Project of Anhui Province/ ; KJ2021ZD0153//The Natural Science Research Project of Anhui Province/ ; wzykjtd202002//Wuhu Institute of Technology level science and technology team/ ; wzykjtd202002//Wuhu Institute of Technology level science and technology team/ ; wzykjtd202002//Wuhu Institute of Technology level science and technology team/ ; },
abstract = {Pathogenic Escherichia coli strains cause diseases in both humans and animals. The limiting factors to prevent as well as control infections from pathogenic E. coli strains are their pathotypes, serotypes, and drug resistance. Herein, a bacteriophage (vB_EcoM-P896) has been isolated from duck sewage. Furthermore, aside from targeting intestinal pathogenic E. coli strains like enteropathogenic E. coli, Shiga toxin-producing E. coli, entero-invasive E. coli, and enteroaggregative E. coli, vB_EcoM-P896 can cause lysis in extraintestinal pathogenic E. coli strains such as avian pathogenic E. coli. Stability analysis revealed that vB_EcoM-P896 was stable under the following conditions: temperature, 4℃-50℃; pH, 3-11. The sequencing of the vB_EcoM-P896 genome was conducted utilizing an HiSeq system (Illumina, San Diego, CA) and subjected to de novo assembling with the aid of Spades 3.11.1. The characteristics of the DNA genome were as follows: size, 170,656 bp; GC content, 40.4%; the number of putative coding regions, 294. Transmission electron microscopy analysis of morphology and genome analysis revealed that the phage vB_EcoM-P896 belonged to the order Caudovirales and the family Myoviridae. The pan-genome analysis of vB_EcoM-P896 was divided into two levels. The first level involved the analysis of 91 strains of muscle tail phages, which were mainly divided into 5 groups. The second level involved the analysis of 24 strains of myophage with high homology. Of the 1480 gene clusters, 23 were shared core genes. Neighbor-joining phylogenetic trees were constructed using the Poisson model with MEGA6.0 based on the conserved sequences of phage proteins, the amino acid sequence of the terminase large subunit, and tail fibrin. Further analysis revealed that vB_EcoM-P896 was a typical T4-like potent phage with potential clinical applications.},
}

@article {pmid38613617,
year = {2024},
author = {Aziz, T and Hangyu, H and Naveed, M and Shabbir, MA and Sarwar, A and Nasbeeb, J and Zhennai, Y and Alharbi, M},
title = {Genotypic Profiling, Functional Analysis, Cholesterol-Lowering Ability, and Angiotensin I-Converting Enzyme (ACE) Inhibitory Activity of Probiotic Lactiplantibacillus plantarum K25 via Different Approaches.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {38613617},
issn = {1867-1314},
support = {2017YFE0131800//National Natural Science Foundation of China/ ; },
abstract = {Due to its alleged health advantages, several uses in biotechnology and food safety, the well-known probiotic strain Lactiplantibacillus plantarum K25 has drawn interest. This in-depth investigation explores the genetic diversity, makeup, and security characteristics of the microbial genome of L. plantarum K25, providing insightful knowledge about its genotypic profile and functional characteristics. Utilizing cutting-edge bioinformatics techniques like comparative genomics, pan-genomics, and genotypic profiling was carried out to reveal the strain's multidimensional potential in various fields. The results not only add to our understanding of the genetic makeup of L. plantarum K25 but also show off its acceptability in various fields, notably in biotechnology and food safety. The explanation of evolutionary links, which highlights L. plantarum K25's aptitude as a probiotic, is one notable finding from this research. Its safety profile, which is emphasized by the absence of genes linked to antibiotic resistance, is crucial and supports its status as a promising probiotic option.},
}

@article {pmid38612691,
year = {2024},
author = {Chen, L and Chen, K and Xi, X and Du, X and Zou, X and Ma, Y and Song, Y and Luo, C and Weining, S},
title = {The Evolution, Expression Patterns, and Domestication Selection Analysis of the Annexin Gene Family in the Barley Pan-Genome.},
journal = {International journal of molecular sciences},
volume = {25},
number = {7},
pages = {},
doi = {10.3390/ijms25073883},
pmid = {38612691},
issn = {1422-0067},
abstract = {Plant annexins constitute a conserved protein family that plays crucial roles in regulating plant growth and development, as well as in responses to both biotic and abiotic stresses. In this study, a total of 144 annexin genes were identified in the barley pan-genome, comprising 12 reference genomes, including cultivated barley, landraces, and wild barley. Their chromosomal locations, physical-chemical characteristics, gene structures, conserved domains, and subcellular localizations were systematically analyzed to reveal the certain differences between wild and cultivated populations. Through a cis-acting element analysis, co-expression network, and large-scale transcriptome analysis, their involvement in growth, development, and responses to various stressors was highlighted. It is worth noting that HvMOREXann5 is only expressed in pistils and anthers, indicating its crucial role in reproductive development. Based on the resequencing data from 282 barley accessions worldwide, genetic variations in thefamily were investigated, and the results showed that 5 out of the 12 identified HvMOREXanns were affected by selection pressure. Genetic diversity and haplotype frequency showed notable reductions between wild and domesticated barley, suggesting that a genetic bottleneck occurred on the annexin family during the barley domestication process. Finally, qRT-PCR analysis confirmed the up-regulation of HvMOREXann7 under drought stress, along with significant differences between wild accessions and varieties. This study provides some insights into the genome organization and genetic characteristics of the annexin gene family in barley at the pan-genome level, which will contribute to better understanding its evolution and function in barley and other crops.},
}

@article {pmid38608279,
year = {2024},
author = {Wong, B and Ferguson, JM and Do, JY and Gamaarachchi, H and Deveson, IW},
title = {Streamlining remote nanopore data access with slow5curl.},
journal = {GigaScience},
volume = {13},
number = {},
pages = {},
doi = {10.1093/gigascience/giae016},
pmid = {38608279},
issn = {2047-217X},
support = {MRF1173594//Australian Medical Research Futures Fund/ ; DE230100178//Australian Research Council/ ; },
abstract = {BACKGROUND: As adoption of nanopore sequencing technology continues to advance, the need to maintain large volumes of raw current signal data for reanalysis with updated algorithms is a growing challenge. Here we introduce slow5curl, a software package designed to streamline nanopore data sharing, accessibility, and reanalysis.

RESULTS: Slow5curl allows a user to fetch a specified read or group of reads from a raw nanopore dataset stored on a remote server, such as a public data repository, without downloading the entire file. Slow5curl uses an index to quickly fetch specific reads from a large dataset in SLOW5/BLOW5 format and highly parallelized data access requests to maximize download speeds. Using all public nanopore data from the Human Pangenome Reference Consortium (>22 TB), we demonstrate how slow5curl can be used to quickly fetch and reanalyze raw signal reads corresponding to a set of target genes from each individual in large cohort dataset (n = 91), minimizing the time, egress costs, and local storage requirements for their reanalysis.

CONCLUSIONS: We provide slow5curl as a free, open-source package that will reduce frictions in data sharing for the nanopore community: https://github.com/BonsonW/slow5curl.},
}

@article {pmid38607544,
year = {2024},
author = {Wang, J and Hu, H and Jiang, X and Zhang, S and Yang, W and Dong, J and Yang, T and Ma, Y and Zhou, L and Chen, J and Nie, S and Liu, C and Ning, Y and Zhu, X and Liu, B and Yang, J and Zhao, J},
title = {Pangenome-Wide Association Study and Transcriptome Analysis Reveal a Novel QTL and Candidate Genes Controlling both Panicle and Leaf Blast Resistance in Rice.},
journal = {Rice (New York, N.Y.)},
volume = {17},
number = {1},
pages = {27},
pmid = {38607544},
issn = {1939-8425},
support = {2020A1515111025//the GuangDong Basic and Applied Basic Research Foundation/ ; 2022NPY00005//Seed industry revitalization project of special fund for rural revitalization strategy in Guangdong Province/ ; 32161143009//the National Natural Science Foundation of China/ ; G2022030024L//the National Project/ ; 2023B1212060042//Guangdong Key Laboratory of New Technology in Rice Breeding/ ; 2023KJ106//the Innovation Team Project of Guangdong Modern Agricultural Industrial System/ ; },
abstract = {Cultivating rice varieties with robust blast resistance is the most effective and economical way to manage the rice blast disease. However, rice blast disease comprises leaf and panicle blast, which are different in terms of resistance mechanisms. While many blast resistant rice cultivars were bred using genes conferring resistance to only leaf or panicle blast, mining durable and effective quantitative trait loci (QTLs) for both panicle and leaf blast resistance is of paramount importance. In this study, we conducted a pangenome-wide association study (panGWAS) on 9 blast resistance related phenotypes using 414 international diverse rice accessions from an international rice panel. This approach led to the identification of 74 QTLs associated with rice blast resistance. One notable locus, qPBR1, validated in a F4:5 population and fine-mapped in a Heterogeneous Inbred Family (HIF), exhibited broad-spectrum, major and durable blast resistance throughout the growth period. Furthermore, we performed transcriptomic analysis of 3 resistant and 3 sensitive accessions at different time points after infection, revealing 3,311 differentially expressed genes (DEGs) potentially involved in blast resistance. Integration of the above results identified 6 candidate genes within the qPBR1 locus, with no significant negative effect on yield. The results of this study provide valuable germplasm resources, QTLs, blast response genes and candidate functional genes for developing rice varieties with enduring and broad-spectrum blast resistance. The qPBR1, in particular, holds significant potential for breeding new rice varieties with comprehensive and durable resistance throughout their growth period.},
}

@article {pmid38604355,
year = {2024},
author = {Yin, Z and Liang, J and Zhang, M and Chen, B and Yu, Z and Tian, X and Deng, X and Peng, L},
title = {Pan-genome insights into adaptive evolution of bacterial symbionts in mixed host-microbe symbioses represented by human gut microbiota Bacteroides cellulosilyticus.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172251},
doi = {10.1016/j.scitotenv.2024.172251},
pmid = {38604355},
issn = {1879-1026},
abstract = {Animal hosts harbor diverse assemblages of microbial symbionts that play crucial roles in the host's lifestyle. The link between microbial symbiosis and host development remains poorly understood. In particular, little is known about the adaptive evolution of gut bacteria in host-microbe symbioses. Recently, symbiotic relationships have been categorized as open, closed, or mixed, reflecting their modes of inter-host transmission and resulting in distinct genomic features. Members of the genus Bacteroides are the most abundant human gut microbiota and possess both probiotic and pathogenic potential, providing an excellent model for studying pan-genome evolution in symbiotic systems. Here, we determined the complete genome of an novel clinical strain PL2022, which was isolated from a blood sample and performed pan-genome analyses on a representative set of Bacteroides cellulosilyticus strains to quantify the influence of the symbiotic relationship on the evolutionary dynamics. B. cellulosilyticus exhibited correlated genomic features with both open and closed symbioses, suggesting a mixed symbiosis. An open pan-genome is characterized by abundant accessory gene families, potential horizontal gene transfer (HGT), and diverse mobile genetic elements (MGEs), indicating an innovative gene pool, mainly associated with genomic islands and plasmids. However, massive parallel gene loss, weak purifying selection, and accumulation of positively selected mutations were the main drivers of genome reduction in B. cellulosilyticus. Metagenomic read recruitment analyses showed that B. cellulosilyticus members are globally distributed and active in human gut habitats, in line with predominant vertical transmission in the human gut. However, existence and/or high abundance were also detected in non-intestinal tissues, other animal hosts, and non-host environments, indicating occasional horizontal transmission to new niches, thereby creating arenas for the acquisition of novel genes. This case study of adaptive evolution under a mixed host-microbe symbiosis advances our understanding of symbiotic pan-genome evolution. Our results highlight the complexity of genetic evolution in this unusual intestinal symbiont.},
}

@article {pmid38605417,
year = {2024},
author = {Roder, T and Pimentel, G and Fuchsmann, P and Stern, MT and von Ah, U and Vergères, G and Peischl, S and Brynildsrud, O and Bruggmann, R and Bär, C},
title = {Scoary2: rapid association of phenotypic multi-omics data with microbial pan-genomes.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {93},
pmid = {38605417},
issn = {1474-760X},
support = {GRS-070/17//Gebert Rüf Stiftung/ ; },
abstract = {Unraveling bacterial gene function drives progress in various areas, such as food production, pharmacology, and ecology. While omics technologies capture high-dimensional phenotypic data, linking them to genomic data is challenging, leaving 40-60% of bacterial genes undescribed. To address this bottleneck, we introduce Scoary2, an ultra-fast microbial genome-wide association studies (mGWAS) software. With its data exploration app and improved performance, Scoary2 is the first tool to enable the study of large phenotypic datasets using mGWAS. As proof of concept, we explore the metabolome of yogurts, each produced with a different Propionibacterium reichii strain and discover two genes affecting carnitine metabolism.},
}

@article {pmid38605254,
year = {2024},
author = {Cunha-Ferreira, IC and Vizzotto, CS and Freitas, MAM and Peixoto, J and Carvalho, LS and Tótola, MR and Thompson, FL and Krüger, RH},
title = {Genomic and physiological characterization of Kitasatospora sp. nov., an actinobacterium with potential for biotechnological application isolated from Cerrado soil.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {38605254},
issn = {1678-4405},
support = {Conselho Nacional de Desenvolvimento Científico e Tecnológico//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; Fundação de Apoio à Pesquisa do Distrito Federal//Fundação de Apoio à Pesquisa do Distrito Federal/ ; Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; },
abstract = {An Actinobacteria - Kitasatospora sp. K002 - was isolated from the soil of Cerrado, a savanna-like Brazilian biome. Herein, we conducted a phylogenetic, phenotypic and physiological characterization, revealing its potential for biotechnological applications. Kitasatospora sp. K002 is an aerobic, non-motile, Gram-positive bacteria that forms grayish-white mycelium on solid cultures and submerged spores with vegetative mycelia on liquid cultures. The strain showed antibacterial activity against Bacillus subtilis, Pseudomonas aeruginosa and Escherichia coli. Genomic analysis indicated that Kitasatospora xanthocidica JCM 4862 is the closest strain to K002, with a dDDH of 32.8-37.8% and an ANI of 86.86% and the pangenome investigations identified a high number of rare genes. A total of 60 gene clusters of 22 different types were detected by AntiSMASH, and 22 gene clusters showed low similarity (< 10%) with known compounds, which suggests the potential production of novel bioactive compounds. In addition, phylogenetic analysis and morphophysiological characterization clearly distinguished Kitasatospora sp. K002 from other related species. Therefore, we propose that Kitasatospora sp. K002 should be recognized as a new species of the genus Kitasatospora - Kitasatospora brasiliensis sp. nov. (type strains = K002).},
}

@article {pmid38605175,
year = {2024},
author = {Lian, Q and Huettel, B and Walkemeier, B and Mayjonade, B and Lopez-Roques, C and Gil, L and Roux, F and Schneeberger, K and Mercier, R},
title = {A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {38605175},
issn = {1546-1718},
support = {TRR 341/1-456082119//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {Although originally primarily a system for functional biology, Arabidopsis thaliana has, owing to its broad geographical distribution and adaptation to diverse environments, developed into a powerful model in population genomics. Here we present chromosome-level genome assemblies of 69 accessions from a global species range. We found that genomic colinearity is very conserved, even among geographically and genetically distant accessions. Along chromosome arms, megabase-scale rearrangements are rare and typically present only in a single accession. This indicates that the karyotype is quasi-fixed and that rearrangements in chromosome arms are counter-selected. Centromeric regions display higher structural dynamics, and divergences in core centromeres account for most of the genome size variations. Pan-genome analyses uncovered 32,986 distinct gene families, 60% being present in all accessions and 40% appearing to be dispensable, including 18% private to a single accession, indicating unexplored genic diversity. These 69 new Arabidopsis thaliana genome assemblies will empower future genetic research.},
}

@article {pmid38600518,
year = {2024},
author = {Hong, A and Oliva, M and Köppl, D and Bannai, H and Boucher, C and Gagie, T},
title = {Pfp-fm: an accelerated FM-index.},
journal = {Algorithms for molecular biology : AMB},
volume = {19},
number = {1},
pages = {15},
pmid = {38600518},
issn = {1748-7188},
support = {R01AI14180/HG/NHGRI NIH HHS/United States ; },
abstract = {FM-indexes are crucial data structures in DNA alignment, but searching with them usually takes at least one random access per character in the query pattern. Ferragina and Fischer [1] observed in 2007 that word-based indexes often use fewer random accesses than character-based indexes, and thus support faster searches. Since DNA lacks natural word-boundaries, however, it is necessary to parse it somehow before applying word-based FM-indexing. In 2022, Deng et al. [2] proposed parsing genomic data by induced suffix sorting, and showed that the resulting word-based FM-indexes support faster counting queries than standard FM-indexes when patterns are a few thousand characters or longer. In this paper we show that using prefix-free parsing-which takes parameters that let us tune the average length of the phrases-instead of induced suffix sorting, gives a significant speedup for patterns of only a few hundred characters. We implement our method and demonstrate it is between 3 and 18 times faster than competing methods on queries to GRCh38, and is consistently faster on queries made to 25,000, 50,000 and 100,000 SARS-CoV-2 genomes. Hence, it seems our method accelerates the performance of count over all state-of-the-art methods with a moderate increase in the memory. The source code for PFP - FM is available at https://github.com/AaronHong1024/afm .},
}

@article {pmid38592762,
year = {2024},
author = {Lazaridi, E and Kapazoglou, A and Gerakari, M and Kleftogianni, K and Passa, K and Sarri, E and Papasotiropoulos, V and Tani, E and Bebeli, PJ},
title = {Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/plants13060758},
pmid = {38592762},
issn = {2223-7747},
abstract = {Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement of genomic technologies such as deciphering of pangenomes, multi-omics tools, marker-assisted selection (MAS), genome-wide association studies (GWAS), and CRISPR/Cas9 gene editing greatly facilitated the exploitation of landraces in modern plant breeding. In this paper, we present a comprehensive overview of the implementation of new genomic technologies and highlight their importance in pinpointing the genetic basis of desirable traits in landraces and indigenous varieties of annual, perennial herbaceous, and woody crop species cultivated in the Mediterranean region. The need for further employment of advanced -omic technologies to unravel the full potential of landraces and indigenous varieties underutilized genetic diversity is also indicated. Ultimately, the large amount of genomic data emerging from the investigation of landraces and indigenous varieties reveals their potential as a source of valuable genes and traits for breeding. The role of landraces and indigenous varieties in mitigating the ongoing risks posed by climate change in agriculture and food security is also highlighted.},
}

@article {pmid38591882,
year = {2024},
author = {Xing, Y and Clark, JR and Chang, JD and Zulk, JJ and Chirman, DM and Piedra, F-A and Vaughan, EE and Hernandez Santos, HJ and Patras, KA and Maresso, AW},
title = {Progress toward a vaccine for extraintestinal pathogenic E. coli (ExPEC) II: efficacy of a toxin-autotransporter dual antigen approach.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0044023},
doi = {10.1128/iai.00440-23},
pmid = {38591882},
issn = {1098-5522},
abstract = {Extraintestinal pathogenic Escherichia coli (ExPEC) is a leading cause of worldwide morbidity and mortality, the top cause of antimicrobial-resistant (AMR) infections, and the most frequent cause of life-threatening sepsis and urinary tract infections (UTI) in adults. The development of an effective and universal vaccine is complicated by this pathogen's pan-genome, its ability to mix and match virulence factors and AMR genes via horizontal gene transfer, an inability to decipher commensal from pathogens, and its intimate association and co-evolution with mammals. Using a pan virulome analysis of >20,000 sequenced E. coli strains, we identified the secreted cytolysin α-hemolysin (HlyA) as a high priority target for vaccine exploration studies. We demonstrate that a catalytically inactive pure form of HlyA, expressed in an autologous host using its own secretion system, is highly immunogenic in a murine host, protects against several forms of ExPEC infection (including lethal bacteremia), and significantly lowers bacterial burdens in multiple organ systems. Interestingly, the combination of a previously reported autotransporter (SinH) with HlyA was notably effective, inducing near complete protection against lethal challenge, including commonly used infection strains ST73 (CFT073) and ST95 (UTI89), as well as a mixture of 10 of the most highly virulent sequence types and strains from our clinical collection. Both HlyA and HlyA-SinH combinations also afforded some protection against UTI89 colonization in a murine UTI model. These findings suggest recombinant, inactive hemolysin and/or its combination with SinH warrant investigation in the development of an E. coli vaccine against invasive disease.},
}

@article {pmid38585972,
year = {2024},
author = {Marin, MG and Wippel, C and Quinones-Olvera, N and Behruznia, M and Jeffrey, BM and Harris, M and Mann, BC and Rosenthal, A and Jacobson, KR and Warren, RM and Li, H and Meehan, CJ and Farhat, MR},
title = {Analysis of the limited M. tuberculosis accessory genome reveals potential pitfalls of pan-genome analysis approaches.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.03.21.586149},
pmid = {38585972},
abstract = {Pan-genome analysis is a fundamental tool in the study of bacterial genome evolution. Benchmarking the accuracy of pan-genome analysis methods is challenging, because it can be significantly influenced by both the methodology used to compare genomes, as well as differences in the accuracy and representativeness of the genomes analyzed. In this work, we curated a collection of 151 Mycobacterium tuberculosis (Mtb) isolates to evaluate sources of variability in pan-genome analysis. Mtb is characterized by its clonal evolution, absence of horizontal gene transfer, and limited accessory genome, making it an ideal test case for this study. Using a state-of-the-art graph-genome approach, we found that a majority of the structural variation observed in Mtb originates from rearrangement, deletion, and duplication of redundant nucleotide sequences. In contrast, we found that pan-genome analyses that focus on comparison of coding sequences (at the amino acid level) can yield surprisingly variable results, driven by differences in assembly quality and the softwares used. Upon closer inspection, we found that coding sequence annotation discrepancies were a major contributor to inflated Mtb accessory genome estimates. To address this, we developed panqc, a software that detects annotation discrepancies and collapses nucleotide redundancy in pan-genome estimates. We characterized the effect of the panqc adjustment on both pan-genome analysis of Mtb and E. coli genomes, and highlight how different levels of genomic diversity are prone to unique biases. Overall, this study illustrates the need for careful methodological selection and quality control to accurately map the evolutionary dynamics of a bacterial species.},
}

@article {pmid38584940,
year = {2024},
author = {Carhuaricra-Huaman, D and Gonzalez, IHL and Ramos, PL and da Silva, AM and Setubal, JC},
title = {Analysis of twelve genomes of the bacterium Kerstersia gyiorum from brown-throated sloths (Bradypus variegatus), the first from a non-human host.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17206},
pmid = {38584940},
issn = {2167-8359},
abstract = {Kerstersia gyiorum is a Gram-negative bacterium found in various animals, including humans, where it has been associated with various infections. Knowledge of the basic biology of K. gyiorum is essential to understand the evolutionary strategies of niche adaptation and how this organism contributes to infectious diseases; however, genomic data about K. gyiorum is very limited, especially from non-human hosts. In this work, we sequenced 12 K. gyiorum genomes isolated from healthy free-living brown-throated sloths (Bradypus variegatus) in the Parque Estadual das Fontes do Ipiranga (São Paulo, Brazil), and compared them with genomes from isolates of human origin, in order to gain insights into genomic diversity, phylogeny, and host specialization of this species. Phylogenetic analysis revealed that these K. gyiorum strains are structured according to host. Despite the fact that sloth isolates were sampled from a single geographic location, the intra-sloth K. gyiorum diversity was divided into three clusters, with differences of more than 1,000 single nucleotide polymorphisms between them, suggesting the circulation of various K. gyiorum lineages in sloths. Genes involved in mobilome and defense mechanisms against mobile genetic elements were the main source of gene content variation between isolates from different hosts. Sloth-specific K. gyiorum genome features include an IncN2 plasmid, a phage sequence, and a CRISPR-Cas system. The broad diversity of defense elements in K. gyiorum (14 systems) may prevent further mobile element flow and explain the low amount of mobile genetic elements in K. gyiorum genomes. Gene content variation may be important for the adaptation of K. gyiorum to different host niches. This study furthers our understanding of diversity, host adaptation, and evolution of K. gyiorum, by presenting and analyzing the first genomes of non-human isolates.},
}

@article {pmid38580497,
year = {2024},
author = {Wolfe, JM},
title = {Pangenomes at the limits of evolution.},
journal = {Trends in ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2024.03.008},
pmid = {38580497},
issn = {1872-8383},
abstract = {Evolutionary pathways can be random or deterministic. In a recent article, Beavan et al. investigate this balance by applying machine learning models to microbial pangenomes. The presence of almost one-third of genes can be reliably inferred, indicating a surprising amount of predictable evolution.},
}

@article {pmid38577974,
year = {2024},
author = {Cannon, EK and Portwood, JL and Hayford, RK and Haley, OC and Gardiner, JM and Andorf, CM and Woodhouse, MR},
title = {Enhanced pan-genomic resources at the maize genetics and genomics database.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyae036},
pmid = {38577974},
issn = {1943-2631},
support = {//US Department of Agriculture/ ; 5030-21000-068-00-D//Agricultural Research Service/ ; 440229//Corn Insects and Crop Genetics Research Unit in Ames, Iowa/ ; },
abstract = {Pan-genomes, encompassing the entirety of genetic sequences found in a collection of genomes within a clade, are more useful than single reference genomes for studying species diversity. This is especially true for a species like Zea mays, which has a particularly diverse and complex genome. Presenting pan-genome data, analyses, and visualization is challenging, especially for a diverse species, but more so when pan-genomic data is linked to extensive gene model and gene data, including classical gene information, markers, insertions, expression and proteomic data, and protein structures as is the case at MaizeGDB. Here, we describe MaizeGDB's expansion to include the genic subset of the Zea pan-genome in a pan-gene data center featuring the maize genomes hosted at MaizeGDB, and the outgroup teosinte Zea genomes from the Pan-Andropoganeae project. The new data center offers a variety of browsing and visualization tools, including sequence alignment visualization, gene trees and other tools, to explore pan-genes in Zea that were calculated by the pipeline Pandagma. Combined, these data will help maize researchers study the complexity and diversity of Zea, and to use the comparative functions to validate pan-gene relationships for a selected gene model.},
}

@article {pmid38576793,
year = {2024},
author = {Borowska-Beszta, M and Smoktunowicz, M and Horoszkiewicz, D and Jonca, J and Waleron, MM and Gawor, J and Mika, A and Sledzinski, T and Waleron, K and Waleron, M},
title = {Comparative genomics, pangenomics, and phenomic studies of Pectobacterium betavasculorum strains isolated from sugar beet, potato, sunflower, and artichoke: insights into pathogenicity, virulence determinants, and adaptation to the host plant.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1352318},
pmid = {38576793},
issn = {1664-462X},
abstract = {INTRODUCTION: Bacteria of genus Pectobacterium, encompassing economically significant pathogens affecting various plants, includes the species P. betavasculorum, initially associated with beetroot infection. However, its host range is much broader. It causes diseases of sunflower, potato, tomato, carrots, sweet potato, radish, squash, cucumber, and chrysanthemum. To explain this phenomenon, a comprehensive pathogenomic and phenomic characterisation of P. betavasculorum species was performed.

METHODS: Genomes of P. betavasculorum strains isolated from potato, sunflower, and artichoke were sequenced and compared with those from sugar beet isolates. Metabolic profiling and pathogenomic analyses were conducted to assess virulence determinants and adaptation potential. Pathogenicity assays were performed on potato tubers and chicory leaves to confirm in silico predictions of disease symptoms. Phenotypic assays were also conducted to assess the strains ability to synthesise homoserine lactones and siderophores.

RESULTS: The genome size ranged from 4.675 to 4.931 kbp, and GC % was between 51.0% and 51.2%. The pangenome of P. betavasculorum is open and comprises, on average, 4,220 gene families. Of these, 83% of genes are the core genome, and 2% of the entire pangenome are unique genes. Strains isolated from sugar beet have a smaller pangenome size and a higher number of unique genes than those from other plants. Interestingly, genomes of strains from artichoke and sunflower share 391 common CDS that are not present in the genomes of other strains from sugar beet or potato. Those strains have only one unique gene. All strains could use numerous sugars as building materials and energy sources and possessed a high repertoire of virulence determinants in the genomes. P. betavasculorum strains were able to cause disease symptoms on potato tubers and chicory leaves. They were also able to synthesise homoserine lactones and siderophores.

DISCUSSION: The findings underscore the adaptability of P. betavasculorum to diverse hosts and environments. Strains adapted to plants with high sugar content in tissues have a different composition of fatty acids in membranes and a different mechanism of replenishing nitrogen in case of deficiency of this compound than strains derived from other plant species. Extensive phenomics and genomic analyses performed in this study have shown that P. betavasculorum species is an agronomically relevant pathogen.},
}

@article {pmid38506894,
year = {2024},
author = {Baek, J and Lawson, J and Rahimzadeh, V},
title = {Investigating the Roles and Responsibilities of Institutional Signing Officials After Data Sharing Policy Reform for Federally Funded Research in the United States: National Survey.},
journal = {JMIR formative research},
volume = {8},
number = {},
pages = {e49822},
pmid = {38506894},
issn = {2561-326X},
abstract = {BACKGROUND: New federal policies along with rapid growth in data generation, storage, and analysis tools are together driving scientific data sharing in the United States. At the same, triangulating human research data from diverse sources can also create situations where data are used for future research in ways that individuals and communities may consider objectionable. Institutional gatekeepers, namely, signing officials (SOs), are therefore at the helm of compliant management and sharing of human data for research. Of those with data governance responsibilities, SOs most often serve as signatories for investigators who deposit, access, and share research data between institutions. Although SOs play important leadership roles in compliant data sharing, we know surprisingly little about their scope of work, roles, and oversight responsibilities.

OBJECTIVE: The purpose of this study was to describe existing institutional policies and practices of US SOs who manage human genomic data access, as well as how these may change in the wake of new Data Management and Sharing requirements for National Institutes of Health-funded research in the United States.

METHODS: We administered an anonymous survey to institutional SOs recruited from biomedical research institutions across the United States. Survey items probed where data generated from extramurally funded research are deposited, how researchers outside the institution access these data, and what happens to these data after extramural funding ends.

RESULTS: In total, 56 institutional SOs participated in the survey. We found that SOs frequently approve duplicate data deposits and impose stricter access controls when data use limitations are unclear or unspecified. In addition, 21% (n=12) of SOs knew where data from federally funded projects are deposited after project funding sunsets. As a consequence, most investigators deposit their scientific data into "a National Institutes of Health-funded repository" to meet the Data Management and Sharing requirements but also within the "institution's own repository" or a third-party repository.

CONCLUSIONS: Our findings inform 5 policy recommendations and best practices for US SOs to improve coordination and develop comprehensive and consistent data governance policies that balance the need for scientific progress with effective human data protections.},
}

@article {pmid38573185,
year = {2024},
author = {Hall, MB and Coin, LJM},
title = {Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data.},
journal = {GigaScience},
volume = {13},
number = {},
pages = {},
doi = {10.1093/gigascience/giae010},
pmid = {38573185},
issn = {2047-217X},
support = {2020/MRF1200856//Australian Government Medical Research Future Fund/ ; //Genomics Health Futures Mission/ ; },
abstract = {BACKGROUND: Culture-free real-time sequencing of clinical metagenomic samples promises both rapid pathogen detection and antimicrobial resistance profiling. However, this approach introduces the risk of patient DNA leakage. To mitigate this risk, we need near-comprehensive removal of human DNA sequences at the point of sequencing, typically involving the use of resource-constrained devices. Existing benchmarks have largely focused on the use of standardized databases and largely ignored the computational requirements of depletion pipelines as well as the impact of human genome diversity.

RESULTS: We benchmarked host removal pipelines on simulated and artificial real Illumina and Nanopore metagenomic samples. We found that construction of a custom kraken database containing diverse human genomes results in the best balance of accuracy and computational resource usage. In addition, we benchmarked pipelines using kraken and minimap2 for taxonomic classification of Mycobacterium reads using standard and custom databases. With a database representative of the Mycobacterium genus, both tools obtained improved specificity and sensitivity, compared to the standard databases for classification of Mycobacterium tuberculosis. Computational efficiency of these custom databases was superior to most standard approaches, allowing them to be executed on a laptop device.

CONCLUSIONS: Customized pangenome databases provide the best balance of accuracy and computational efficiency when compared to standard databases for the task of human read removal and M. tuberculosis read classification from metagenomic samples. Such databases allow for execution on a laptop, without sacrificing accuracy, an especially important consideration in low-resource settings. We make all customized databases and pipelines freely available.},
}

@article {pmid38567256,
year = {2024},
author = {Olbrich, M and Bartels, L and Wohlers, I},
title = {Sequencing technologies and hardware-accelerated parallel computing transform computational genomics research.},
journal = {Frontiers in bioinformatics},
volume = {4},
number = {},
pages = {1384497},
pmid = {38567256},
issn = {2673-7647},
}

@article {pmid38567138,
year = {2024},
author = {Jiang, M and Chen, M and Zeng, J and Du, Z and Xiao, J},
title = {A comprehensive evaluation of the potential of three next-generation short-read-based plant pan-genome construction strategies for the identification of novel non-reference sequence.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1371222},
pmid = {38567138},
issn = {1664-462X},
abstract = {Pan-genome studies are important for understanding plant evolution and guiding the breeding of crops by containing all genomic diversity of a certain species. Three short-read-based strategies for plant pan-genome construction include iterative individual, iteration pooling, and map-to-pan. Their performance is very different under various conditions, while comprehensive evaluations have yet to be conducted nowadays. Here, we evaluate the performance of these three pan-genome construction strategies for plants under different sequencing depths and sample sizes. Also, we indicate the influence of length and repeat content percentage of novel sequences on three pan-genome construction strategies. Besides, we compare the computational resource consumption among the three strategies. Our findings indicate that map-to-pan has the greatest recall but the lowest precision. In contrast, both two iterative strategies have superior precision but lower recall. Factors of sample numbers, novel sequence length, and the percentage of novel sequences' repeat content adversely affect the performance of all three strategies. Increased sequencing depth improves map-to-pan's performance, while not affecting the other two iterative strategies. For computational resource consumption, map-to-pan demands considerably more than the other two iterative strategies. Overall, the iterative strategy, especially the iterative pooling strategy, is optimal when the sequencing depth is less than 20X. Map-to-pan is preferable when the sequencing depth exceeds 20X despite its higher computational resource consumption.},
}

@article {pmid38564163,
year = {2024},
author = {Marlin, R and Loger, JS and Joachim, C and Ebring, C and Robert-Siegwald, G and Pennont, S and Rose, M and Raguette, K and Suez-Panama, V and Ulric-Gervaise, S and Lusbec, S and Bera, O and Vallard, A and Aline-Fardin, A and Colomba, E and Jean-Laurent, M},
title = {Copy number signatures and CCNE1 amplification reveal the involvement of replication stress in high-grade endometrial tumors oncogenesis.},
journal = {Cellular oncology (Dordrecht)},
volume = {},
number = {},
pages = {},
pmid = {38564163},
issn = {2211-3436},
abstract = {PURPOSE: Managing high-grade endometrial cancer in Martinique poses significant challenges. The diversity of copy number alterations in high-grade endometrial tumors, often associated with a TP53 mutation, is a key factor complicating treatment. Due to the high incidence of high-grade tumors with poor prognosis, our study aimed to characterize the molecular signature of these tumors within a cohort of 25 high-grade endometrial cases.

METHODS: We conducted a comprehensive pangenomic analysis to categorize the copy number alterations involved in these tumors. Whole-Exome Sequencing (WES) and Homologous Recombination (HR) analysis were performed. The alterations obtained from the WES were classified into various signatures using the Copy Number Signatures tool available in COSMIC.

RESULTS: We identified several signatures that correlated with tumor stage and disctinct prognoses. These signatures all seem to be linked to replication stress, with CCNE1 amplification identified as the primary driver of oncogenesis in over 70% of tumors analyzed.

CONCLUSION: The identification of CCNE1 amplification, which is currently being explored as a therapeutic target in clinical trials, suggests new treatment strategies for high-grade endometrial cancer. This finding holds particular significance for Martinique, where access to care is challenging.},
}

@article {pmid38560215,
year = {2024},
author = {Comba-González, NB and Chaves-Moreno, D and Santamaría-Vanegas, J and Montoya-Castaño, D},
title = {A pan-genomic assessment: Delving into the genome of the marine epiphyte Bacillus altitudinis strain 19_A and other very close Bacillus strains from multiple environments.},
journal = {Heliyon},
volume = {10},
number = {7},
pages = {e27820},
doi = {10.1016/j.heliyon.2024.e27820},
pmid = {38560215},
issn = {2405-8440},
abstract = {Marine macroalgae are the habitat of epiphytic bacteria and provide several conditions for a beneficial biological interaction to thrive. Although Bacillus is one of the most abundant epiphytic genera, genomic information on marine macroalgae-associated Bacillus species remains scarce. In this study, we further investigated our previously published genome of the epiphytic strain Bacillus altitudinis 19_A to find features that could be translated to potential metabolites produced by this microorganism, as well as genes that play a role in its interaction with its macroalgal host. To achieve this goal, we performed a pan-genome analysis of Bacillus sp. and a codon bias assessment, including the genome of the strain Bacillus altitudinis 19_A and 29 complete genome sequences of closely related Bacillus strains isolated from soil, marine environments, plants, extreme environments, air, and food. This genomic analysis revealed that Bacillus altitudinis 19_A possessed unique genes encoding proteins involved in horizontal gene transfer, DNA repair, transcriptional regulation, and bacteriocin biosynthesis. In this comparative analysis, codon bias was not associated with the habitat of the strains studied. Some accessory genes were identified in the Bacillus altitudinis 19_A genome that could be related to its epiphytic lifestyle, as well as gene clusters for the biosynthesis of a sporulation-killing factor and a bacteriocin, showing their potential as a source of antimicrobial peptides. Our results provide a comprehensive view of the Bacillus altitudinis 19_A genome to understand its adaptation to the marine environment and its potential as a producer of bioactive compounds.},
}

@article {pmid38559026,
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 = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.03.15.585215},
pmid = {38559026},
abstract = {Portable genomic sequencers such as Oxford Nanopore's MinION enable real-time applications in both clinical and environmental health, e.g., detection of bacterial outbreaks. 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. For instance, metagenomics classifiers usually require a large amount of memory or specific operating systems/libraries. In this work, 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 (e.g., selection of bacteria of public health priority), making it ideal for running on smartphones or tablets. We indexed both OCTOPUS and Kraken2 on a bacterial database with ∼4,000 reference genomes, then simulated a positive (bacterial genomes from the same species, but different genomes) and two negative (viral, mammalian) Nanopore test sets. On the bacterial test set OCTOPUS yielded sensitivity and precision comparable to Kraken2 (94.4% and 99.8% versus 94.5% and 99.1%, respectively). On non-bacterial sequences (mammals and viral), OCTOPUS dramatically decreased (4-to 16-fold) the false positive rate when compared to Kraken2 (2.1% and 0.7% versus 8.2% and 11.2%, respectively). We also developed customized databases including viruses, and the World Health Organization's set of bacteria of concern for drug resistance, tested with real Nanopore data on an Android smartphone. OCTOPUS is publicly available at https://github.com/DataIntellSystLab/OCTOPUS and https://github.com/Ruiz-HCI-Lab/OctopusMobile .},
}

@article {pmid38558270,
year = {2024},
author = {Montecillo, JAV},
title = {Comparative genomics of the genus Halioglobus reveals the genetic basis for the reclassification of Halioglobus pacificus as Parahalioglobus pacificus gen. nov. comb. nov.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {38558270},
issn = {1618-1905},
abstract = {The genus Halioglobus is one of the environmentally relevant members of the family Halieaceae, class Gammaproteobacteria. At present, the genus is composed of three validly published species. However, in the recent study of the family Halieaceae, the species Halioglobus pacificus was observed to branch outside of the main clade formed by the members of Halioglobus, suggesting its distinct taxonomic placement within the family. In the present study, the taxonomic placement of H. pacificus was reassessed using comparative genomics. Phylogenomic analysis revealed the paraphyletic relationship of H. pacificus with the type species of the genus Halioglobus, and further demonstrated its genus-level placement. This phylogenetic relationship was reinforced by the average nucleotide and amino acid identity values shared by H. pacificus with the members of the family Halieaceae. Moreover, the results of the pan-genome analysis, together with the phenotype data, further supported the exclusion of H. pacificus from the genus Halioglobus. Based on these findings, the species H. pacificus is thereby assigned to a new genus Parahalioglobus gen. nov. as Parahalioglobus pacificus comb. nov.},
}

@article {pmid38555312,
year = {2024},
author = {Yang, Y and Wang, H and Tu, J and Li, Y and Guan, H},
title = {Comprehensive genomic analysis of Burkholderia arboris PN-1 reveals its biocontrol potential against Fusarium solani-induced root rot in Panax notoginseng.},
journal = {Current genetics},
volume = {70},
number = {1},
pages = {4},
pmid = {38555312},
issn = {1432-0983},
support = {YJSJJ22-A15//Postgraduate research Innovation Fund Project in Yunnan Normal University/ ; 202202AE090025//Major Science and Technology Special Project of Yunnan Province/ ; 202305AF150027//Yunnan Academician Expert Workstation/ ; YSZJGZZ-2021062//Yunnan (Kunming) Academician Expert Workstation/ ; },
abstract = {Panax notoginseng (Burkill) F.H. Chen, a valuable traditional Chinese medicine, faces significant yield and quality challenges stemming from root rot primarily caused by Fusarium solani. Burkholderia arboris PN-1, isolated from the rhizosphere soil of P. notoginseng, demonstrated a remarkable ability to inhibit the growth of F. solani. This study integrates phenotypic, phylogenetic, and genomic analyses to enhance our understanding of the biocontrol mechanisms employed by B. arboris PN-1. Phenotype analysis reveals that B. arboris PN-1 effectively suppresses P. notoginseng root rot both in vitro and in vivo. The genome of B. arboris PN-1 comprises three circular chromosomes (contig 1: 3,651,544 bp, contig 2: 1,355,460 bp, and contig 3: 3,471,056 bp), with a 66.81% GC content, housing 7,550 protein-coding genes. Notably, no plasmids were detected. Phylogenetic analysis places PN-1 in close relation to B. arboris AU14372, B. arboris LMG24066, and B. arboris MEC_B345. Average nucleotide identity (ANI) values confirm the PN-1 classification as B. arboris. Comparative analysis with seven other B. arboris strains identified 4,628 core genes in B. arboris PN-1. The pan-genome of B. arboris appears open but may approach closure. Whole-genome sequencing revealed 265 carbohydrate-active enzymes and identified 9 gene clusters encoding secondary metabolites. This comprehensive investigation enhances our understanding of B. arboris genomes, paving the way for their potential as effective biocontrol agents against fungal plant pathogens in the future.},
}

@article {pmid38550074,
year = {2024},
author = {International, BR},
title = {Retracted: Epi-Gene: An R-Package for Easy Pan-Genome Analysis.},
journal = {BioMed research international},
volume = {2024},
number = {},
pages = {9830450},
doi = {10.1155/2024/9830450},
pmid = {38550074},
issn = {2314-6141},
abstract = {[This retracts the article DOI: 10.1155/2021/5585586.].},
}

@article {pmid38543563,
year = {2024},
author = {Grizon, A and Theil, S and Helinck, S and Gerber, P and Bonnarme, P and Chassard, C},
title = {Genomic Characterization of Wild Lactobacillus delbrueckii Strains Reveals Low Diversity but Strong Typicity.},
journal = {Microorganisms},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/microorganisms12030512},
pmid = {38543563},
issn = {2076-2607},
support = {convention CIFRE N° 2020/0839//Association Nationale de la Recherche et de la Technologie/ ; },
abstract = {Investigating the diversity of a given species could give clues for the development of autochthonous starter cultures. However, few studies have focused on the intraspecies diversity of Lactobacillus delbrueckii strains, a technologically important lactic acid bacterium for the dairy industry. For this reason, Lactobacillus delbrueckii strains from the Saint-Nectaire Protected Designation of Origin (PDO) area were isolated and characterized. Genetic diversity was determined based on core genome phylogenetic reconstruction and pangenome analysis, while phenotypic assessments encompassed proteolysis and volatile compound production potential. A total of 15 L. delbrueckii ssp. lactis unique new strains were obtained. The genetic analysis and further proteolytic activities measurement revealed low variability among these Saint-Nectaire strains, while substantial genetic variability was observed within the L. delbrueckii ssp. lactis subspecies as a whole. The volatile compound profiles slightly differed among strains, and some strains produced volatile compounds that could be of particular interest for cheese flavor development. While the genetic diversity among Saint-Nectaire strains was relatively modest compared to overall subspecies diversity, their distinct characteristics and pronounced differentiation from publicly available genomes position them as promising candidates for developing autochthonous starter cultures for cheese production.},
}

@article {pmid38541621,
year = {2024},
author = {Park, S and Kim, I and Chhetri, G and Jung, Y and Woo, H and Seo, T},
title = {Draft Genome Sequence Analyses of Two Novel Marinobacter suadae sp. nov. and Wenyingzhuangia gilva sp. nov. Isolated from the Root of Suaeda japonica Makino.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/life14030296},
pmid = {38541621},
issn = {2075-1729},
support = {2022R1F1A1070108//National Research Foundation of Korea/ ; NIBR202304204//National Institute of Biological Resources/ ; },
abstract = {Gram-negative, rod-shaped, and aerobic bacteria designated chi1[T] and chi5[T] were isolated from the root of Suaeda japonica Makino. Phylogenetics utilizing 16S rRNA and whole-genome sequences of the two novel strains chi1[T] and chi5[T] confirmed that they were related to the genera Marinobacter and Wenyingzhuangia, respectively. For the novel strains chi1[T] and chi5[T], the digital DNA-DNA hybridization values (19-20% and 22.1-36.6%, respectively) and average nucleotide identity values (74.4-76.5% and 79.1-88.9%, respectively) fell within the range for the genera Marinobacter and Wenyingzhuangia, respectively. Pangenome analyses of the novel strains chi1[T] and chi5[T] revealed 357 and 368 singletons genes, respectively. The genomic DNA G + C contents of the strains chi1[T] and chi5[T] were 57.2% and 31.5%, respectively. The major fatty acids of strain chi1[T] were C12:0, C16:0, and summed feature 3 (C16:1ω6c and/or C16:1ω7c), while those of the strain chi5[T] were iso-C15:0 3OH, iso-C17:0 3OH, and iso-C15:0. Data from the phylogenetic, phylogenomic, pangenome, genomic, physiological, and biochemical analyses indicated that the novel strains were distinct. Therefore, we propose the names Marinobacter suadae (type strain chi1[T] = KACC 23259[T] = TBRC 17652[T]) and Wenyingzhangia gilva (type strain chi5[T] = KACC 23262[T] = TBRC 17900[T]) for the studied bacterial strains.},
}

@article {pmid38537199,
year = {2024},
author = {Meng, T and Jiao, H and Zhang, Y and Zhou, Y and Chen, S and Wang, X and Yang, B and Sun, J and Geng, X and Ayhan, DH and Guo, L},
title = {FoPGDB: a pangenome database of Fusarium oxysporum, a cross-kingdom fungal pathogen.},
journal = {Database : the journal of biological databases and curation},
volume = {2024},
number = {},
pages = {},
doi = {10.1093/database/baae017},
pmid = {38537199},
issn = {1758-0463},
support = {//National Natural Science Foundation of China/ ; //Taishan Scholars Program of Shandong Province/ ; //Shandong Provincial Science and Technology Innovation Fund/ ; //National Natural Science Foundation of China/ ; //Taishan Scholars Program of Shandong Province/ ; //Shandong Provincial Science and Technology Innovation Fund/ ; },
abstract = {Pangenomes, capturing the genetic diversity of a species or genus, are essential to understanding the ecology, pathobiology and evolutionary mechanisms of fungi that cause infection in crops and humans. However, fungal pangenome databases remain unavailable. Here, we report the first fungal pangenome database, specifically for Fusarium oxysporum species complex (FOSC), a group of cross-kingdom pathogens causing devastating vascular wilt to over 100 plant species and life-threatening fusariosis to immunocompromised humans. The F. oxysporum Pangenome Database (FoPGDB) is a comprehensive resource integrating 35 high-quality FOSC genomes, coupled with robust analytical tools. FoPGDB allows for both gene-based and graph-based exploration of the F. oxysporum pangenome. It also curates a large repository of putative effector sequences, crucial for understanding the mechanisms of FOSC pathogenicity. With an assortment of functionalities including gene search, genomic variant exploration and tools for functional enrichment, FoPGDB provides a platform for in-depth investigations of the genetic diversity and adaptability of F. oxysporum. The modular and user-friendly interface ensures efficient data access and interpretation. FoPGDB promises to be a valuable resource for F. oxysporum research, contributing to our understanding of this pathogen's pangenomic landscape and aiding in the development of novel disease management strategies. Database URL: http://www.fopgdb.site.},
}

@article {pmid38534692,
year = {2024},
author = {Karampatakis, T and Tsergouli, K and Behzadi, P},
title = {Pan-Genome Plasticity and Virulence Factors: A Natural Treasure Trove for Acinetobacter baumannii.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/antibiotics13030257},
pmid = {38534692},
issn = {2079-6382},
abstract = {Acinetobacter baumannii is a Gram-negative pathogen responsible for a variety of community- and hospital-acquired infections. It is recognized as a life-threatening pathogen among hospitalized individuals and, in particular, immunocompromised patients in many countries. A. baumannii, as a member of the ESKAPE group, encompasses high genomic plasticity and simultaneously is predisposed to receive and exchange the mobile genetic elements (MGEs) through horizontal genetic transfer (HGT). Indeed, A. baumannii is a treasure trove that contains a high number of virulence factors. In accordance with these unique pathogenic characteristics of A. baumannii, the authors aim to discuss the natural treasure trove of pan-genome and virulence factors pertaining to this bacterial monster and try to highlight the reasons why this bacterium is a great concern in the global public health system.},
}

@article {pmid38532808,
year = {2024},
author = {Bundhoo, E and Ghoorah, AW and Jaufeerally-Fakim, Y},
title = {Large-scale Pan Genomic Analysis of Mycobacterium tuberculosis Reveals Key Insights Into Molecular Evolutionary Rate of Specific Processes and Functions.},
journal = {Evolutionary bioinformatics online},
volume = {20},
number = {},
pages = {11769343241239463},
pmid = {38532808},
issn = {1176-9343},
abstract = {Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis (TB), an infectious disease that is a major killer worldwide. Due to selection pressure caused by the use of antibacterial drugs, Mtb is characterised by mutational events that have given rise to multi drug resistant (MDR) and extensively drug resistant (XDR) phenotypes. The rate at which mutations occur is an important factor in the study of molecular evolution, and it helps understand gene evolution. Within the same species, different protein-coding genes evolve at different rates. To estimate the rates of molecular evolution of protein-coding genes, a commonly used parameter is the ratio dN/dS, where dN is the rate of non-synonymous substitutions and dS is the rate of synonymous substitutions. Here, we determined the estimated rates of molecular evolution of select biological processes and molecular functions across 264 strains of Mtb. We also investigated the molecular evolutionary rates of core genes of Mtb by computing the dN/dS values, and estimated the pan genome of the 264 strains of Mtb. Our results show that the cellular amino acid metabolic process and the kinase activity function evolve at a significantly higher rate, while the carbohydrate metabolic process evolves at a significantly lower rate for M. tuberculosis. These high rates of evolution correlate well with Mtb physiology and pathogenicity. We further propose that the core genome of M. tuberculosis likely experiences varying rates of molecular evolution which may drive an interplay between core genome and accessory genome during M. tuberculosis evolution.},
}

@article {pmid38529905,
year = {2024},
author = {Crowley, C and Selvaraj, A and Hariharan, A and Healy, CM and Moran, GP},
title = {Fusobacterium nucleatum subsp. polymorphum recovered from malignant and potentially malignant oral disease exhibit heterogeneity in adhesion phenotypes and adhesin gene copy number, shaped by inter-subspecies horizontal gene transfer and recombination-derived mosaicism.},
journal = {Microbial genomics},
volume = {10},
number = {3},
pages = {},
doi = {10.1099/mgen.0.001217},
pmid = {38529905},
issn = {2057-5858},
abstract = {Fusobacterium nucleatum is an anaerobic commensal of the oral cavity associated with periodontitis and extra-oral diseases, including colorectal cancer. Previous studies have shown an increased relative abundance of this bacterium associated with oral dysplasia or within oral tumours. Using direct culture, we found that 75 % of Fusobacterium species isolated from malignant or potentially malignant oral mucosa were F. nucleatum subsp. polymorphum. Whole genome sequencing and pangenome analysis with Panaroo was carried out on 76 F. nucleatum subsp. polymorphum genomes. F. nucleatum subsp. polymorphum was shown to possesses a relatively small core genome of 1604 genes in a pangenome of 7363 genes. Phylogenetic analysis based on the core genome shows the isolates can be separated into three main clades with no obvious genotypic associations with disease. Isolates recovered from healthy and diseased sites in the same patient are generally highly related. A large repertoire of adhesins belonging to the type V secretion system (TVSS) could be identified with major variation in repertoire and copy number between strains. Analysis of intergenic recombination using fastGEAR showed that adhesin complement is shaped by horizontal gene transfer and recombination. Recombination events at TVSS adhesin genes were not only common between lineages of subspecies polymorphum, but also between different subspecies of F. nucleatum. Strains of subspecies polymorphum with low copy numbers of TVSS adhesin encoding genes tended to have the weakest adhesion to oral keratinocytes. This study highlights the genetic heterogeneity of F. nucleatum subsp. polymorphum and provides a new framework for defining virulence in this organism.},
}

@article {pmid38529502,
year = {2024},
author = {Zhou, Q and Ghezelji, M and Hari, A and Ford, MKB and Holley, C and , and Mirabello, L and Chanock, S and Sahinalp, SC and Numanagić, I},
title = {Geny: A Genotyping Tool for Allelic Decomposition of Killer Cell Immunoglobulin-Like Receptor Genes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.02.27.582413},
pmid = {38529502},
abstract = {Accurate genotyping of Killer cell Immunoglobulin-like Receptor (KIR) genes plays a pivotal role in enhancing our understanding of innate immune responses, disease correlations, and the advancement of personalized medicine. However, due to the high variability of the KIR region and high level of sequence similarity among different KIR genes, the currently available genotyping methods are unable to accurately infer copy numbers, genotypes and haplotypes of individual KIR genes from next-generation sequencing data. Here we introduce Geny, a new computational tool for precise genotyping of KIR genes. Geny utilizes available KIR haplotype databases and proposes a novel combination of expectation-maximization filtering schemes and integer linear programming-based combinatorial optimization models to resolve ambiguous reads, provide accurate copy number estimation and estimate the haplotype of each copy for the genes within the KIR region. We evaluated Geny on a large set of simulated short-read datasets covering the known validated KIR region assemblies and a set of Illumina short-read samples sequenced from 25 validated samples from the Human Pangenome Reference Consortium collection and showed that it outperforms the existing genotyping tools in terms of accuracy, precision and recall. We envision Geny becoming a valuable resource for understanding immune system response and consequently advancing the field of patient-centric medicine.},
}

@article {pmid38524570,
year = {2024},
author = {Nwabor, LC and Chukamnerd, A and Nwabor, OF and Surachat, K and Pomwised, R and Jeenkeawpiam, K and Chusri, S},
title = {Genotypic and phenotypic mechanisms underlying antimicrobial resistance and synergistic efficacy of rifampicin-based combinations against carbapenem-resistant Acinetobacter baumannii.},
journal = {Heliyon},
volume = {10},
number = {6},
pages = {e27326},
pmid = {38524570},
issn = {2405-8440},
abstract = {PURPOSE: Carbapenem-resistant Acinetobacter baumannii (CRAB) is an urgent concern to public health. This study focuses on exploring the resistance mechanisms and the in vitro results of using rifampicin in combination with conventional antibiotics for the management of CRAB.

METHODS: The synergistic and bactericidal effects of rifampicin with conventional antibiotics were evaluated using chequerboard assay and time-kill assay, while the phenotypic and genotypic characteristics of resistant determinants were performed by efflux pump detection and whole genome sequencing on 29 isolates from ICU patients with underlying health diseases.

RESULTS: The isolates showed multidrug resistance, with over 60% showing addictive responses to rifampicin-based combinations at FICI ranging from 0.6 to 0.8. The time-kill assay revealed 99 % killing for rifampicin and minocycline combination in one isolate at 1/4 MIC rifampicin plus 1/4 MIC minocycline, while a bacteriostatic effect was observed at 1/2 MIC rifampici plus 1/2 MIC for a second isolate. Combination with tigecycline resulted in a 99% killing in two out of three isolates with a 2.5-3 log reduction in CFU at 1/4 MIC rifampicin plus 1/4 MIC tigecycline. Rifampicin plus colistin exhibited bactericidal activity against three out of four isolates. The combinations of rifampicin with ciprofloxacin, chloramphenicol, and trimethoprim-sulfamethoxazole were ineffective against the isolates. In addition, a 4-fold reduction in rifampicin MIC was observed in 2 out of 14 isolates in the presence of an efflux pump inhibitor. The pan-genome study demonstrated a progressive evolution with an accessory genome estimated to cover 58% of the matrix. Seven of the ten sequenced isolates belong to sequence type 2 (ST2), while one isolate each was assigned to ST164, ST16, and ST25. Furthermore, 11 plasmids, 34 antimicrobial resistance (AMR) genes, and 65 virulence-associated genes were predicted from the whole genome data. The blaOXA-23blaADC-25, blaOXA-66, blaPER-7, aph(6)-Id, armA, and arr-3 were prevalent among the isolates. Sequence alignment of the bacteria genome to the reference strain revealed a deleterious mutation in the rpoB gene of 4 isolates.

CONCLUSION: The study suggests that rifampicin in combination with either minocycline, tigecycline, or colistin might be a treatment option for CRAB clinical isolates. In addition, genotypic analysis of the bacteria isolates may inform the clinician of the suitable drug regimen for the management of specific bacteria variants.},
}

@article {pmid38521963,
year = {2024},
author = {Sengupta, P and Muthamilselvi Sivabalan, SK and Singh, NK and Raman, K and Venkateswaran, K},
title = {Genomic, functional, and metabolic enhancements in multidrug-resistant Enterobacter bugandensis facilitating its persistence and succession in the International Space Station.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {62},
pmid = {38521963},
issn = {2049-2618},
support = {19-12829-26//2012 Space Biology NNH12ZTT001N/ ; 19-12829-26//2012 Space Biology NNH12ZTT001N/ ; MTR/2020/000490//Science and Engineering Board (SERB) MATRICS/ ; },
abstract = {BACKGROUND: The International Space Station (ISS) stands as a testament to human achievement in space exploration. Despite its highly controlled environment, characterised by microgravity, increased CO 2 levels, and elevated solar radiation, microorganisms occupy a unique niche. These microbial inhabitants play a significant role in influencing the health and well-being of astronauts on board. One microorganism of particular interest in our study is Enterobacter bugandensis, primarily found in clinical specimens including the human gastrointestinal tract, and also reported to possess pathogenic traits, leading to a plethora of infections.

RESULTS: Distinct from their Earth counterparts, ISS E. bugandensis strains have exhibited resistance mechanisms that categorise them within the ESKAPE pathogen group, a collection of pathogens recognised for their formidable resistance to antimicrobial treatments. During the 2-year Microbial Tracking 1 mission, 13 strains of multidrug-resistant E. bugandensis were isolated from various locations within the ISS. We have carried out a comprehensive study to understand the genomic intricacies of ISS-derived E. bugandensis in comparison to terrestrial strains, with a keen focus on those associated with clinical infections. We unravel the evolutionary trajectories of pivotal genes, especially those contributing to functional adaptations and potential antimicrobial resistance. A hypothesis central to our study was that the singular nature of the stresses of the space environment, distinct from any on Earth, could be driving these genomic adaptations. Extending our investigation, we meticulously mapped the prevalence and distribution of E. bugandensis across the ISS over time. This temporal analysis provided insights into the persistence, succession, and potential patterns of colonisation of E. bugandensis in space. Furthermore, by leveraging advanced analytical techniques, including metabolic modelling, we delved into the coexisting microbial communities alongside E. bugandensis in the ISS across multiple missions and spatial locations. This exploration revealed intricate microbial interactions, offering a window into the microbial ecosystem dynamics within the ISS.

CONCLUSIONS: Our comprehensive analysis illuminated not only the ways these interactions sculpt microbial diversity but also the factors that might contribute to the potential dominance and succession of E. bugandensis within the ISS environment. The implications of these findings are twofold. Firstly, they shed light on microbial behaviour, adaptation, and evolution in extreme, isolated environments. Secondly, they underscore the need for robust preventive measures, ensuring the health and safety of astronauts by mitigating risks associated with potential pathogenic threats. Video Abstract.},
}

@article {pmid38517169,
year = {2024},
author = {Paulay, A and Grimaud, GM and Caballero, R and Laroche, B and Leclerc, M and Labarthe, S and Maguin, E},
title = {Design of a proteolytic module for improved metabolic modeling of Bacteroides caccae.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0015324},
doi = {10.1128/msystems.00153-24},
pmid = {38517169},
issn = {2379-5077},
abstract = {The gut microbiota plays a crucial role in health and is significantly modulated by human diets. In addition to Western diets which are rich in proteins, high-protein diets are used for specific populations or indications, mainly weight loss. In this study, we investigated the effect of protein supplementation on Bacteroides caccae, a Gram-negative gut symbiont. The supplementation with whey proteins led to a significant increase in growth rate, final biomass, and short-chain fatty acids production. A comprehensive genomic analysis revealed that B. caccae possesses a set of 156 proteases with putative intracellular and extracellular localization and allowed to identify amino acid transporters and metabolic pathways. We developed a fully curated genome-scale metabolic model of B. caccae that incorporated its proteolytic activity and simulated its growth and production of fermentation-related metabolites in response to the different growth media. We validated the model by comparing the predicted phenotype to experimental data. The model accurately predicted B. caccae's growth and metabolite production (R[2] = 0.92 for the training set and R[2] = 0.89 for the validation set). We found that accounting for both ATP consumption related to proteolysis, and whey protein accessibility is necessary for accurate predictions of metabolites production. These results provide insights into B. caccae's adaptation to a high-protein diet and its ability to utilize proteins as a source of nutrition. The proposed model provides a useful tool for understanding the feeding mechanism of B. caccae in the gut microbiome.IMPORTANCEMicrobial proteolysis is understudied despite the availability of dietary proteins for the gut microbiota. Here, the proteolytic potential of the gut symbiont Bacteroides caccae was analyzed for the first time using pan-genomics. This sketches a well-equipped bacteria for protein breakdown, capable of producing 156 different proteases with a broad spectrum of cleavage targets. This functional potential was confirmed by the enhancement of growth and metabolic activities at high protein levels. Proteolysis was included in a B. caccae metabolic model which was fitted with the experiments and validated on external data. This model pinpoints the links between protein availability and short-chain fatty acids production, and the importance for B. caccae to gain access to glutamate and asparagine to promote growth. This integrated approach can be generalized to other symbionts and upscaled to complex microbiota to get insights into the ecological impact of proteins on the gut microbiota.},
}

@article {pmid38514651,
year = {2024},
author = {Xie, S and Cui, L and Liao, Z and Zhu, J and Ren, S and Niu, K and Li, H and Jiang, F and Wu, J and Wang, J and Wu, J and Song, B and Wu, W and Peng, C},
title = {Genomic analysis of lumpy skin disease virus asian variants and evaluation of its cellular tropism.},
journal = {NPJ vaccines},
volume = {9},
number = {1},
pages = {65},
pmid = {38514651},
issn = {2059-0105},
support = {32172822//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32172822//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32172822//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32172822//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32172822//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32172822//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32172822//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32172822//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32172822//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32172822//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32172822//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32172822//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32172822//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Lumpy skin disease virus (LSDV) is a poxvirus that mainly affects cattle and can lead to symptoms such as severe reduction in milk production as well as infertility and mortality, which has resulted in dramatic economic loss in affected countries in Africa, Europe, and Asia. In this study, we successfully isolated two strains of LSDV from different geographical regions in China. Comparative genomic analyses were performed by incorporating additional LSDV whole genome sequences reported in other areas of Asia. Our analyses revealed that LSDV exhibited an 'open' pan-genome. Phylogenetic analysis unveiled distinct branches of LSDV evolution, signifying the prevalence of multiple lineages of LSDV across various regions in Asia. In addition, a reporter LSDV expressing eGFP directed by a synthetic poxvirus promoter was generated and used to evaluate the cell tropism of LSDV in various mammalian and avian cell lines. Our results demonstrated that LSDV replicated efficiently in several mammalian cell lines, including human A549 cells. In conclusion, our results underscore the necessity for strengthening LSD outbreak control measures and continuous epidemiological surveillance.},
}

@article {pmid38509359,
year = {2024},
author = {Zepeda-Rivera, M and Minot, SS and Bouzek, H and Wu, H and Blanco-Míguez, A and Manghi, P and Jones, DS and LaCourse, KD and Wu, Y and McMahon, EF and Park, SN and Lim, YK and Kempchinsky, AG and Willis, AD and Cotton, SL and Yost, SC and Sicinska, E and Kook, JK and Dewhirst, FE and Segata, N and Bullman, S and Johnston, CD},
title = {A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {38509359},
issn = {1476-4687},
abstract = {Fusobacterium nucleatum (Fn), a bacterium present in the human oral cavity and rarely found in the lower gastrointestinal tract of healthy individuals[1], is enriched in human colorectal cancer (CRC) tumours[2-5]. High intratumoural Fn loads are associated with recurrence, metastases and poorer patient prognosis[5-8]. Here, to delineate Fn genetic factors facilitating tumour colonization, we generated closed genomes for 135 Fn strains; 80 oral strains from individuals without cancer and 55 unique cancer strains cultured from tumours from 51 patients with CRC. Pangenomic analyses identified 483 CRC-enriched genetic factors. Tumour-isolated strains predominantly belong to Fn subspecies animalis (Fna). However, genomic analyses reveal that Fna, considered a single subspecies, is instead composed of two distinct clades (Fna C1 and Fna C2). Of these, only Fna C2 dominates the CRC tumour niche. Inter-Fna analyses identified 195 Fna C2-associated genetic factors consistent with increased metabolic potential and colonization of the gastrointestinal tract. In support of this, Fna C2-treated mice had an increased number of intestinal adenomas and altered metabolites. Microbiome analysis of human tumour tissue from 116 patients with CRC demonstrated Fna C2 enrichment. Comparison of 62 paired specimens showed that only Fna C2 is tumour enriched compared to normal adjacent tissue. This was further supported by metagenomic analysis of stool samples from 627 patients with CRC and 619 healthy individuals. Collectively, our results identify the Fna clade bifurcation, show that specifically Fna C2 drives the reported Fn enrichment in human CRC and reveal the genetic underpinnings of pathoadaptation of Fna C2 to the CRC niche.},
}

@article {pmid38509222,
year = {2024},
author = {Xie, L and Gong, X and Yang, K and Huang, Y and Zhang, S and Shen, L and Sun, Y and Wu, D and Ye, C and Zhu, QH and Fan, L},
title = {Technology-enabled great leap in deciphering plant genomes.},
journal = {Nature plants},
volume = {},
number = {},
pages = {},
pmid = {38509222},
issn = {2055-0278},
support = {2022C02032//Hainan Provincial Department of Science and Technology (Department of Science and Technology of Hainan Province)/ ; },
abstract = {Plant genomes provide essential and vital basic resources for studying many aspects of plant biology and applications (for example, breeding). From 2000 to 2020, 1,144 genomes of 782 plant species were sequenced. In the past three years (2021-2023), 2,373 genomes of 1,031 plant species, including 793 newly sequenced species, have been assembled, representing a great leap. The 2,373 newly assembled genomes, of which 63 are telomere-to-telomere assemblies and 921 have been generated in pan-genome projects, cover the major phylogenetic clades. Substantial advances in read length, throughput, accuracy and cost-effectiveness have notably simplified the achievement of high-quality assemblies. Moreover, the development of multiple software tools using different algorithms offers the opportunity to generate more complete and complex assemblies. A database named N3: plants, genomes, technologies has been developed to accommodate the metadata associated with the 3,517 genomes that have been sequenced from 1,575 plant species since 2000. We also provide an outlook for emerging opportunities in plant genome sequencing.},
}

@article {pmid38503725,
year = {2024},
author = {Zhao, X and Yu, J and Chanda, B and Zhao, J and Wu, S and Zheng, Y and Sun, H and Levi, A and Ling, KS and Fei, Z},
title = {Genomic and pangenomic analyses provide insights into the population history and genomic diversification of bottle gourd.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19673},
pmid = {38503725},
issn = {1469-8137},
support = {2015-51181-24285//National Institute of Food and Agriculture/ ; 2020-51181-32139//National Institute of Food and Agriculture/ ; },
abstract = {Bottle gourd (Lagenaria siceraria (Mol.) Strandl.) is an economically important vegetable crop and one of the earliest domesticated crops. However, the population history and genomic diversification of bottle gourd have not been extensively studied. We generated a comprehensive bottle gourd genome variation map from genome sequences of 197 world-wide representative accessions, which enables a genome-wide association study for identifying genomic loci associated with resistance to zucchini yellow mosaic virus, and constructed a bottle gourd pangenome that harbors 1534 protein-coding genes absent in the reference genome. Demographic analyses uncover that domesticated bottle gourd originated in Southern Africa c. 12 000 yr ago, and subsequently radiated to the New World via the Atlantic drift and to Eurasia through the efforts of early farmers in the initial Holocene. The identified highly differentiated genomic regions among different bottle gourd populations harbor many genes contributing to their local adaptations such as those related to disease resistance and stress tolerance. Presence/absence variation analysis of genes in the pangenome reveals numerous genes including those involved in abiotic/biotic stress responses that have been under selection during the world-wide expansion of bottle gourds. The bottle gourd variation map and pangenome provide valuable resources for future functional studies and genomics-assisted breeding.},
}

@article {pmid38502137,
year = {2024},
author = {Guo, X and Zhang, Z and Chen, Q and Wang, L and Xu, X and Wei, Z and Zhang, Y and Chen, K and Wang, Z and Lu, X and Liang, Q},
title = {Whole Genome Sequencing Highlights the Pathogenic Profile in Nocardia Keratitis.},
journal = {Investigative ophthalmology & visual science},
volume = {65},
number = {3},
pages = {26},
doi = {10.1167/iovs.65.3.26},
pmid = {38502137},
issn = {1552-5783},
abstract = {PURPOSE: Nocardia keratitis is a serious and sight-threatening condition. This study aims to reveal the virulence and antimicrobial resistance gene profile of Nocardia strains using whole genome sequencing.

METHODS: Whole-genome sequencing was performed on 23 cornea-derived Nocardia strains. Together with genomic data from the respiratory tract and the environment, 141 genomes were then utilized for phylogenetic and pan-genome analyses, followed by virulence and antibiotic resistance analysis. The correlations between virulence genes and pathogenicity were experimentally validated, including the characteristics of Nocardia colonies and clinical and histopathological evaluations of Nocardia keratitis mice models.

RESULTS: Whole-genome sequencing of 141 Nocardia strains revealed a mean of 220 virulence genes contributed to bacterial pathogenesis. The mce gene family analysis led to the categorization of strains from the cornea into groups A, B, and C. The colonies of group C had the largest diameter, height, and fastest growth rate. The size of corneal ulcers and the clinical scores showed a significant increase in mouse models induced by group C. The relative expression levels of pro-inflammatory cytokines (CD4, IFN-γ, IL-6Rα, and TNF-α) in the lesion area exhibited an increasing trend from group A to group C. Antibiotic resistance genes (ARGs) spanned nine distinct drug classes, four resistance mechanisms, and seven primary antimicrobial resistance gene families.

CONCLUSIONS: Whole genome sequencing highlights the pathogenic role of mce gene family in Nocardia keratitis. Its distribution pattern may contribute to the distinct characteristics of the growth of Nocardia colonies and the clinical severity of the mice models.},
}

@article {pmid38501935,
year = {2024},
author = {Piper, KR and Ikhimiukor, OO and Souza, SSR and Garcia-Aroca, T and Andam, CP},
title = {Evolutionary dynamics of the accessory genomes of Staphylococcus aureus.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0075123},
doi = {10.1128/msphere.00751-23},
pmid = {38501935},
issn = {2379-5042},
abstract = {Staphylococcus aureus is a ubiquitous commensal and opportunistic bacterial pathogen that can cause a wide gamut of infections, which are exacerbated by the presence of multidrug-resistant and methicillin-resistant S. aureus. S. aureus is genetically heterogeneous and consists of numerous distinct lineages. Using 558 complete genomes of S. aureus, we aim to determine how the accessory genome content among phylogenetic lineages of S. aureus is structured and has evolved. Bayesian hierarchical clustering identified 10 sequence clusters, of which seven contained major sequence types (ST 1, 5, 8, 30, 59, 239, and 398). The seven sequence clusters differed in their accessory gene content, including genes associated with antimicrobial resistance and virulence. Focusing on the two largest clusters, BAPS8 and BAPS10, and each consisting mostly of ST5 and ST8, respectively, we found that the structure and connected components in the co-occurrence networks of accessory genomes varied between them. These differences are explained, in part, by the variation in the rates at which the two sequence clusters gained and lost accessory genes, with the highest rate of gene accumulation occurring recently in their evolutionary histories. We also identified a divergent group within BAPS10 that has experienced high gene gain and loss early in its history. Together, our results show highly variable and dynamic accessory genomes in S. aureus that are structured by the history of the specific lineages that carry them.IMPORTANCEStaphylococcus aureus is an opportunistic, multi-host pathogen that can cause a variety of benign and life-threatening infections. Our results revealed considerable differences in the structure and evolution of the accessory genomes of major lineages within S. aureus. Such genomic variation within a species can have important implications on disease epidemiology, pathogenesis of infection, and interactions with the vertebrate host. Our findings provide important insights into the underlying genetic basis for the success of S. aureus as a highly adaptable and resistant pathogen, which will inform current efforts to control and treat staphylococcal diseases.},
}

@article {pmid38500021,
year = {2024},
author = {Zouagui, R and Zouagui, H and Aurag, J and Ibrahimi, A and Sbabou, L},
title = {Functional analysis and comparative genomics of Rahnella perminowiae S11P1 and Variovorax sp. S12S4, two plant growth-promoting rhizobacteria isolated from Crocus sativus L. (saffron) rhizosphere.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {289},
pmid = {38500021},
issn = {1471-2164},
abstract = {BACKGROUND: Rahnella perminowiae S11P1 and Variovorax sp. S12S4 are two plant growth-promoting rhizobacteria that were previously isolated from the rhizosphere of Crocus sativus L. (saffron), and have demonstrated interesting PGP activities and promising results when used as inoculants in field trials. To further elucidate the molecular mechanisms underlying their beneficial effects on plant growth, comprehensive genome mining of S11P1 and S12S4 and comparative genomic analysis with closely related strains were conducted.

RESULTS: Functional annotation of the two strains predicted a large number of genes involved in auxin and siderophore production, nitrogen fixation, sulfur metabolism, organic acid biosynthesis, pyrroloquinoline quinone production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, volatile organic compounds production, and polyamine biosynthesis. In addition, numerous genes implicated in plant-bacteria interactions, such as those involved in chemotaxis and quorum sensing, were predicted. Moreover, the two strains carried genes involved in bacterial fitness under abiotic stress conditions. Comparative genomic analysis revealed an open pan-genomic structure for the two strains. COG annotation showed that higher fractions of core and accessory genes were involved in the metabolism and transport of carbohydrates and amino acids, suggesting the metabolic versatility of the two strains as effective rhizosphere colonizers. Furthermore, this study reports the first comparison of Multilocus sequence analysis (MLSA) and core-based phylogenies of the Rahnella and Variovorax genera.

CONCLUSIONS: The present study unveils the molecular mechanisms underlying plant growth promotion and biocontrol activity of S11P1 and S12S4, and provides a basis for their further biotechnological application in agriculture.},
}

@article {pmid38496489,
year = {2024},
author = {Rinker, DC and Sauters, TJC and Steffen, K and Gumilang, A and Raja, HA and Rangel-Grimaldo, M and Pinzan, CF and de Castro, PA and Dos Reis, TF and Delbaje, E and Houbraken, J and Goldman, GH and Oberlies, NH and Rokas, A},
title = {Strain heterogeneity in a non-pathogenic fungus highlights factors contributing to virulence.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.03.08.583994},
pmid = {38496489},
abstract = {Fungal pathogens exhibit extensive strain heterogeneity, including variation in virulence. Whether closely related non-pathogenic species also exhibit strain heterogeneity remains unknown. Here, we comprehensively characterized the pathogenic potentials (i.e., the ability to cause morbidity and mortality) of 16 diverse strains of Aspergillus fischeri , a non-pathogenic close relative of the major pathogen Aspergillus fumigatus . In vitro immune response assays and in vivo virulence assays using a mouse model of pulmonary aspergillosis showed that A. fischeri strains varied widely in their pathogenic potential. Furthermore, pangenome analyses suggest that A. fischeri genomic and phenotypic diversity is even greater. Genomic, transcriptomic, and metabolomic profiling identified several pathways and secondary metabolites associated with variation in virulence. Notably, strain virulence was associated with the simultaneous presence of the secondary metabolites hexadehydroastechrome and gliotoxin. We submit that examining the pathogenic potentials of non-pathogenic close relatives is key for understanding the origins of fungal pathogenicity.},
}

@article {pmid38495945,
year = {2024},
author = {Lecomte, L and Árnyasi, M and Ferchaud, AL and Kent, M and Lien, S and Stenløkk, K and Sylvestre, F and Bernatchez, L and Mérot, C},
title = {Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations.},
journal = {Evolutionary applications},
volume = {17},
number = {3},
pages = {e13653},
pmid = {38495945},
issn = {1752-4571},
abstract = {Genomic structural variants (SVs) are now recognized as an integral component of intraspecific polymorphism and are known to contribute to evolutionary processes in various organisms. However, they are inherently difficult to detect and genotype from readily available short-read sequencing data, and therefore remain poorly documented in wild populations. Salmonid species displaying strong interpopulation variability in both life history traits and habitat characteristics, such as Atlantic salmon (Salmo salar), offer a prime context for studying adaptive polymorphism, but the contribution of SVs to fine-scale local adaptation has yet to be explored. Here, we performed a comparative analysis of SVs, single nucleotide polymorphisms (SNPs) and small indels (<50 bp) segregating in the Romaine and Puyjalon salmon, two putatively locally adapted populations inhabiting neighboring rivers (Québec, Canada) and showing pronounced variation in life history traits, namely growth, fecundity, and age at maturity and smoltification. We first catalogued polymorphism using a hybrid SV characterization approach pairing both short- (16X) and long-read sequencing (20X) for variant discovery with graph-based genotyping of SVs across 60 salmon genomes, along with characterization of SNPs and small indels from short reads. We thus identified 115,907 SVs, 8,777,832 SNPs and 1,089,321 short indels, with SVs covering 4.8 times more base pairs than SNPs. All three variant types revealed a highly congruent population structure and similar patterns of F ST and density variation along the genome. Finally, we performed outlier detection and redundancy analysis (RDA) to identify variants of interest in the putative local adaptation of Romaine and Puyjalon salmon. Genes located near these variants were enriched for biological processes related to nervous system function, suggesting that observed variation in traits such as age at smoltification could arise from differences in neural development. This study therefore demonstrates the feasibility of large-scale SV characterization and highlights its relevance for salmonid population genomics.},
}

@article {pmid38492232,
year = {2024},
author = {Poretsky, E and Cagirici, HB and Andorf, CM and Sen, TZ},
title = {Harnessing the predicted maize pan-interactome for putative gene function prediction and prioritization of candidate genes for important traits.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkae059},
pmid = {38492232},
issn = {2160-1836},
abstract = {The recent assembly and annotation of the 26 maize nested association mapping (NAM) population founder inbreds have enabled large-scale pan-genomic comparative studies. These studies have expanded our understanding of agronomically important traits by integrating pan-transcriptomic data with trait-specific gene candidates from previous association mapping results. In contrast to the availability of pan-transcriptomic data, obtaining reliable protein-protein interaction (PPI) data has remained a challenge due to its high cost and complexity. We generated predicted PPI networks for each of the 26 genomes using the established STRING database. The individual genome-interactomes were then integrated to generate core- and pan-interactomes. We deployed the PPI clustering algorithm ClusterONE to identify numerous PPI clusters that were functionally annotated using gene ontology (GO) functional enrichment, demonstrating a diverse range of enriched GO terms across different clusters. Additional cluster annotations were generated by integrating gene co-expression data and gene description annotations, providing additional useful information. We show that the functionally annotated PPI clusters establish a useful framework for protein function prediction and prioritization of candidate genes of interest. Our study not only provides a comprehensive resource of predicted PPI networks for 26 maize genomes, but also offers annotated interactome clusters for predicting protein functions and prioritizing gene candidates. The source code for the Python implementation of the analysis workflow and a standalone web application for accessing the analysis results are available at https://github.com/eporetsky/PanPPI.},
}

@article {pmid38491145,
year = {2024},
author = {Wang, Y and Tang, H and Wang, X and Sun, Y and Joseph, PV and Paterson, AH},
title = {Detection of colinear blocks and synteny and evolutionary analyses based on utilization of MCScanX.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {38491145},
issn = {1750-2799},
abstract = {As different taxa evolve, gene order often changes slowly enough that chromosomal 'blocks' with conserved gene orders (synteny) are discernible. The MCScanX toolkit (https://github.com/wyp1125/MCScanX) was published in 2012 as freely available software for the detection of such 'colinear blocks' and subsequent synteny and evolutionary analyses based on genome-wide gene location and protein sequence information. Owing to its simplicity and high efficiency for colinear block detection, MCScanX provides a powerful tool for conducting diverse synteny and evolutionary analyses. Moreover, the detection of colinear blocks has been embraced as an integral step for pangenome graph construction. Here, new application trends of MCScanX are explored, striving to better connect this increasingly used tool to other tools and accelerate insight generation from exponentially growing sequence data. We provide a detailed protocol that covers how to install MCScanX on diverse platforms, tune parameters, prepare input files from data from the National Center for Biotechnology Information, run MCScanX and its visualization and evolutionary analysis tools, and connect MCScanX with external tools, including MCScanX-transposed, Circos and SynVisio. This protocol is easily implemented by users with minimal computational background and is adaptable to new data of interest to them. The data and utility programs for this protocol can be obtained from http://bdx-consulting.com/mcscanx-protocol .},
}

@article {pmid38488860,
year = {2024},
author = {Freddi, S and Rajabal, V and Tetu, SG and Gillings, MR and Penesyan, A},
title = {Microbial biofilms on macroalgae harbour diverse integron gene cassettes.},
journal = {Microbiology (Reading, England)},
volume = {170},
number = {3},
pages = {},
doi = {10.1099/mic.0.001446},
pmid = {38488860},
issn = {1465-2080},
abstract = {Integrons are genetic platforms that capture, rearrange and express mobile modules called gene cassettes. The best characterized gene cassettes encode antibiotic resistance, but the function of most integron gene cassettes remains unknown. Functional predictions suggest that many gene cassettes could encode proteins that facilitate interactions with other cells and with the extracellular environment. Because cell interactions are essential for biofilm stability, we sequenced gene cassettes from biofilms growing on the surface of the marine macroalgae Ulva australis and Sargassum linearifolium. Algal samples were obtained from coastal rock platforms around Sydney, Australia, using seawater as a control. We demonstrated that integrons in microbial biofilms did not sample genes randomly from the surrounding seawater, but harboured specific functions that potentially provided an adaptive advantage to both the bacterial cells in biofilm communities and their macroalgal host. Further, integron gene cassettes had a well-defined spatial distribution, suggesting that each bacterial biofilm acquired these genetic elements via sampling from a large but localized pool of gene cassettes. These findings suggest two forms of filtering: a selective acquisition of different integron-containing bacterial species into the distinct biofilms on Ulva and Sargassum surfaces, and a selective retention of unique populations of gene cassettes at each sampling location.},
}

@article {pmid38488392,
year = {2024},
author = {Wang, M and Li, X and Liu, X and Hou, X and He, Y and Yu, J-H and Hu, S and Yin, H and Xie, B-B},
title = {Annotation of 2,507 Saccharomyces cerevisiae genomes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0358223},
doi = {10.1128/spectrum.03582-23},
pmid = {38488392},
issn = {2165-0497},
abstract = {Saccharomyces cerevisiae (baker's yeast, budding yeast) is one of the most important model organisms for biological research and is a crucial microorganism in industry. Currently, a huge number of Saccharomyces cerevisiae genome sequences are available at the public domain. However, these genomes are distributed at different websites and a large number of them are released without annotation information. To provide one complete annotated genome data resource, we collected 2,507 Saccharomyces cerevisiae genome assemblies and re-annotated 2,506 assemblies using a custom annotation pipeline, producing a total of 15,407,164 protein-coding gene models. With a custom pipeline, all these gene sequences were clustered into families. A total of 1,506 single-copy genes were selected as marker genes, which were then used to evaluate the genome completeness and base qualities of all assemblies. Pangenomic analyses were performed based on a selected subset of 847 medium-high-quality genomes. Statistical comparisons revealed a number of gene families showing copy number variations among different organism sources. To the authors' knowledge, this study represents the largest genome annotation project of S. cerevisiae so far, providing rich genomic resources for the future studies of the model organism S. cerevisiae and its relatives.IMPORTANCESaccharomyces cerevisiae (baker's yeast, budding yeast) is one of the most important model organisms for biological research and is a crucial microorganism in industry. Though a huge number of Saccharomyces cerevisiae genome sequences are available at the public domain, these genomes are distributed at different websites and most are released without annotation, hindering the efficient reuse of these genome resources. Here, we collected 2,507 genomes for Saccharomyces cerevisiae, performed genome annotation, and evaluated the genome qualities. All the obtained data have been deposited at public repositories and are freely accessible to the community. This study represents the largest genome annotation project of S. cerevisiae so far, providing one complete annotated genome data set for S. cerevisiae, an important workhorse for fundamental biology, biotechnology, and industry.},
}

@article {pmid38488280,
year = {2024},
author = {Giacomini, JJ and Torres-Morales, J and Tang, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL},
title = {Spatial ecology of Haemophilus and Aggregatibacter in the human oral cavity.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0401723},
doi = {10.1128/spectrum.04017-23},
pmid = {38488280},
issn = {2165-0497},
abstract = {UNLABELLED: Haemophilus and Aggregatibacter are two of the most common bacterial genera in the human oral cavity, encompassing both commensals and pathogens of substantial ecological and medical significance. In this study, we conducted a metapangenomic analysis of oral Haemophilus and Aggregatibacter species to uncover genomic diversity, phylogenetic relationships, and habitat specialization within the human oral cavity. Using three metrics-pangenomic gene content, phylogenomics, and average nucleotide identity (ANI)-we first identified distinct species and sub-species groups among these genera. Mapping of metagenomic reads then revealed clear patterns of habitat specialization, such as Aggregatibacter species predominantly in dental plaque, a distinctive Haemophilus parainfluenzae sub-species group on the tongue dorsum, and H. sp. HMT-036 predominantly in keratinized gingiva and buccal mucosa. In addition, we found that supragingival plaque samples contained predominantly only one out of the three taxa, H. parainfluenzae, Aggregatibacter aphrophilus, and A. sp. HMT-458, suggesting independent niches or a competitive relationship. Functional analyses revealed the presence of key metabolic genes, such as oxaloacetate decarboxylase, correlated with habitat specialization, suggesting metabolic versatility as a driving force. Additionally, heme synthesis distinguishes H. sp. HMT-036 from closely related Haemophilus haemolyticus, suggesting that the availability of micronutrients, particularly iron, was important in the evolutionary ecology of these species. Overall, our study exemplifies the power of metapangenomics to identify factors that may affect ecological interactions within microbial communities, including genomic diversity, habitat specialization, and metabolic versatility.

IMPORTANCE: Understanding the microbial ecology of the mouth is essential for comprehending human physiology. This study employs metapangenomics to reveal that various Haemophilus and Aggregatibacter species exhibit distinct ecological preferences within the oral cavity of healthy individuals, thereby supporting the site-specialist hypothesis. Additionally, it was observed that the gene pool of different Haemophilus species correlates with their ecological niches. These findings shed light on the significance of key metabolic functions in shaping microbial distribution patterns and interspecies interactions in the oral ecosystem.},
}

@article {pmid38487210,
year = {2023},
author = {Grizon, A and Theil, S and Callon, C and Gerber, P and Helinck, S and Dugat-Bony, E and Bonnarme, P and Chassard, C},
title = {Genetic and technological diversity of Streptococcus thermophilus isolated from the Saint-Nectaire PDO cheese-producing area.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1245510},
doi = {10.3389/fmicb.2023.1245510},
pmid = {38487210},
issn = {1664-302X},
abstract = {Streptococcus thermophilus is of major importance for cheese manufacturing to ensure rapid acidification; however, studies indicate that intensive use of commercial strains leads to the loss of typical characteristics of the products. To strengthen the link between the product and its geographical area and improve the sensory qualities of cheeses, cheese-producing protected designations of origin (PDO) are increasingly interested in the development of specific autochthonous starter cultures. The present study is therefore investigating the genetic and functional diversity of S. thermophilus strains isolated from a local cheese-producing PDO area. Putative S. thermophilus isolates were isolated and identified from milk collected in the Saint-Nectaire cheese-producing PDO area and from commercial starters. Whole genomes of isolates were sequenced, and a comparative analysis based on their pan-genome was carried out. Important functional properties were studied, including acidifying and proteolytic activities. Twenty-two isolates representative of the diversity of the geographical area and four commercial strains were selected for comparison. The resulting phylogenetic trees do not correspond to the geographical distribution of isolates. The clustering based on the pan-genome analysis indicates that isolates are divided into five distinct groups. A Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation of the accessory genes indicates that the accessory gene contents of isolates are involved in different functional categories. High variability in acidifying activities and less diversity in proteolytic activities were also observed. These results indicate that high genetic and functional variabilities of the species S. thermophilus may arise from a small (1,800 km[2]) geographical area and may be exploited to meet demand for use as autochthonous starters.},
}

@article {pmid38486452,
year = {2024},
author = {Shi, T and Zhang, X and Hou, Y and Jia, C and Dan, X and Zhang, Y and Jiang, Y and Lai, Q and Feng, J and Feng, J and Ma, T and Wu, J and Liu, S and Zhang, L and Long, Z and Chen, L and Street, NR and Ingvarsson, PK and Liu, J and Yin, T and Wang, J},
title = {The super-pangenome of Populus unveil genomic facets for its adaptation and diversification in widespread forest trees.},
journal = {Molecular plant},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molp.2024.03.009},
pmid = {38486452},
issn = {1752-9867},
abstract = {Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pan-genomes with transcriptomes, methylomes and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pan-genes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142,202 structural variants (SVs) across species, which intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180 bp presence/absence variant impacting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com/). Together, the present pioneering super-pangenome resource in forest trees not only aid in the advancement of breeding efforts of this globally important tree genus but also offer valuable insights into potential avenues for comprehending tree biology.},
}

@article {pmid38478130,
year = {2024},
author = {Wisal, A and Saeed, N and Aurongzeb, M and Shafique, M and Sohail, S and Anwar, W and Basharat, Z and Irfan, M and Ullah, A and Hassan, SS},
title = {Bridging drug discovery through hierarchical subtractive genomics against asd, trpG, and secY of pneumonia causing MDR Staphylococcus aureus.},
journal = {Molecular genetics and genomics : MGG},
volume = {299},
number = {1},
pages = {34},
pmid = {38478130},
issn = {1617-4623},
abstract = {Staphylococcus aureus (S. aureus) is an opportunistic gram-positive, non-motile, and non-sporulating bacteria that induces pneumonia, a provocative lung infection affecting mainly the terminal bronchioles and the small air sacs known as alveoli. Recently, it has developed antibiotic resistance to the available consortium as per the WHO reports; thereby, novel remedial targets and resilient medications to forestall and cure this illness are desperately needed. Here, using pan-genomics, a total of 1,387 core proteins were identified. Subtractive proteome analyses further identified 12 proteins that are vital for bacteria. One membrane protein (secY) and two cytoplasmic proteins (asd and trpG) were chosen as possible therapeutic targets concerning minimum % host identity, essentiality, and other cutoff values, such as high resistance in the MDR S. aureus. The UniProt AA sequences of the selected targets were modelled and docked against 3 drug-like chemical libraries. The top-ranked compounds i.e., ZINC82049692, ZINC85492658 and 3a of Isosteviol derivative for Aspartate-semialdehyde dehydrogenase (asd); ZINC38222743, ZINC70455378, and 5 m Isosteviol derivative for Anthranilate synthase component II (trpG); and finally, ZINC72292296, ZINC85632684, and 7 m Isosteviol derivative for Protein translocase subunit secY (secY), were further subjected to molecular dynamics studies for thermodynamic stability and energy calculation. Our study proposes new therapeutic targets in S. aureus, some of which have previously been reported in other pathogenic microorganisms. Owing to further experimental validation, we anticipate that the adapted methodology and the predicted results in this work could make major contributions towards novel drug discovery and their targets in S. aureus caused pneumonia.},
}

@article {pmid38472486,
year = {2024},
author = {Martínez-Gallardo, MJ and Villicaña, C and Yocupicio-Monroy, M and Alcaraz-Estrada, SL and Salazar-Salinas, J and Mendoza-Vázquez, OF and Damazo-Hernández, G and León-Félix, J},
title = {Comparative genomic analysis of Pseudomonas aeruginosa strains susceptible and resistant to carbapenems and aztreonam isolated from patients with healthcare-associated infections in a Mexican hospital.},
journal = {Molecular genetics and genomics : MGG},
volume = {299},
number = {1},
pages = {29},
pmid = {38472486},
issn = {1617-4623},
support = {E05//Ciencia y Tecnología ISSSTE/ ; },
abstract = {Pseudomonas aeruginosa (PA) is an important opportunistic pathogen that causes different infections on immunocompromised patients. Within PA accessory genome, differences in virulence, antibiotic resistance and biofilm formation have been described between strains, leading to the emergence of multidrug-resistant strains. The genome sequences of 17 strains isolated from patients with healthcare-associated infections in a Mexican hospital were genomically and phylogenetically analyzed and antibiotic resistance genes, virulence genes, and biofilm formation genes were detected. Fifteen of the 17 strains were resistant to at least two of the carbapenems meropenem, imipenem, and the monobactam aztreonam. The antibiotic resistance (mexA, mexB, and oprM) and the biofilm formation (pslA and pslD) genes were detected in all strains. Differences were found between strains in accessory genome size. The strains had different sequence types, and seven strains had sequence types associated with global high risk epidemic PA clones. All strains were represented in two groups among PA global strains. In the 17 strains, horizontally acquired resistance genes to aminoglycosides and beta-lactams were found, mainly, and between 230 and 240 genes that encode virulence factors. The strains under study were variable in terms of their accessory genome, antibiotic resistance, and virulence genes. With these characteristics, we provide information about the genomic diversity of clinically relevant PA strains.},
}

@article {pmid38470044,
year = {2024},
author = {Liu, D and Xie, L-S and Lian, S and Li, K and Yang, Y and Wang, W-Z and Hu, S and Liu, S-J and Liu, C and He, Z},
title = {Anaerostipes hadrus, a butyrate-producing bacterium capable of metabolizing 5-fluorouracil.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0081623},
doi = {10.1128/msphere.00816-23},
pmid = {38470044},
issn = {2379-5042},
abstract = {UNLABELLED: Anaerostipes hadrus (A. hadrus) is a dominant species in the human gut microbiota and considered a beneficial bacterium for producing probiotic butyrate. However, recent studies have suggested that A. hadrus may negatively affect the host through synthesizing fatty acid and metabolizing the anticancer drug 5-fluorouracil, indicating that the impact of A. hadrus is complex and unclear. Therefore, comprehensive genomic studies on A. hadrus need to be performed. We integrated 527 high-quality public A. hadrus genomes and five distinct metagenomic cohorts. We analyzed these data using the approaches of comparative genomics, metagenomics, and protein structure prediction. We also performed validations with culture-based in vitro assays. We constructed the first large-scale pan-genome of A. hadrus (n = 527) and identified 5-fluorouracil metabolism genes as ubiquitous in A. hadrus genomes as butyrate-producing genes. Metagenomic analysis revealed the wide and stable distribution of A. hadrus in healthy individuals, patients with inflammatory bowel disease, and patients with colorectal cancer, with healthy individuals carrying more A. hadrus. The predicted high-quality protein structure indicated that A. hadrus might metabolize 5-fluorouracil by producing bacterial dihydropyrimidine dehydrogenase (encoded by the preTA operon). Through in vitro assays, we validated the short-chain fatty acid production and 5-fluorouracil metabolism abilities of A. hadrus. We observed for the first time that A. hadrus can convert 5-fluorouracil to α-fluoro-β-ureidopropionic acid, which may result from the combined action of the preTA operon and adjacent hydA (encoding bacterial dihydropyrimidinase). Our results offer novel understandings of A. hadrus, exceptionally functional features, and potential applications.

IMPORTANCE: This work provides new insights into the evolutionary relationships, functional characteristics, prevalence, and potential applications of Anaerostipes hadrus.},
}

@article {pmid38469580,
year = {2024},
author = {Yakubu, B and Appiah, EM and Adu, AF},
title = {Pangenome Analysis of Helicobacter pylori Isolates from Selected Areas of Africa Indicated Diverse Antibiotic Resistance and Virulence Genes.},
journal = {International journal of genomics},
volume = {2024},
number = {},
pages = {5536117},
pmid = {38469580},
issn = {2314-4378},
abstract = {The challenge facing Helicobacter pylori (H. pylori) infection management in some parts of Africa is the evolution of drug-resistant species, the lack of gold standard in diagnostic methods, and the ineffectiveness of current vaccines against the bacteria. It is being established that even though clinical consequences linked to the bacteria vary geographically, there is rather a generic approach to treatment. This situation has remained problematic in the successful fight against the bacteria in parts of Africa. As a result, this study compared the genomes of selected H. pylori isolates from selected areas of Africa and evaluated their virulence and antibiotic drug resistance, those that are highly pathogenic and are associated with specific clinical outcomes and those that are less virulent and rarely associated with clinical outcomes. 146 genomes of H. pylori isolated from selected locations of Africa were sampled, and bioinformatic tools such as Abricate, CARD RGI, MLST, Prokka, Roary, Phandango, Google Sheets, and iTOLS were used to compare the isolates and their antibiotic resistance or susceptibility. Over 20 k virulence and AMR genes were observed. About 95% of the isolates were genetically diverse, 90% of the isolates harbored shell genes, and 50% harbored cloud and core genes. Some isolates did not retain the cagA and vacA genes. Clarithromycin, metronidazole, amoxicillin, and tinidazole were resistant to most AMR genes (vacA, cagA, oip, and bab). Conclusion. This study found both virulence and AMR genes in all H. pylori strains in all the selected geographies around Africa with differing quantities. MLST, Pangenome, and ORF analyses showed disparities among the isolates. This in general could imply diversities in terms of genetics, evolution, and protein production. Therefore, generic administration of antibiotics such as clarithromycin, amoxicillin, and erythromycin as treatment methods in the African subregion could be contributing to the spread of the bacterium's antibiotic resistance.},
}

@article {pmid38463963,
year = {2024},
author = {Young, MG and Straub, TJ and Worby, CJ and Metsky, HC and Gnirke, A and Bronson, RA and van Dijk, LR and Desjardins, CA and Matranga, C and Qu, J and Dodson, K and Schreiber, HL and Manson, AL and Hultgren, SJ and Earl, AM},
title = {Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pan-genome hybrid selection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.02.29.582780},
pmid = {38463963},
abstract = {Low-abundance members of microbial communities are difficult to study in their native habitat. This includes Escherichia coli , a minor, but common inhabitant of the gastrointestinal tract and opportunistic pathogen, including of the urinary tract, where it causes most infections. While our understanding of the interactions between uropathogenic Escherichia coli (UPEC) and the bladder is increasing, comparatively little is known about UPEC in its pre-infection reservoir, partly due to its low abundance there (<1% relative abundance). In order to specifically and sensitively explore the genomes and transcriptomes of diverse E. coli from gastrointestinal communities, we developed E. coli PanSelect, a set of probes designed to enrich E. coli 's broad pangenome. First we demonstrated the ability of PanSelect to enrich diverse strains in an unbiased way using a mock community of known composition. Then we enriched E. coli DNA and RNA from human stool microbiomes by 158 and 30-fold, respectively. We also used E. coli PanSelect to explore the gene content and transcriptome of E. coli within the gut microbiomes of women with history of recurrent urinary tract infection (rUTI), finding differential regulation of pathways that suggests that the rUTI gut environment promotes respiratory vs fermentative metabolism. E. coli PanSelect technology holds promise for investigations of native in vivo biology of diverse E. coli in the gut and other environments, where it is a minor component of the microbial community, using unbiased, culture-free shotgun sequencing. This method could also be generally applied to other highly diverse, low abundance bacteria.},
}

@article {pmid38463499,
year = {2024},
author = {Li, H and Marin, M and Farhat, MR},
title = {Exploring gene content with pangenome gene graphs.},
journal = {ArXiv},
volume = {},
number = {},
pages = {},
pmid = {38463499},
issn = {2331-8422},
abstract = {MOTIVATION: The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is applicable to collections of large eukaryotic genomes such as the human pangenome.

RESULTS: We developed pangene, a computational tool to identify gene orientation, gene order and gene copy-number changes in a collection of genomes. Pangene aligns a set of input protein sequences to the genomes, resolves redundancies between protein sequences and constructs a gene graph with each genome represented as a walk in the graph. It additionally finds subgraphs that encodes gene content changes. Applied to the human pangenome, pangene identifies known gene-level variations and reveals complex haplotypes that are not well studied before. Pangene also works with high-quality bacterial pangenome and reports similar numbers of core and accessory genes in comparison to existing tools.

Source code at https://github.com/lh3/pangene; pre-built pangene graphs can be downloaded from https://zenodo.org/records/8118576 and visualized at https://pangene.bioinweb.org.},
}

@article {pmid38461665,
year = {2024},
author = {Feng, NX and Li, DW and Zhang, F and Bin, H and Huang, YT and Xiang, L and Liu, BL and Cai, QY and Li, YW and Xu, DL and Xie, Y and Mo, CH},
title = {Biodegradation of phthalate acid esters and whole-genome analysis of a novel Streptomyces sp. FZ201 isolated from natural habitats.},
journal = {Journal of hazardous materials},
volume = {469},
number = {},
pages = {133972},
doi = {10.1016/j.jhazmat.2024.133972},
pmid = {38461665},
issn = {1873-3336},
abstract = {Di-n-butyl phthalate (DBP) is one of the most extensively used phthalic acid esters (PAEs) and is considered to be an emerging, globally concerning pollutant. The genus Streptomyces holds promise as a degrader of various organic pollutants, but PAE biodegradation mechanisms by Streptomyces species remain unsolved. In this study, a novel PAE-degrading Streptomyces sp. FZ201 isolated from natural habitats efficiently degraded various PAEs. FZ201 had strong resilience against DBP and exhibited immediate degradation, with kinetics adhering to a first-order model. The comprehensive biodegradation of DBP involves de-esterification, β-oxidation, trans-esterification, and aromatic ring cleavage. FZ201 contains numerous catabolic genes that potentially facilitate PAE biodegradation. The DBP metabolic pathway was reconstructed by genome annotation and intermediate identification. Streptomyces species have an open pangenome with substantial genome expansion events during the evolutionary process, enabling extensive genetic diversity and highly plastic genomes within the Streptomyces genus. FZ201 had a diverse array of highly expressed genes associated with the degradation of PAEs, potentially contributing significantly to its adaptive advantage and efficiency of PAE degradation. Thus, FZ201 is a promising candidate for remediating highly PAE-contaminated environments. These findings enhance our preliminary understanding of the molecular mechanisms employed by Streptomyces for the removal of PAEs.},
}

@article {pmid38459435,
year = {2024},
author = {Zhu, L and Liu, H and Li, X and Shi, Y and Yin, X and Pi, X},
title = {Whole-genome sequencing and analysis of Chryseobacterium arthrosphaerae from Rana nigromaculata.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {80},
pmid = {38459435},
issn = {1471-2180},
support = {2022SNJF072//Zhejiang Provincial Science and Technology Cooperation Plan of "Three Rural Areas and Nine Rural Areas"/ ; 2022SNJF072//Zhejiang Provincial Science and Technology Cooperation Plan of "Three Rural Areas and Nine Rural Areas"/ ; 2022SNJF072//Zhejiang Provincial Science and Technology Cooperation Plan of "Three Rural Areas and Nine Rural Areas"/ ; 2022SNJF072//Zhejiang Provincial Science and Technology Cooperation Plan of "Three Rural Areas and Nine Rural Areas"/ ; 2022SNJF072//Zhejiang Provincial Science and Technology Cooperation Plan of "Three Rural Areas and Nine Rural Areas"/ ; 2022SNJF072//Zhejiang Provincial Science and Technology Cooperation Plan of "Three Rural Areas and Nine Rural Areas"/ ; },
abstract = {Chryseobacterium arthrosphaerae strain FS91703 was isolated from Rana nigromaculata in our previous study. To investigate the genomic characteristics, pathogenicity-related genes, antimicrobial resistance, and phylogenetic relationship of this strain, PacBio RS II and Illumina HiSeq 2000 platforms were used for the whole genome sequencing. The genome size of strain FS91703 was 5,435,691 bp and GC content was 37.78%. A total of 4,951 coding genes were predicted; 99 potential virulence factors homologs were identified. Analysis of antibiotic resistance genes revealed that strain FS91703 harbored 10 antibiotic resistance genes in 6 categories and 2 multidrug-resistant efflux pump genes, including adeG and farA. Strain FS91703 was sensitive to β-lactam combination drugs, cephem, monobactam and carbapenems, intermediately resistant to phenicol, and resistant to penicillin, aminoglycosides, tetracycline, fluoroquinolones, and folate pathway inhibitors. Phylogenetic analysis revealed that strain FS91703 and C. arthrosphaerae CC-VM-7[T] were on the same branch of the phylogenetic tree based on 16 S rRNA; the ANI value between them was 96.99%; and the DDH values were 80.2, 72.2 and 81.6% by three default calculation formulae. These results suggested that strain FS91703 was a species of C. arthrosphaerae. Pan-genome analysis showed FS91703 had 566 unique genes compared with 13 other C. arthrosphaerae strains, and had a distant phylogenetic relationship with the other C. arthrosphaerae strains of the same branch in phylogenetic tree based on orthologous genes. The results of this study suggest that strain FS91703 is a multidrug-resistant and highly virulent bacterium, that differs from other C. arthrosphaerae strains at the genomic level. The knowledge about the genomic characteristics and antimicrobial resistance of strain FS91703 provides valuable insights into this rare species, as well as guidance for the treatment of the disease caused by FS91703 in Rana nigromaculata.},
}

@article {pmid38450165,
year = {2024},
author = {Zhou, Y and Tu, T and Yao, X and Luo, Y and Yang, Z and Ren, M and Zhang, G and Yu, Y and Lu, A and Wang, Y},
title = {Pan-genome analysis of Streptococcus suis serotype 2 highlights genes associated with virulence and antibiotic resistance.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1362316},
pmid = {38450165},
issn = {1664-302X},
abstract = {Streptococcus suis serotype 2 (SS2) is a Gram-positive bacterium. It is a common and significant pathogen in pigs and a common cause of zoonotic meningitis in humans. It can lead to sepsis, endocarditis, arthritis, and pneumonia. If not diagnosed and treated promptly, it has a high mortality rate. The pan-genome of SS2 is open, and with an increasing number of genes, the core genome and accessory genome may exhibit more pronounced differences. Due to the diversity of SS2, the genes related to its virulence and resistance are still unclear. In this study, a strain of SS2 was isolated from a pig farm in Sichuan Province, China, and subjected to whole-genome sequencing and characterization. Subsequently, we conducted a Pan-Genome-Wide Association Study (Pan-GWAS) on 230 strains of SS2. Our analysis indicates that the core genome is composed of 1,458 genes related to the basic life processes of the bacterium. The accessory genome, consisting of 4,337 genes, is highly variable and a major contributor to the genetic diversity of SS2. Furthermore, we identified important virulence and resistance genes in SS2 through pan-GWAS. The virulence genes of SS2 are mainly associated with bacterial adhesion. In addition, resistance genes in the core genome may confer natural resistance of SS2 to fluoroquinolone and glycopeptide antibiotics. This study lays the foundation for further research on the virulence and resistance of SS2, providing potential new drug and vaccine targets against SS2.},
}

@article {pmid38448140,
year = {2024},
author = {Mathur, S and Singh, D and Ranjan, R},
title = {Recent advances in plant translational genomics for crop improvement.},
journal = {Advances in protein chemistry and structural biology},
volume = {139},
number = {},
pages = {335-382},
doi = {10.1016/bs.apcsb.2023.11.009},
pmid = {38448140},
issn = {1876-1631},
abstract = {The growing population, climate change, and limited agricultural resources put enormous pressure on agricultural systems. A plateau in crop yields is occurring and extreme weather events and urbanization threaten the livelihood of farmers. It is imperative that immediate attention is paid to addressing the increasing food demand, ensuring resilience against emerging threats, and meeting the demand for more nutritious, safer food. Under uncertain conditions, it is essential to expand genetic diversity and discover novel crop varieties or variations to develop higher and more stable yields. Genomics plays a significant role in developing abundant and nutrient-dense food crops. An alternative to traditional breeding approach, translational genomics is able to improve breeding programs in a more efficient and precise manner by translating genomic concepts into practical tools. Crop breeding based on genomics offers potential solutions to overcome the limitations of conventional breeding methods, including improved crop varieties that provide more nutritional value and are protected from biotic and abiotic stresses. Genetic markers, such as SNPs and ESTs, contribute to the discovery of QTLs controlling agronomic traits and stress tolerance. In order to meet the growing demand for food, there is a need to incorporate QTLs into breeding programs using marker-assisted selection/breeding and transgenic technologies. This chapter primarily focuses on the recent advances that are made in translational genomics for crop improvement and various omics techniques including transcriptomics, metagenomics, pangenomics, single cell omics etc. Numerous genome editing techniques including CRISPR Cas technology and their applications in crop improvement had been discussed.},
}

@article {pmid38439049,
year = {2024},
author = {Chen, C and Wu, S and Sun, Y and Zhou, J and Chen, Y and Zhang, J and Birchler, JA and Han, F and Yang, N and Su, H},
title = {Three near-complete genome assemblies reveal substantial centromere dynamics from diploid to tetraploid in Brachypodium genus.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {63},
pmid = {38439049},
issn = {1474-760X},
support = {2021YFF1000800//National Key Research and Development Program of China/ ; 32170571//National Natural Science Foundation of China/ ; 2021ZKPY008//Fundamental Research Funds for the Central Universities/ ; No. B21HJ0504//Hainan Yazhou Bay Seed Laboratory/ ; },
abstract = {BACKGROUND: Centromeres are critical for maintaining genomic stability in eukaryotes, and their turnover shapes genome architectures and drives karyotype evolution. However, the co-evolution of centromeres from different species in allopolyploids over millions of years remains largely unknown.

RESULTS: Here, we generate three near-complete genome assemblies, a tetraploid Brachypodium hybridum and its two diploid ancestors, Brachypodium distachyon and Brachypodium stacei. We detect high degrees of sequence, structural, and epigenetic variations of centromeres at base-pair resolution between closely related Brachypodium genomes, indicating the appearance and accumulation of species-specific centromere repeats from a common origin during evolution. We also find that centromere homogenization is accompanied by local satellite repeats bursting and retrotransposon purging, and the frequency of retrotransposon invasions drives the degree of interspecies centromere diversification. We further investigate the dynamics of centromeres during alloploidization process, and find that dramatic genetics and epigenetics architecture variations are associated with the turnover of centromeres between homologous chromosomal pairs from diploid to tetraploid. Additionally, our pangenomes analysis reveals the ongoing variations of satellite repeats and stable evolutionary homeostasis within centromeres among individuals of each Brachypodium genome with different polyploidy levels.

CONCLUSIONS: Our results provide unprecedented information on the genomic, epigenomic, and functional diversity of highly repetitive DNA between closely related species and their allopolyploid genomes at both coarse and fine scale.},
}

@article {pmid38438804,
year = {2024},
author = {Niu, D and Feng, N and Xi, S and Xu, J and Su, Y},
title = {Genomics-based analysis of four porcine-derived lactic acid bacteria strains and their evaluation as potential probiotics.},
journal = {Molecular genetics and genomics : MGG},
volume = {299},
number = {1},
pages = {24},
pmid = {38438804},
issn = {1617-4623},
support = {2022YFD1300402//Key Technologies Research and Development Program/ ; 31872362//National Natural Science Foundation of China/ ; 32072688//National Natural Science Foundation of China/ ; },
abstract = {The search for probiotics and exploration of their functions are crucial for livestock farming. Recently, porcine-derived lactic acid bacteria (LAB) have shown great potential as probiotics. However, research on the evaluation of porcine-derived LAB as potential probiotics through genomics-based analysis is relatively limited. The present study analyzed four porcine-derived LAB strains (Lactobacillus johnsonii L16, Latilactobacillus curvatus ZHA1, Ligilactobacillus salivarius ZSA5 and Ligilactobacillus animalis ZSB1) using genomic techniques and combined with in vitro tests to evaluate their potential as probiotics. The genome sizes of the four strains ranged from 1,897,301 bp to 2,318,470 bp with the GC contents from 33.03 to 41.97%. Pan-genomic analysis and collinearity analysis indicated differences among the genomes of four strains. Carbohydrate active enzymes analysis revealed that L. johnsonii L16 encoded more carbohydrate active enzymes than other strains. KEGG pathway analysis and in vitro tests confirmed that L. johnsonii L16 could utilize a wide range of carbohydrates and had good utilization capacity for each carbohydrate. The four strains had genes related to acid tolerance and were tolerant to low pH, with L. johnsonii L16 showing the greatest tolerance. The four strains contained genes related to bile salt tolerance and were able to tolerate 0.1% bile salt. Four strains had antioxidant related genes and exhibited antioxidant activity in in vitro tests. They contained the genes linked with organic acid biosynthesis and exhibited antibacterial activity against enterotoxigenic Escherichia coli K88 (ETEC K88) and Salmonella 6,7:c:1,5, wherein, L. johnsonii L16 and L. salivarius ZSA5 had gene clusters encoding bacteriocin. Results suggest that genome analysis combined with in vitro tests is an effective approach for evaluating different strains as probiotics. The findings of this study indicate that L. johnsonii L16 has the potential as a probiotic strain among the four strains and provide theoretical basis for the development of probiotics in swine production.},
}