@article {pmid37728044,
year = {2023},
author = {Lin, Y and Zhu, Y and Cui, Y and Qian, H and Yuan, Q and Chen, R and Lin, Y and Chen, J and Zhou, X and Shi, C and He, H and Hu, T and Gu, C and Yu, X and Zhu, X and Wang, Y and Qian, Q and Zhang, C and Wang, F and Shang, L},
title = {Identification of natural allelic variation in TTL1 controlling thermotolerance and grain size by a rice super pan-genome.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.13568},
pmid = {37728044},
issn = {1744-7909},
abstract = {Continuously increasing global temperatures present great challenges to food security. Grain size, one of the critical components determining grain yield in rice (Oryza sativa L.), is a prime target for genetic breeding. Thus, there is an immediate need for genetic improvement in rice to maintain grain yield under heat stress. However, quantitative trait loci (QTLs) endowing heat stress tolerance and grain size in rice are extremely rare. Here, we identified a novel negative regulator with pleiotropic effects, Thermo-Tolerance and grain Length 1 (TTL1), from the super pan-genomic and transcriptomic data. Loss-of-function mutations in TTL1 enhanced heat tolerance, and caused an increase in grain size by coordinating cell expansion and proliferation. TTL1 was shown to function as a transcriptional regulator and localized to the nucleus and cell membrane. Furthermore, haplotype analysis showed that hap [L] and hap [S] of TTL1 were obviously correlated with variations of thermotolerance and grain size in a core collection of cultivars. Genome evolution analysis of available rice germplasms suggested that TTL1 was selected during domestication of the indica and japonica rice subspecies, but still had much breeding potential for increasing grain length and thermotolerance. These findings provide insights into TTL1 as a novel potential target for development of high-yield and thermotolerant rice varieties. This article is protected by copyright. All rights reserved.},
}

@article {pmid37727231,
year = {2023},
author = {Rios Galicia, B and Sáenz, JS and Yergaliyev, T and Camarinha-Silva, A and Seifert, J},
title = {Host specific adaptations of Ligilactobacillus aviarius to poultry.},
journal = {Current research in microbial sciences},
volume = {5},
number = {},
pages = {100199},
pmid = {37727231},
issn = {2666-5174},
abstract = {The genus Ligilactobacillus encompasses species adapted to vertebrate hosts and fermented food. Their genomes encode adaptations to the host lifestyle. Reports of gut microbiota from chicken and turkey gastrointestinal tract have shown a high persistence of Ligilactobacillus aviarius along the digestive system compared to other species found in the same host. However, its adaptations to poultry as a host has not yet been described. In this work, the pan-genome of Ligilactobacillus aviarius was explored to describe the functional adaptability to the gastrointestinal environment. The core genome is composed of 1179 gene clusters that are present at least in one copy that codifies to structural, ribosomal and biogenesis proteins. The rest of the identified regions were classified into three different functional clusters of orthologous groups (clusters) that codify carbohydrate metabolism, envelope biogenesis, viral defence mechanisms, and mobilome inclusions. The pan-genome of Ligilactobacillus aviarius is a closed pan-genome, frequently found in poultry and highly prevalent across chicken faecal samples. The genome of L. aviarius codifies different clusters of glycoside hydrolases and glycosyltransferases that mediate interactions with the host cells. Accessory features, such as antiviral mechanisms and prophage inclusions, variate amongst strains from different GIT sections. This information provides hints about the interaction of this species with viral particles and other bacterial species. This work highlights functional adaptability traits present in L. aviarius that make it a dominant key member of the poultry gut microbiota and enlightens the convergent ecological relation of this species to the poultry gut environment.},
}

@article {pmid37722405,
year = {2023},
author = {Low, SJ and O'Neill, MT and Kerry, WJ and Krysiak, M and Papadakis, G and Whitehead, LW and Savic, I and Prestedge, J and Williams, L and Cooney, JP and Tran, T and Lim, CK and Caly, L and Towns, JM and Bradshaw, CS and Fairley, C and Chow, EPF and Chen, MY and Pellegrini, M and Pasricha, S and Williamson, DA},
title = {Rapid detection of monkeypox virus using a CRISPR-Cas12a mediated assay: a laboratory validation and evaluation study.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2666-5247(23)00148-9},
pmid = {37722405},
issn = {2666-5247},
abstract = {BACKGROUND: The 2022 outbreak of mpox (formerly known as monkeypox) led to the spread of monkeypox virus (MPXV) in over 110 countries, demanding effective disease management and surveillance. As current diagnostics rely largely on centralised laboratory testing, our objective was to develop a simple rapid point-of-care assay to detect MPXV in clinical samples using isothermal amplification coupled with CRISPR and CRISPR-associated protein (Cas) technology.

METHODS: In this proof-of-concept study, we developed a portable isothermal amplification CRISPR-Cas12a-based assay for the detection of MPXV. We designed a panel of 22 primer-guide RNA sets using pangenome and gene-agnostic approaches, and subsequently shortlisted the three sets producing the strongest signals for evaluation of analytical sensitivity and specificity using a fluorescence-based readout. The set displaying 100% specificity and the lowest limit of detection (LOD) was selected for further assay validation using both a fluorescence-based and lateral-flow readout. Assay specificity was confirmed using a panel of viral and bacterial pathogens. Finally, we did a blind concordance study on genomic DNA extracted from 185 clinical samples, comparing assay results with a gold-standard quantitative PCR (qPCR) assay. We identified the optimal time to detection and analysed the performance of the assay relative to qPCR using receiver operating characteristic (ROC) curves. We also assessed the compatibility with lateral-flow strips, both visually and computationally, where strips were interpreted blinded to the fluorescence results on the basis of the presence or absence of test bands.

FINDINGS: With an optimal run duration of approximately 45 min from isothermal amplification to CRISPR-assay readout, the MPXV recombinase polymerase amplification CRISPR-Cas12a-based assay with the selected primer-guide set had an LOD of 1 copy per μL and 100% specificity against tested viral pathogens. Blinded concordance testing of 185 clinical samples resulted in 100% sensitivity (95% CI 89·3-100) and 99·3% specificity (95% CI 95·7-100) using the fluorescence readout. For optimal time to detection by fluorescence readout, we estimated the areas under the ROC curve to be 0·98 at 2 min and 0·99 at 4 min. Lateral-flow strips had 100% sensitivity (89·3-100) and 98·6% specificity (94·7-100) with both visual and computational assessment. Overall, lateral-flow results were highly concordant with fluorescence-based readouts (179 of 185 tests, 96·8% concordant), with discrepancies associated with low viral load samples.

INTERPRETATION: Our assay for the diagnosis of mpox displayed good performance characteristics compared with qPCR. Although optimisation of the assay will be required before deployment, its usability and versatility present a potential solution to MPXV detection in low-resource and remote settings, as well as a means of community-based, on-site testing.

FUNDING: Victorian Medical Research Accelerator Fund and the Australian Government Department of Health.},
}

@article {pmid37714713,
year = {2023},
author = {Dai, X and Bian, P and Hu, D and Luo, F and Huang, Y and Jiao, S and Wang, X and Gong, M and Li, R and Cai, Y and Wen, J and Yang, Q and Deng, W and Nanaei, HA and Wang, Y and Wang, F and Zhang, Z and Rosen, BD and Heller, R and Jiang, Y},
title = {A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.277481.122},
pmid = {37714713},
issn = {1549-5469},
abstract = {Chinese indicine cattle harbor a much higher genetic diversity compared with other domestic cattle, but their genome architecture remains uninvestigated. Using PacBio HiFi sequencing data from 10 Chinese indicine cattle across southern China, we assembled 20 high-quality partially phased genomes and integrated them into a multiassembly graph containing 148.5 Mb (5.6%) of novel sequence. We identified 156,009 high-confidence nonredundant structural variants (SVs) and 206 SV hotspots spanning ∼195 Mb of gene-rich sequence. We detected 34,249 archaic introgressed fragments in Chinese indicine cattle covering 1.93 Gb (73.3%) of the genome. We inferred an average of 3.8%, 3.2%, 1.4%, and 0.5% of introgressed sequence originating, respectively, from banteng-like, kouprey-like, gayal-like, and gaur-like Bos species, as well as 0.6% of unknown origin. Introgression from multiple donors might have contributed to the genetic diversity of Chinese indicine cattle. Altogether, this study highlights the contribution of interspecies introgression to the genomic architecture of an important livestock population and shows how exotic genomic elements can contribute to the genetic variation available for selection.},
}

@article {pmid37710174,
year = {2023},
author = {Mahboob, S and Ullah, N and Farhan Ul Haque, M and Rauf, W and Iqbal, M and Ali, A and Rahman, M},
title = {Genomic characterization and comparative genomic analysis of HS-associated Pasteurella multocida serotype B:2 strains from Pakistan.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {546},
pmid = {37710174},
issn = {1471-2164},
support = {NRPU-7254//Higher Education Commision, Pakistan/ ; },
abstract = {BACKGROUND: Haemorrhagic septicaemia (HS) is a highly fatal and predominant disease in livestock, particularly cattle and buffalo in the tropical regions of the world. Pasteurella multocida (P. multocida), serotypes B:2 and E:2, are reported to be the main causes of HS wherein serotype B:2 is more common in Asian countries including Pakistan and costs heavy financial losses every year. As yet, very little molecular and genomic information related to the HS-associated serotypes of P. multocida isolated from Pakistan is available. Therefore, this study aimed to explore the characteristics of novel bovine isolates of P. multocida serotype B:2 at the genomic level and perform comparative genomic analysis of various P. multocida strains from Pakistan to better understand the genetic basis of pathogenesis and virulence.

RESULTS: To understand the genomic variability and pathogenomics, we characterized three HS-associated P. multocida serotype B:2 strains isolated from the Faisalabad (PM1), Peshawar (PM2) and Okara (PM3) districts of Punjab, Pakistan. Together with the other nine publicly available Pakistani-origin P. multocida strains and a reference strain Pm70, a comparative genomic analysis was performed. The sequenced strains were characterized as serotype B and belong to ST-122. The strains contain no plasmids; however, each strain contains at least two complete prophages. The pan-genome analysis revealed a higher number of core genes indicating a close resemblance to the studied genomes and very few genes (1%) of the core genome serve as a part of virulence, disease, and defense mechanisms. We further identified that studied P. multocida B:2 strains harbor common antibiotic resistance genes, specifically PBP3 and EF-Tu. Remarkably, the distribution of virulence factors revealed that OmpH and plpE were not present in any P. multocida B:2 strains while the presence of these antigens was reported uniformly in all serotypes of P. multocida.

CONCLUSION: This study's findings indicate the absence of OmpH and PlpE in the analyzed P. multocida B:2 strains, which are known surface antigens and provide protective immunity against P. multocida infection. The availability of additional genomic data on P. multocida B:2 strains from Pakistan will facilitate the development of localized therapeutic agents and rapid diagnostic tools specifically targeting HS-associated P. multocida B:2 strains.},
}

@article {pmid37710263,
year = {2023},
author = {Zhu, Q and Dovletgeldiyev, A and Shen, C and Li, K and Hu, S and He, Z},
title = {Comparative genomic analysis of Fusobacterium nucleatum reveals high intra-species diversity and cgmlst marker construction.},
journal = {Gut pathogens},
volume = {15},
number = {1},
pages = {43},
pmid = {37710263},
issn = {1757-4749},
abstract = {BACKGROUND: Fusobacterium nucleatum is a one of the most important anaerobic opportunistic pathogens in the oral and intestinal tracts of human and animals. It can cause various diseases such as infections, Lemierre's syndrome, oral cancer and colorectal cancer. The comparative genomic studies on the population genome level, have not been reported.

RESULTS: We analyzed all publicly available Fusobacterium nucleatums' genomic data for a comparative genomic study, focusing on the pan-genomic features, virulence genes, plasmid genomes and developed cgmlst molecular markers. We found the pan-genome shows a clear open tendency and most of plasmids in Fusobacterium nucleatum are mainly transmitted intraspecifically.

CONCLUSIONS: Our comparative analysis of Fusobacterium nucleatum systematically revealed the open pan-genomic features and phylogenetic tree based on cgmlst molecular markers. What's more, we also identified common plasmid typing among genomes. We hope that our study will provide a theoretical basis for subsequent functional studies.},
}

@article {pmid37695773,
year = {2023},
author = {Le Naour-Vernet, M and Charriat, F and Gracy, J and Cros-Arteil, S and Ravel, S and Veillet, F and Meusnier, I and Padilla, A and Kroj, T and Cesari, S and Gladieux, P},
title = {Adaptive evolution in virulence effectors of the rice blast fungus Pyricularia oryzae.},
journal = {PLoS pathogens},
volume = {19},
number = {9},
pages = {e1011294},
doi = {10.1371/journal.ppat.1011294},
pmid = {37695773},
issn = {1553-7374},
abstract = {Plant pathogens secrete proteins called effectors that target host cellular processes to promote disease. Recently, structural genomics has identified several families of fungal effectors that share a similar three-dimensional structure despite remarkably variable amino-acid sequences and surface properties. To explore the selective forces that underlie the sequence variability of structurally-analogous effectors, we focused on MAX effectors, a structural family of effectors that are major determinants of virulence in the rice blast fungus Pyricularia oryzae. Using structure-informed gene annotation, we identified 58 to 78 MAX effector genes per genome in a set of 120 isolates representing seven host-associated lineages. The expression of MAX effector genes was primarily restricted to the early biotrophic phase of infection and strongly influenced by the host plant. Pangenome analyses of MAX effectors demonstrated extensive presence/absence polymorphism and identified gene loss events possibly involved in host range adaptation. However, gene knock-in experiments did not reveal a strong effect on virulence phenotypes suggesting that other evolutionary mechanisms are the main drivers of MAX effector losses. MAX effectors displayed high levels of standing variation and high rates of non-synonymous substitutions, pointing to widespread positive selection shaping the molecular diversity of MAX effectors. The combination of these analyses with structural data revealed that positive selection acts mostly on residues located in particular structural elements and at specific positions. By providing a comprehensive catalog of amino acid polymorphism, and by identifying the structural determinants of the sequence diversity, our work will inform future studies aimed at elucidating the function and mode of action of MAX effectors.},
}

@article {pmid37695632,
year = {2023},
author = {Naveed, M and Mahmood, S and Aziz, T and Azeem, A and Hussain, I and Waseem, M and Ali, A and Alharbi, M and Alshammari, A and Alasmari, AF},
title = {Designing a novel chimeric multi-epitope vaccine subunit against Staphylococcus argenteus through artificial intelligence approach integrating pan-genome analysis, in vitro identification, and immunogenicity profiling.},
journal = {Journal of biomolecular structure & dynamics},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/07391102.2023.2256881},
pmid = {37695632},
issn = {1538-0254},
abstract = {Staphylococcus argenteus is a newly identified pathogen that causes respiratory tract infections, skin infections, such as cellulitis, abscesses, and impetigo, and currently, there is no licensed vaccine available against it. To develop a vaccine against S. argenteus, a bacterial pan-genome analysis was applied to identify potential vaccine candidates. A total of 4908 core proteins were retrieved and utilized for identifying four proteins, including SG38 Panton-Valentine leukocidin LukS-PV protein, SG62 staphylococcal enterotoxin type A protein, SG39 enterotoxin B protein, and SG43 enterotoxin type C3 protein as potential vaccine candidates. Epitopes were predicted for these proteins using different types of B and T-cell epitope prediction tools, and only those with a non-toxic profile, antigenic, non-allergenic, and immunogenic were selected. The selected epitopes were linked to each other to form a multi-epitope vaccine construct, which was further linked to the PADRE sequence (AKFVAAWTLKAAA) and 50s ribosomal L7/L12 protein to enhance the vaccine's antigenicity. The three-dimensional structure of the vaccine construct was assessed to determine its binding affinity with key Toll-like receptor 9 (TLR-9) and Toll-like receptor 5 (TLR-5) immune cell receptors. Our findings demonstrate that the vaccine exhibits favorable binding interactions with these immune cell receptors, indicating its potential efficacy. Molecular dynamic simulations further confirmed the accessibility of vaccine epitopes to the host immune system, substantiating its ability to elicit protective immune responses. Taken together, this study highlights the promising candidacy of the modeled vaccine construct for future in vivo and in vitro experimental investigations.Communicated by Ramaswamy H. Sarma.},
}

@article {pmid37692398,
year = {2023},
author = {Villacís, JE and Castelán-Sánchez, HG and Rojas-Vargas, J and Rodríguez-Cruz, UE and Albán, V and Reyes, JA and Meza-Rodríguez, PM and Dávila-Ramos, S and Villavicencio, F and Galarza, M and Gestal, MC},
title = {Emergence of Raoultella ornithinolytica in human infections from different hospitals in Ecuador with OXA-48-producing resistance.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1216008},
doi = {10.3389/fmicb.2023.1216008},
pmid = {37692398},
issn = {1664-302X},
abstract = {PURPOSE: The purpose of this study was to highlight the clinical and molecular features of 13 Raoultella ornithinolytica strains isolated from clinical environments in Ecuador, and to perform comparative genomics with previously published genomes of Raoultella spp. As Raoultella is primarily found in environmental, clinical settings, we focused our work on identifying mechanisms of resistance that can provide this bacterium an advantage to establish and persist in hospital environments.

METHODS: We analyzed 13 strains of Raoultella ornithinolytica isolated from patients with healthcare associated infections (HAI) in three hospitals in Quito and one in Santo Domingo de Los Tsáchilas, Ecuador, between November 2017 and April 2018. These isolates were subjected to phenotypic antimicrobial susceptibility testing, end-point polymerase chain reaction (PCR) to detect the presence of carbapenemases and whole-genome sequencing.

RESULTS: Polymerase chain reaction revealed that seven isolates were positive isolates for blaOXA-48 and one for blaKPC-2 gene. Of the seven strains that presented the blaOXA-48 gene, six harbored it on an IncFII plasmid, one was inserted into the bacterial chromosome. The blaKPC gene was detected in an IncM2/IncR plasmid. From the bioinformatics analysis, nine genomes had the gene blaOXA-48, originating from Ecuador. Moreover, all R. ornithinolytica strains contained the ORN-1 gene, which confers resistance for β-lactams, such as penicillins and cephalosporins. Comparative genome analysis of the strains showed that the pangenome of R. ornithinolytica is considered an open pangenome, with 27.77% of core genes, which could be explained by the fact that the antibiotic resistance genes in the ancestral reconstruction are relatively new, suggesting that this genome is constantly incorporating new genes.

CONCLUSION: These results reveal the genome plasticity of R. ornithinolytica, particularly in acquiring antibiotic-resistance genes. The genomic surveillance and infectious control of these uncommon species are important since they may contribute to the burden of antimicrobial resistance and human health.},
}

@article {pmid37690289,
year = {2023},
author = {Sarker, P and Mitro, A and Hoque, H and Hasan, MN and Nurnabi Azad Jewel, GM},
title = {Identification of potential novel therapeutic drug target against Elizabethkingia anophelis by integrative pan and subtractive genomic analysis: An in silico approach.},
journal = {Computers in biology and medicine},
volume = {165},
number = {},
pages = {107436},
doi = {10.1016/j.compbiomed.2023.107436},
pmid = {37690289},
issn = {1879-0534},
abstract = {Elizabethkingia anophelis is a human pathogen responsible for severe nosocomial infections in neonates and immunocompromised patients. The significantly higher mortality rate from E. anophelis infections and the lack of available regimens highlight the critical need to explore novel drug targets. The current study investigated effective novel drug targets by employing a comprehensive in silico subtractive genomic approach integrated with pangenomic analysis of E. anophelis strains. A total of 2809 core genomic proteins were found by pangenomic analysis of non-paralogous proteins. Subsequently, 156 pathogen-specific, 442 choke point, 202 virulence factor, 53 antibiotic resistant and 119 host-pathogen interacting proteins were identified in E. anophelis. By subtractive genomic approach, at first 791 proteins were found to be indispensable for the survival of E. anophelis. 558 and 315 proteins were detected as non-homologous to human and gut microflora respectively. Following that 245 cytoplasmic, 245 novel, and 23 broad-spectrum targets were selected and finally four proteins were considered as potential therapeutic targets of E. anophelis based on highest degree score in PPI network. Among those, three proteins were subjected to molecular docking and subsequent MD simulation as one protein did not contain a plausible binding pocket with sufficient surface area and volume. All the complexes were found to be stable and compact in 100 ns molecular dynamics simulation studies as measured by RMSD, RMSF, and Rg. These three short-listed targets identified in this study may lead to the development of novel antimicrobials capable of curing infections and pave the way to prevent and control the disease progression caused by the deadly agent E. anophelis.},
}

@article {pmid37684624,
year = {2023},
author = {Nageeb, WM and Hetta, HF},
title = {Pangenome analysis of Corynebacterium striatum: insights into a neglected multidrug-resistant pathogen.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {252},
pmid = {37684624},
issn = {1471-2180},
abstract = {BACKGROUND: Over the past two decades, Corynebacterium striatum has been increasingly isolated from clinical cultures with most isolates showing increased antimicrobial resistance (AMR) to last resort agents. Advances in the field of pan genomics would facilitate the understanding of the clinical significance of such bacterial species previously thought to be among commensals paving the way for identifying new drug targets and control strategies.

METHODS: We constructed a pan-genome using 310 genome sequences of C. striatum. Pan-genome analysis was performed using three tools including Roary, PIRATE, and PEPPAN. AMR genes and virulence factors have been studied in relation to core genome phylogeny. Genomic Islands (GIs), Integrons, and Prophage regions have been explored in detail.

RESULTS: The pan-genome ranges between a total of 5253-5857 genes with 2070 - 1899 core gene clusters. Some antimicrobial resistance genes have been identified in the core genome portion, but most of them were located in the dispensable genome. In addition, some well-known virulence factors described in pathogenic Corynebacterium species were located in the dispensable genome. A total of 115 phage species have been identified with only 44 intact prophage regions.

CONCLUSION: This study presents a detailed comparative pangenome report of C. striatum. The species show a very slowly growing pangenome with relatively high number of genes in the core genome contributing to lower genomic variation. Prophage elements carrying AMR and virulence elements appear to be infrequent in the species. GIs appear to offer a prominent role in mobilizing antibiotic resistance genes in the species and integrons occur at a frequency of 50% in the species. Control strategies should be directed against virulence and resistance determinants carried on the core genome and those frequently occurring in the accessory genome.},
}

@article {pmid37679681,
year = {2023},
author = {Wang, Y and Xu, X and Chen, H and Yang, F and Xu, B and Wang, K and Liu, Q and Liang, G and Zhang, R and Jiao, X and Zhang, Y},
title = {Assessment of beneficial effects and identification of host adaptation-associated genes of Ligilactobacillus salivarius isolated from badgers.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {530},
pmid = {37679681},
issn = {1471-2164},
support = {PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; },
abstract = {BACKGROUND: Ligilactobacillus salivarius has been frequently isolated from the gut microbiota of humans and domesticated animals and has been studied as a candidate probiotic. Badger (Meles meles) is known as a "generalist" species that consumes complex foods and exhibits tolerance and resistance to certain pathogens, which can be partly attributed to the beneficial microbes such as L. salivarius in the gut microbiota. However, our understanding of the beneficial traits and genomic features of badger-originated L. salivarius remains elusive.

RESULTS: In this study, nine L. salivarius strains were isolated from wild badgers' feces, one of which exhibited good probiotic properties. Complete genomes of the nine L. salivarius strains were generated, and comparative genomic analysis was performed with the publicly available complete genomes of L. salivarius obtained from humans and domesticated animals. The strains originating from badgers harbored a larger genome, a higher number of protein-coding sequences, and functionally annotated genes than those originating from humans and chickens. The pan-genome phylogenetic tree demonstrated that the strains originating from badgers formed a separate clade, and totally 412 gene families (12.6% of the total gene families in the pan-genome) were identified as genes gained by the last common ancestor of the badger group. The badger group harbored significantly more gene families responsible for the degradation of complex carbohydrate substrates and production of polysaccharides than strains from other hosts; many of these were acquired by gene gain events.

CONCLUSIONS: A candidate probiotic and nine L. salivarius complete genomes were obtained from the badgers' gut microbiome, and several beneficial genes were identified to be specifically present in the badger-originated strains that were gained in the evolution. Our study provides novel insights into the adaptation of L. salivarius to the intestinal habitat of wild badgers and provides valuable strain and genome resources for the development of L. salivarius as a probiotic.},
}

@article {pmid37679363,
year = {2023},
author = {Liu, F and Zhao, J and Sun, H and Xiong, C and Sun, X and Wang, X and Wang, Z and Jarret, R and Wang, J and Tang, B and Xu, H and Hu, B and Suo, H and Yang, B and Ou, L and Li, X and Zhou, S and Yang, S and Liu, Z and Yuan, F and Pei, Z and Ma, Y and Dai, X and Wu, S and Fei, Z and Zou, X},
title = {Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {5487},
pmid = {37679363},
issn = {2041-1723},
support = {1855585//National Science Foundation (NSF)/ ; },
abstract = {Pepper (Capsicum spp.) is one of the earliest cultivated crops and includes five domesticated species, C. annuum var. annuum, C. chinense, C. frutescens, C. baccatum var. pendulum and C. pubescens. Here, we report a pepper graph pan-genome and a genome variation map of 500 accessions from the five domesticated Capsicum species and close wild relatives. We identify highly differentiated genomic regions among the domesticated peppers that underlie their natural variations in flowering time, characteristic flavors, and unique resistances to biotic and abiotic stresses. Domestication sweeps detected in C. annuum var. annuum and C. baccatum var. pendulum are mostly different, and the common domestication traits, including fruit size, shape and pungency, are achieved mainly through the selection of distinct genomic regions between these two cultivated species. Introgressions from C. baccatum into C. chinense and C. frutescens are detected, including those providing genetic sources for various biotic and abiotic stress tolerances.},
}

@article {pmid37676357,
year = {2023},
author = {Huang, B and Yan, H and Sun, M and Jin, Y},
title = {Novel discovery in roles of structural variations and RWP-RK transcription factors in heat tolerance for pearl millet.},
journal = {Stress biology},
volume = {3},
number = {1},
pages = {12},
doi = {10.1007/s44154-023-00092-3},
pmid = {37676357},
issn = {2731-0450},
abstract = {Global warming adversely affects crop production worldwide. Massive efforts have been undertaken to study mechanisms regulating heat tolerance in plants. However, the roles of structural variations (SVs) in heat stress tolerance remain unclear. In a recent article, Yan et al. (Nat Genet 1-12, 2023) constructed the first pan-genome of pearl millet (Pennisetum glaucum) and identified key SVs linked to genes involved in regulating plant tolerance to heat stress for an important crop with a superior ability to thrive in extremely hot and arid climates. Through multi-omics analyses integrating by pan-genomics, comparative genomics, transcriptomics, population genetics and and molecular biological technologies, they found RWP-RK transcription factors cooperating with endoplasmic reticulum-related genes play key roles in heat tolerance in pearl millet. The results in this paper provided novel insights to advance the understanding of the genetic and genomic basis of heat tolerance and an exceptional resource for molecular breeding to improve heat tolerance in pearl millet and other crops.},
}

@article {pmid37676306,
year = {2023},
author = {González-Gómez, JP and Lozano-Aguirre, LF and Medrano-Félix, JA and Chaidez, C and Gerba, CP and Betancourt, WQ and Castro-Del Campo, N},
title = {Evaluation of nuclear and mitochondrial phylogenetics for the subtyping of Cyclospora cayetanensis.},
journal = {Parasitology research},
volume = {},
number = {},
pages = {},
pmid = {37676306},
issn = {1432-1955},
abstract = {Cyclospora cayetanensis is an enteric coccidian parasite responsible for gastrointestinal disease transmitted through contaminated food and water. It has been documented in several countries, mostly with low-socioeconomic levels, although major outbreaks have hit developed countries. Detection methods based on oocyst morphology, staining, and molecular testing have been developed. However, the current MLST panel offers an opportunity for enhancement, as amplification of all molecular markers remains unfeasible in the majority of samples. This study aims to address this challenge by evaluating two approaches for analyzing the genetic diversity of C. cayetanensis and identifying reliable markers for subtyping: core homologous genes and mitochondrial genome analysis. A pangenome was constructed using 36 complete genomes of C. cayetanensis, and a haplotype network and phylogenetic analysis were conducted using 33 mitochondrial genomes. Through the analysis of the pangenome, 47 potential markers were identified, emphasizing the need for more sequence data to achieve comprehensive characterization. Additionally, the analysis of mitochondrial genomes revealed 19 single-nucleotide variations that can serve as characteristic markers for subtyping this parasite. These findings not only contribute to the selection of molecular markers for C. cayetanensis subtyping, but they also drive the knowledge toward the potential development of a comprehensive genotyping method for this parasite.},
}

@article {pmid37671027,
year = {2023},
author = {Lee, H and Greer, SU and Pavlichin, DS and Zhou, B and Urban, AE and Weissman, T and , and Ji, HP},
title = {Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome.},
journal = {Cell reports methods},
volume = {3},
number = {8},
pages = {100543},
pmid = {37671027},
issn = {2667-2375},
abstract = {The human pangenome, a new reference sequence, addresses many limitations of the current GRCh38 reference. The first release is based on 94 high-quality haploid assemblies from individuals with diverse backgrounds. We employed a k-mer indexing strategy for comparative analysis across multiple assemblies, including the pangenome reference, GRCh38, and CHM13, a telomere-to-telomere reference assembly. Our k-mer indexing approach enabled us to identify a valuable collection of universally conserved sequences across all assemblies, referred to as "pan-conserved segment tags" (PSTs). By examining intervals between these segments, we discerned highly conserved genomic segments and those with structurally related polymorphisms. We found 60,764 polymorphic intervals with unique geo-ethnic features in the pangenome reference. In this study, we utilized ultra-conserved sequences (PSTs) to forge a link between human pangenome assemblies and reference genomes. This methodology enables the examination of any sequence of interest within the pangenome, using the reference genome as a comparative framework.},
}

@article {pmid37668148,
year = {2023},
author = {Mentasti, M and David, S and Turton, J and Morgan, M and Turner, L and Westlake, J and Jenkins, J and Williams, C and Rey, S and Watkins, J and Daniel, V and Mitchell, S and Forbes, G and Wootton, M and Jones, L},
title = {Clonal expansion and rapid characterization of Klebsiella pneumoniae ST1788, an otherwise uncommon strain spreading in Wales, UK.},
journal = {Microbial genomics},
volume = {9},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001104},
pmid = {37668148},
issn = {2057-5858},
abstract = {A multidrug-resistant strain of Klebsiella pneumoniae (Kp) sequence type (ST) 1788, an otherwise uncommon ST worldwide, was isolated from 65 patients at 11 hospitals and 11 general practices across South and West Wales, UK, between February 2019 and November 2021. A collection of 97 Kp ST1788 isolates (including 94 from Wales) was analysed to investigate the diversity and spread across Wales and to identify molecular marker(s) to aid development of a strain-specific real-time PCR. Whole genome sequencing (WGS) was performed with Illumina technology and the data were used to perform phylogenetic analyses. Pan-genome analysis of further Kp genome collections was used to identify an ST1788-specific gene target; a real-time PCR was then validated against a panel of 314 strains and 218 broth-enriched screening samples. Low genomic diversity was demonstrated amongst the 94 isolates from Wales. Evidence of spread within and across healthcare facilities was found. A yersiniabactin locus and the KL2 capsular locus were identified in 85/94 (90.4 %) and 94/94 (100 %) genomes respectively; bla SHV-232, bla TEM-1, bla CTX-M-15 and bla OXA-1 were simultaneously carried by 86/94 (91.5 %) isolates; 4/94 (4.3 %) isolates also carried bla OXA-48 carbapenemase. Aminoglycoside and fluoroquinolone resistance markers were found in 94/94 (100 %) and 86/94 (91.5 %) isolates respectively. The ST1788-specific real-time PCR was 100 % sensitive and specific. Our analyses demonstrated recent clonal expansion and spread of Kp ST1788 in the community and across healthcare facilities in South and West Wales with isolates carrying well-defined antimicrobial resistance and virulence markers. An ST1788-specific marker was also identified, enabling rapid and reliable preliminary characterization of isolates by real-time PCR. This study confirms the utility of WGS in investigating novel strains and in aiding proactive implementation of molecular tools to assist infection control specialists.},
}

@article {pmid37667515,
year = {2023},
author = {Baker, JL},
title = {Illuminating the oral microbiome and its host interactions: recent Advancements in omics and bioinformatics technologies in the context of oral microbiome research.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuad051},
pmid = {37667515},
issn = {1574-6976},
abstract = {The oral microbiota has an enormous impact on human health, with oral dysbiosis now linked to many oral and systemic diseases. Recent advancements in sequencing, mass spectrometry, bioinformatics, computational biology, and machine learning are revolutionizing oral microbiome research, enabling analysis at an unprecedented scale and level of resolution using omics approaches. This review contains a comprehensive perspective of the current state-of-the-art tools available to perform genomics, metagenomics, phylogenomics, pangenomics, transcriptomics, proteomics, metabolomics, lipidomics, and multi-omics analysis on (all) microbiomes, and then provides examples of how the techniques have been applied to research of the oral microbiome, specifically. Key findings of these studies and remaining challenges for the field are highlighted. Although the methods discussed here are placed in the context of their contributions to oral microbiome research specifically, they are pertinent to the study of any microbiome, and the intended audience of this includes researchers would simply like to get an introduction to microbial omics and/or an update on the latest omics methods. Continued research of the oral microbiota using omics approaches is crucial and will lead to dramatic improvements in human health, longevity, and quality of life.},
}

@article {pmid37662009,
year = {2023},
author = {Li, Z and Zhou, X and Liao, D and Liu, R and Zhao, X and Wang, J and Zhong, Q and Zeng, Z and Peng, Y and Tan, Y and Yang, Z},
title = {Comparative genomics and DNA methylation analysis of Pseudomonas aeruginosa clinical isolate PA3 by single-molecule real-time sequencing reveals new targets for antimicrobials.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1180194},
pmid = {37662009},
issn = {2235-2988},
abstract = {INTRODUCTION: Pseudomonas aeruginosa (P.aeruginosa) is an important opportunistic pathogen with broad environmental adaptability and complex drug resistance. Single-molecule real-time (SMRT) sequencing technique has longer read-length sequences, more accuracy, and the ability to identify epigenetic DNA alterations.

METHODS: This study applied SMRT technology to sequence a clinical strain P. aeruginosa PA3 to obtain its genome sequence and methylation modification information. Genomic, comparative, pan-genomic, and epigenetic analyses of PA3 were conducted.

RESULTS: General genome annotations of PA3 were discovered, as well as information about virulence factors, regulatory proteins (RPs), secreted proteins, type II toxin-antitoxin (TA) pairs, and genomic islands. A genome-wide comparison revealed that PA3 was comparable to other P. aeruginosa strains in terms of identity, but varied in areas of horizontal gene transfer (HGT). Phylogenetic analysis showed that PA3 was closely related to P. aeruginosa 60503 and P. aeruginosa 8380. P. aeruginosa's pan-genome consists of a core genome of roughly 4,300 genes and an accessory genome of at least 5,500 genes. The results of the epigenetic analysis identified one main methylation sites, N6-methyladenosine (m6A) and 1 motif (CATNNNNNNNTCCT/AGGANNNNNNNATG). 16 meaningful methylated sites were picked. Among these, purH, phaZ, and lexA are of great significance playing an important role in the drug resistance and biological environment adaptability of PA3, and the targeting of these genes may benefit further antibacterial studies.

DISUCSSION: This study provided a detailed visualization and DNA methylation information of the PA3 genome and set a foundation for subsequent research into the molecular mechanism of DNA methyltransferase-controlled P. aeruginosa pathogenicity.},
}

@article {pmid37659733,
year = {2023},
author = {Sharma, N and Raman, H and Wheeler, D and Kalenahalli, Y and Sharma, R},
title = {Data-driven approaches to improve water-use efficiency and drought resistance in crop plants.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {},
number = {},
pages = {111852},
doi = {10.1016/j.plantsci.2023.111852},
pmid = {37659733},
issn = {1873-2259},
abstract = {With the increasing population, there lies a pressing demand for food, feed and fibre, while the changing climatic conditions pose severe challenges for agricultural production worldwide. Water is the lifeline for crop production; thus, enhancing crop water-use efficiency (WUE) and improving drought resistance in crop varieties are crucial for overcoming these challenges. Genetically-driven improvements in yield, WUE and drought tolerance traits can buffer the worst effects of climate change on crop production in dry areas. While traditional crop breeding approaches have delivered impressive results in increasing yield, the methods remain time-consuming and are often limited by the existing allelic variation present in the germplasm. Significant advances in breeding and high-throughput omics technologies in parallel with smart agriculture practices have created avenues to dramatically speed up the process of trait improvement by leveraging the vast volumes of genomic and phenotypic data. For example, individual genome and pan-genome assemblies, along with transcriptomic, metabolomic and proteomic data from germplasm collections, characterised at phenotypic levels, could be utilised to identify marker-trait associations and superior haplotypes for crop genetic improvement. In addition, these omics approaches enable the identification of genes involved in pathways leading to the expression of a trait, thereby providing an understanding of the genetic, physiological and biochemical basis of trait variation. These data-driven gene discoveries and validation approaches are essential for crop improvement pipelines, including genomic breeding, speed breeding and gene editing. Herein, we provide an overview of prospects presented using big data-driven approaches (including artificial intelligence and machine learning) to harness new genetic gains for breeding programs and develop drought-tolerant crop varieties with favourable WUE and high-yield potential traits.},
}

@article {pmid37655941,
year = {2023},
author = {Meyer, S and Laval, L and Pimenta, M and González-Flores, Y and Gaschet, M and Couvé-Deacon, E and Barraud, O and Dagot, C and Ploy, MC},
title = {[Tracking transfers of resistance-carrying bacteria between animals, humans and the environment].},
journal = {Comptes rendus biologies},
volume = {},
number = {},
pages = {},
doi = {10.5802/crbiol.114},
pmid = {37655941},
issn = {1768-3238},
abstract = {The fight against antibiotic resistance must incorporate the "One Health" concept to be effective. This means having a holistic approach embracing the different ecosystems, human, animal, and environment. Transfers of resistance genes may exist between these three domains and different stresses related to the exposome may influence these transfers. Various targeted or pan-genomic molecular biology techniques can be used to better characterise the dissemination of bacterial clones and to identify exchanges of genes and mobile genetic elements between ecosystems.},
}

@article {pmid37653687,
year = {2023},
author = {Dixon, TA and Walker, RSK and Pretorius, IS},
title = {Visioning synthetic futures for yeast research within the context of current global techno-political trends.},
journal = {Yeast (Chichester, England)},
volume = {},
number = {},
pages = {},
doi = {10.1002/yea.3897},
pmid = {37653687},
issn = {1097-0061},
support = {//Australian Research Council/ ; },
abstract = {Yeast research is entering into a new period of scholarship, with new scientific tools, new questions to ask and new issues to consider. The politics of emerging and critical technology can no longer be separated from the pursuit of basic science in fields, such as synthetic biology and engineering biology. Given the intensifying race for technological leadership, yeast research is likely to attract significant investment from government, and that it offers huge opportunities to the curious minded from a basic research standpoint. This article provides an overview of new directions in yeast research with a focus on Saccharomyces cerevisiae, and places these trends in their geopolitical context. At the highest level, yeast research is situated within the ongoing convergence of the life sciences with the information sciences. This convergent effect is most strongly pronounced in areas of AI-enabled tools for the life sciences, and the creation of synthetic genomes, minimal genomes, pan-genomes, neochromosomes and metagenomes using computer-assisted design tools and methodologies. Synthetic yeast futures encompass basic and applied science questions that will be of intense interest to government and nongovernment funding sources. It is essential for the yeast research community to map and understand the context of their research to ensure their collaborations turn global challenges into research opportunities.},
}

@article {pmid37646934,
year = {2023},
author = {Bayer, PE and Edwards, D},
title = {Investigating Pangenome Graphs Using Wheat Panache.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2703},
number = {},
pages = {23-29},
pmid = {37646934},
issn = {1940-6029},
abstract = {Pangenome graphs quickly become the central data structure representing the diversity of variation we see across related genomes. Pangenome graphs have been published for some species, including plants of agronomic interest. However, visualizing these graphs is not easy as the graphs are large, and variants within these graphs are complex. Tools are needed to visualize graph data structures. Here, we present a workflow to search and visualize a wheat pangenome graph using Wheat Panache. The approach presented assists researchers interested in wheat genomics.},
}

@article {pmid37645952,
year = {2023},
author = {McLaughlin, M and Fiebig, A and Crosson, S},
title = {XRE Transcription Factors Conserved in Caulobacter and φCbK Modulate Adhesin Development and Phage Production.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.08.20.554034},
pmid = {37645952},
abstract = {Upon infection, transcriptional shifts in both a host bacterium and its invading phage determine host and viral fitness. The xenobiotic response element (XRE) family of transcription factors (TFs), which are commonly encoded by bacteria and phages, regulate diverse features of bacterial cell physiology and impact phage infection dynamics. Through a pangenome analysis of Caulobacter species isolated from soil and aquatic ecosystems, we uncovered an apparent radiation of a paralogous XRE TF gene cluster, several of which have established functions in the regulation of holdfast adhesin development and biofilm formation in C. crescentus . We further discovered related XRE TFs across the class Alphaproteobacteria and its phages, including the φCbK Caulophage, suggesting that members of this gene cluster impact host-phage interactions. Here we show that that a closely related group of XRE proteins, encoded by both C. crescentus and φCbK, can form heteromeric associations and control the transcription of a common gene set, influencing processes including holdfast development and the production of φCbK virions. The φCbK XRE paralog, tgrL , is highly expressed at the earliest stages of infection and can directly repress transcription of hfiA , a potent holdfast inhibitor, and gafYZ , a transcriptional activator of prophage-like gene transfer agents (GTAs) encoded on the C. crescentus chromosome. XRE proteins encoded from the C. crescentus chromosome also directly repress gafYZ transcription, revealing a functionally redundant set of host regulators that may protect against spurious production of GTA particles and inadvertent cell lysis. Deleting host XRE transcription factors reduced φCbK burst size, while overexpressing these genes or φCbK tgrL rescued this burst defect. We conclude that an XRE TF gene cluster, shared by C. crescentus and φCbK, plays an important role in adhesion regulation under phage-free conditions, and influences host-phage dynamics during infection.},
}

@article {pmid37645873,
year = {2023},
author = {Shivakumar, VS and Ahmed, OY and Kovaka, S and Zakeri, M and Langmead, B},
title = {Sigmoni: classification of nanopore signal with a compressed pangenome index.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.08.15.553308},
pmid = {37645873},
abstract = {Improvements in nanopore sequencing necessitate efficient classification methods, including pre-filtering and adaptive sampling algorithms that enrich for reads of interest. Signal-based approaches circumvent the computational bottleneck of basecalling. But past methods for signal-based classification do not scale efficiently to large, repetitive references like pangenomes, limiting their utility to partial references or individual genomes. We introduce Sigmoni: a rapid, multiclass classification method based on the r -index that scales to references of hundreds of Gbps. Sigmoni quantizes nanopore signal into a discrete alphabet of picoamp ranges. It performs rapid, approximate matching using matching statistics, classifying reads based on distributions of picoamp matching statistics and co-linearity statistics. Sigmoni is 10-100 × faster than previous methods for adaptive sampling in host depletion experiments with improved accuracy, and can query reads against large microbial or human pangenomes.},
}

@article {pmid37644736,
year = {2023},
author = {Le, VV and Ko, SR and Kang, M and Jeong, S and Oh, HM and Ahn, CY},
title = {Comparative Genome analysis of the Genus Curvibacter and the Description of Curvibacter microcysteis sp. nov. and Curvibacter cyanobacteriorum sp. nov., Isolated from Fresh Water during the Cyanobacterial Bloom Period.},
journal = {Journal of microbiology and biotechnology},
volume = {33},
number = {11},
pages = {1-10},
doi = {10.4014/jmb.2306.06017},
pmid = {37644736},
issn = {1738-8872},
abstract = {The three Gram-negative, catalase- and oxidase-positive bacterial strains RS43T, HBC28, and HBC61[T], were isolated from fresh water and subjected to a polyphasic study. Comparison of 16S rRNA gene sequence initially indicated that strains RS43[T], HBC28, and HBC61[T] were closely related to species of genus Curvibacter and shared the highest sequence similarity of 98.14%, 98.21%, and 98.76%, respectively, with Curvibacter gracilis 7-1[T]. Phylogenetic analysis based on genome sequences placed all strains within the genus Curvibacter. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the three strains and related type strains supported their recognition as two novel genospecies in the genus Curvibacter. Comparative genomic analysis revealed that the genus possessed an open pangenome. Based on KEGG BlastKOALA analyses, Curvibacter species have the potential to metabolize benzoate, phenylacetate, catechol, and salicylate, indicating their potential use in the elimination of these compounds from the water systems. The results of polyphasic characterization indicated that strain RS43T and HBC61[T] represent two novel species, for which the name Curvibacter microcysteis sp. nov. (type strain RS43[T] (=KCTC 92793T=LMG 32714[T]) and Curvibacter cyanobacteriorum sp. nov. (type strain HBC61[T] =KCTC 92794[T] =LMG 32713[T]) are proposed.},
}

@article {pmid37639729,
year = {2023},
author = {Prajapati, A and Yogisharadhya, R and Mohanty, NN and Mendem, SK and Chanda, MM and Siddaramappa, S and Shivachandra, SB},
title = {Comparative genome analysis of Pasteurella multocida strains of porcine origin.},
journal = {Genome},
volume = {},
number = {},
pages = {},
doi = {10.1139/gen-2023-0021},
pmid = {37639729},
issn = {1480-3321},
abstract = {Pasteurella multocida causes acute/chronic pasteurellosis in porcine resulting in considerable economic losses globally. The draft genomes of two Indian strains NIVEDIPm17 (serogroup D) and NIVEDIPm36 (serogroup A) were sequenced. A total of 2182- 2284 coding sequences (CDSs) were predicted along with 5-6 rRNA and 45-46 tRNA genes in the genomes. Multi locus sequence analysis and LPS genotyping showed the presence of ST50: genotype 07 and ST74: genotype 06 in NIVEDIPm17 and NIVEDIPm36, respectively. Pangenome analysis of 61 strains showed the presence of 1653 core genes, 167 soft core genes, 750 shell genes, and 1820 cloud genes. Analysis of virulence-associated genes in 61 genomes indicated the presence of nanB, exbB, exbD. ptfA, ompA, ompH, fur, plpB, fimA, sodA, sodC, tonB, and omp87 in all strains. The 61 genomes contained genes encoding tetracycline (54%), streptomycin (48%), sulphonamide (28%), tigecycline (25%), chloramphenicol (21%), amikacin (7%), cephalosporin (5%) and trimethoprim (5%) resistance. MLST revealed that ST50 was the most common (34%), followed by ST74 (26%), ST13 (24%), ST287 (5%), ST09 (5%), ST122 (3%), and ST07 (2%). SNP and core genome-based phylogenetic analysis clustered the strains in to 3 major clusters. In conclusion, we described the various virulence factors, mobile genetic elements and antimicrobial resistance genes in pangenome of P. multocida of porcine origin besides a rare presence of LPS genotype 7 in serogroup D..},
}

@article {pmid37636268,
year = {2023},
author = {Yang, Z and Guarracino, A and Biggs, PJ and Black, MA and Ismail, N and Wold, JR and Merriman, TR and Prins, P and Garrison, E and de Ligt, J},
title = {Pangenome graphs in infectious disease: a comprehensive genetic variation analysis of Neisseria meningitidis leveraging Oxford Nanopore long reads.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1225248},
pmid = {37636268},
issn = {1664-8021},
abstract = {Whole genome sequencing has revolutionized infectious disease surveillance for tracking and monitoring the spread and evolution of pathogens. However, using a linear reference genome for genomic analyses may introduce biases, especially when studies are conducted on highly variable bacterial genomes of the same species. Pangenome graphs provide an efficient model for representing and analyzing multiple genomes and their variants as a graph structure that includes all types of variations. In this study, we present a practical bioinformatics pipeline that employs the PanGenome Graph Builder and the Variation Graph toolkit to build pangenomes from assembled genomes, align whole genome sequencing data and call variants against a graph reference. The pangenome graph enables the identification of structural variants, rearrangements, and small variants (e.g., single nucleotide polymorphisms and insertions/deletions) simultaneously. We demonstrate that using a pangenome graph, instead of a single linear reference genome, improves mapping rates and variant calling for both simulated and real datasets of the pathogen Neisseria meningitidis. Overall, pangenome graphs offer a promising approach for comparative genomics and comprehensive genetic variation analysis in infectious disease. Moreover, this innovative pipeline, leveraging pangenome graphs, can bridge variant analysis, genome assembly, population genetics, and evolutionary biology, expanding the reach of genomic understanding and applications.},
}

@article {pmid37630674,
year = {2023},
author = {Aguirre-Sánchez, JR and Quiñones, B and Ortiz-Muñoz, JA and Prieto-Alvarado, R and Vega-López, IF and Martínez-Urtaza, J and Lee, BG and Chaidez, C},
title = {Comparative Genomic Analyses of Virulence and Antimicrobial Resistance in Citrobacter werkmanii, an Emerging Opportunistic Pathogen.},
journal = {Microorganisms},
volume = {11},
number = {8},
pages = {},
doi = {10.3390/microorganisms11082114},
pmid = {37630674},
issn = {2076-2607},
support = {CRIS Project Number 2030-42000-055-00D//United States Department of Agriculture (USDA), Agricultural Research Service (ARS)/ ; Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA)//Centro de Investigación y Desarrollo A. C. (CIAD) in Culiacán, Sinaloa/ ; },
abstract = {Citrobacter werkmanii is an emerging and opportunistic human pathogen found in developing countries and is a causative agent of wound, urinary tract, and blood infections. The present study conducted comparative genomic analyses of a C. werkmanii strain collection from diverse geographical locations and sources to identify the relevant virulence and antimicrobial resistance genes. Pangenome analyses divided the examined C. werkmanii strains into five distinct clades; the subsequent classification identified genes with functional roles in carbohydrate and general metabolism for the core genome and genes with a role in secretion, adherence, and the mobilome for the shell and cloud genomes. A maximum-likelihood phylogenetic tree with a heatmap, showing the virulence and antimicrobial genes' presence or absence, demonstrated the presence of genes with functional roles in secretion systems, adherence, enterobactin, and siderophore among the strains belonging to the different clades. C. werkmanii strains in clade V, predominantly from clinical sources, harbored genes implicated in type II and type Vb secretion systems as well as multidrug resistance to aminoglycoside, beta-lactamase, fluoroquinolone, phenicol, trimethoprim, macrolides, sulfonamide, and tetracycline. In summary, these comparative genomic analyses have demonstrated highly pathogenic and multidrug-resistant genetic profiles in C. werkmanii strains, indicating a virulence potential for this commensal and opportunistic human pathogen.},
}

@article {pmid37630640,
year = {2023},
author = {van der Lee, TAJ and van Gent-Pelzer, MPE and Jonkheer, EM and Brankovics, B and Houwers, IM and van der Wolf, JM and Bonants, PJM and van Duivenbode, I and Vreeburg, RAM and Nas, M and Smit, S},
title = {An Efficient Triplex TaqMan Quantitative PCR to Detect a Blackleg-Causing Lineage of Pectobacterium brasiliense in Potato Based on a Pangenome Analysis.},
journal = {Microorganisms},
volume = {11},
number = {8},
pages = {},
doi = {10.3390/microorganisms11082080},
pmid = {37630640},
issn = {2076-2607},
support = {TU-16022//Dutch Ministry of Agriculture, Nature and Food Safety/ ; },
abstract = {P. brasiliense is an important bacterial pathogen causing blackleg (BL) in potatoes. Nevertheless, P. brasiliense is often detected in seed lots that do not develop any of the typical blackleg symptoms in the potato crop when planted. Field bioassays identified that P. brasiliense strains can be categorized into two distinct classes, some able to cause blackleg symptoms and some unable to do it. A comparative pangenomic approach was performed on 116 P. brasiliense strains, of which 15 were characterized as BL-causing strains and 25 as non-causative. In a genetically homogeneous clade comprising all BL-causing P. brasiliense strains, two genes only present in the BL-causing strains were identified, one encoding a predicted lysozyme inhibitor Lprl (LZI) and one encoding a putative Toll/interleukin-1 receptor (TIR) domain-containing protein. TaqMan assays for the specific detection of BL-causing P. brasiliense were developed and integrated with the previously developed generic P. brasiliense assay into a triplex TaqMan assay. This simultaneous detection makes the scoring more efficient as only a single tube is needed, and it is more robust as BL-causing strains of P. brasiliense should be positive for all three assays. Individual P. brasiliense strains were found to be either positive for all three assays or only for the P. brasiliense assay. In potato samples, the mixed presence of BL-causing and not BL-causing P. brasiliense strains was observed as shown by the difference in Ct value of the TaqMan assays. However, upon extension of the number of strains, it became clear that in recent years additional BL-causing lineages of P. brasiliense were detected for which additional assays must be developed.},
}

@article {pmid37630590,
year = {2023},
author = {Mevada, V and Patel, R and Dudhagara, P and Chaudhari, R and Vohra, M and Khan, V and J H Shyu, D and Chen, YY and Zala, D},
title = {Whole Genome Sequencing and Pan-Genomic Analysis of Multidrug-Resistant Vibrio cholerae VC01 Isolated from a Clinical Sample.},
journal = {Microorganisms},
volume = {11},
number = {8},
pages = {},
doi = {10.3390/microorganisms11082030},
pmid = {37630590},
issn = {2076-2607},
abstract = {Cholera, a disease caused by the Vibrio cholerae bacteria, threatens public health worldwide. The organism mentioned above has a significant historical record of being identified as a prominent aquatic environmental pollutant capable of adapting its phenotypic and genotypic traits to react to host patients effectively. This study aims to elucidate the heterogeneity of the sporadic clinical strain of V. cholerae VC01 among patients residing in Silvasa. The study involved conducting whole-genome sequencing of the isolate obtained from patients exhibiting symptoms, including those not commonly observed in clinical practice. The strain was initially identified through a combination of biochemical analysis, microscopy, and 16s rRNA-based identification, followed by type strain-based identification. The investigation demonstrated the existence of various genetic alterations and resistance profiles against multiple drugs, particularly chloramphenicol (catB9), florfenicol (floR), oxytetracycline (tet(34)), sulfonamide (sul2), and Trimethoprim (dfrA1). The pan-genomic analysis indicated that 1099 distinct clusters were detected within the genome sequences of recent isolates worldwide. The present study helps to establish a correlation between the mutation and the coexistence of antimicrobial resistance toward current treatment.},
}

@article {pmid37628823,
year = {2023},
author = {Li, H and Song, K and Zhang, X and Wang, D and Dong, S and Liu, Y and Yang, L},
title = {Application of Multi-Perspectives in Tea Breeding and the Main Directions.},
journal = {International journal of molecular sciences},
volume = {24},
number = {16},
pages = {},
doi = {10.3390/ijms241612643},
pmid = {37628823},
issn = {1422-0067},
support = {SDAIT-25-01//The Foundation of Innovation Team Project for Modern Agricultural Industrious Technology System of Shandong Province/ ; YDZX2022123//Special Funds for Local Scientific and Technological Development Guided by the Central Government/ ; },
abstract = {Tea plants are an economically important crop and conducting research on tea breeding contributes to enhancing the yield and quality of tea leaves as well as breeding traits that satisfy the requirements of the public. This study reviews the current status of tea plants germplasm resources and their utilization, which has provided genetic material for the application of multi-omics, including genomics and transcriptomics in breeding. Various molecular markers for breeding were designed based on multi-omics, and available approaches in the direction of high yield, quality and resistance in tea plants breeding are proposed. Additionally, future breeding of tea plants based on single-cellomics, pangenomics, plant-microbe interactions and epigenetics are proposed and provided as references. This study aims to provide inspiration and guidance for advancing the development of genetic breeding in tea plants, as well as providing implications for breeding research in other crops.},
}

@article {pmid37623951,
year = {2023},
author = {Pitta, JLLP and Bezerra, MF and Fernandes, DLRDS and Block, T and Novaes, AS and Almeida, AMP and Rezende, AM},
title = {Genomic Analysis of Yersinia pestis Strains from Brazil: Search for Virulence Factors and Association with Epidemiological Data.},
journal = {Pathogens (Basel, Switzerland)},
volume = {12},
number = {8},
pages = {},
doi = {10.3390/pathogens12080991},
pmid = {37623951},
issn = {2076-0817},
abstract = {Yersinia pestis, the etiological agent of the plague, is considered a genetically homogeneous species. Brazil is currently in a period of epidemiological silence but plague antibodies are still detected in sentinel animals, suggesting disease activity in the sylvatic cycle. The present study deployed an in silico approach to analyze virulence factors among 407 Brazilian genomes of Y. pestis belonging to the Fiocruz Collection (1966-1997). The pangenome analysis associated several known virulence factors of Y. pestis in clades according to the presence or absence of genes. Four main strain clades (C, E, G, and H) exhibited the absence of various virulence genes. Notably, clade G displayed the highest number of absent genes, while clade E showed a significant absence of genes related to the T6SS secretion system and clade H predominantly demonstrated the absence of plasmid-related genes. These results suggest attenuation of virulence in these strains over time. The cgMLST analysis associated genomic and epidemiological data highlighting evolutionary patterns related to the isolation years and outbreaks of Y. pestis in Brazil. Thus, the results contribute to the understanding of the genetic diversity and virulence within Y. pestis and the potential for utilizing genomic data in epidemiological investigations.},
}

@article {pmid37620118,
year = {2023},
author = {Horsfield, ST and Tonkin-Hill, G and Croucher, NJ and Lees, JA},
title = {Accurate and fast graph-based pangenome annotation and clustering with ggCaller.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.277733.123},
pmid = {37620118},
issn = {1549-5469},
abstract = {Bacterial genomes differ in both gene content and sequence mutations, which underlies extensive phenotypic diversity, including variation in susceptibility to antimicrobials or vaccine-induced immunity. To identify and quantify important variants, all genes within a population must be predicted, functionally annotated and clustered, representing the pangenome. Despite the volume of genome data available, gene prediction and annotation are currently conducted in isolation on individual genomes, which is computationally inefficient and frequently inconsistent across genomes. Here, we introduce the open-source software graph-gene-caller (ggCaller). ggCaller combines gene prediction, functional annotation, and clustering into a single workflow using population-wide de Bruijn Graphs, removing redundancy in gene annotation, and resulting in more accurate gene predictions and orthologue clustering. We applied ggCaller to simulated and real-world bacterial datasets containing hundreds or thousands of genomes, comparing it to current state-of-the-art tools. ggCaller has considerable speed-ups with equivalent or greater accuracy, particularly with datasets containing complex sources of error, such as assembly contamination or fragmentation. ggCaller is also an important extension to bacterial genome-wide association studies, enabling querying of annotated graphs for functional analyses. We highlight this application by functionally annotating DNA sequences with significant associations to tetracycline and macrolide resistance in Streptococcus pneumoniae, identifying key resistance determinants that were missed when using only a single reference genome. ggCaller is a novel bacterial genome analysis tool with applications in bacterial evolution and epidemiology.},
}

@article {pmid37612339,
year = {2023},
author = {Jang, J and Jung, J and Lee, YH and Lee, S and Baik, M and Kim, H},
title = {Chromosome-level genome assembly of Korean native cattle and pangenome graph of 14 Bos taurus assemblies.},
journal = {Scientific data},
volume = {10},
number = {1},
pages = {560},
pmid = {37612339},
issn = {2052-4463},
support = {NRF-2021R1A2C2094111//National Research Foundation of Korea (NRF)/ ; },
abstract = {This study presents the first chromosome-level genome assembly of Hanwoo, an indigenous Korean breed of Bos taurus taurus. This is the first genome assembly of Asian taurus breed. Also, we constructed a pangenome graph of 14 B. taurus genome assemblies. The contig N50 was over 55 Mb, the scaffold N50 was over 89 Mb and a genome completeness of 95.8%, as estimated by BUSCO using the mammalian set, indicated a high-quality assembly. 48.7% of the genome comprised various repetitive elements, including DNAs, tandem repeats, long interspersed nuclear elements, and simple repeats. A total of 27,314 protein-coding genes were identified, including 25,302 proteins with inferred gene names and 2,012 unknown proteins. The pangenome graph of 14 B. taurus autosomes revealed 528.47 Mb non-reference regions in total and 61.87 Mb Hanwoo-specific regions. Our Hanwoo assembly and pangenome graph provide valuable resources for studying B. taurus populations.},
}

@article {pmid37610465,
year = {2023},
author = {Szuhaj, M and Kakuk, B and Wirth, R and Rákhely, G and Kovács, KL and Bagi, Z},
title = {Regulation of the methanogenesis pathways by hydrogen at transcriptomic level in time.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {37610465},
issn = {1432-0614},
support = {2020-3.1.2-ZFR-KVG-2020-00009//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; K143198//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; FK123902//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; 2019-2.1.13-TÉT_IN-2020-00016//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; PD 132145//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; },
abstract = {The biomethane formation from 4 H2 + CO2 by pure cultures of two methanogens, Methanocaldococcus fervens and Methanobacterium thermophilum, has been studied. The goal of the study was to understand the regulation of the enzymatic steps associated with biomethane biosynthesis by H2, using metagenomic, pan-genomic, and transcriptomic approaches. Methanogenesis in the autotrophic methanogen M. fervens could be easily "switched off" and "switched on" by H2/CO2 within about an hour. In contrast, the heterotrophic methanogen M. thermophilum was practically insensitive to the addition of the H2/CO2 trigger although this methanogen also converted H2/CO2 to CH4. From practical points of view, the regulatory function of H2/CO2 suggests that in the power-to-gas (P2G) renewable excess electricity conversion and storage systems, the composition of the biomethane-generating methanogenic community is essential for sustainable operation. In addition to managing the specific hydrogenotrophic methanogenesis biochemistry, H2/CO2 affected several, apparently unrelated, metabolic pathways. The redox-regulated overall biochemistry and symbiotic relationships in the methanogenic communities should be explored in order to make the P2G technology more efficient. KEY POINTS : • Hydrogenotrophic methanogens may respond distinctly to H2/CO2 in bio-CH4 formation. • H2/CO2 can also activate metabolic routes, which are apparently unrelated to methanogenesis. • Sustainable conversion of the fluctuating renewable electricity to bio-CH4 is an option.},
}

@article {pmid37608158,
year = {2023},
author = {Guo, Y},
title = {Pangenome and the diversity of potato species.},
journal = {Nature food},
volume = {4},
number = {8},
pages = {638},
doi = {10.1038/s43016-023-00830-w},
pmid = {37608158},
issn = {2662-1355},
}

@article {pmid37599459,
year = {2023},
author = {Alsaiari, AA and Hakami, MA and Alotaibi, BS and Alkhalil, SS and Alkhorayef, N and Khan, K and Jalal, K},
title = {Delineating multi-epitopes vaccine designing from membrane protein CL5 against all monkeypox strains: a pangenome reverse vaccinology approach.},
journal = {Journal of biomolecular structure & dynamics},
volume = {},
number = {},
pages = {1-22},
doi = {10.1080/07391102.2023.2248301},
pmid = {37599459},
issn = {1538-0254},
abstract = {The recently identified monkeypox virus (MPXV or mpox) is a zoonotic orthopox virus that infects humans and causes diseases with traits like smallpox. The world health organization (WHO) estimates that 3-6% of MPXV cases result in death. As it might impact everyone globally, like COVID, and become the next pandemic, the cure for this disease is important for global public health. The high incidence and disease ratio of MPXV necessitates immediate efforts to design a unique vaccine candidate capable of addressing MPXV diseases. Here, we used a computational pan-genome-based vaccine design strategy for all currently reported 19 MPXV strains acquired from different regions of the world. Thus, this study's objective was to develop a new and safe vaccine candidate against MPXV by targeting the membrane CL5 protein; identified after the pangenome analysis. Proteomics and reverse vaccinology have covered up all of the MPXV epitopes that would usually stimulate robust host immune responses. Following this, only two mapped (MHC-I, MHC-II, and B-cell) epitopes were observed to be extremely effective that can be used in the construction of CL5 protein vaccine candidates. The suggested vaccine (V5) candidate from eight vaccine models was shown to be antigenic, non-allergenic, and stable (with 213 amino acids). The vaccine's candidate efficacy was evaluated by using many in silico methods to predict, improve, and validate its 3D structure. Molecular docking and molecular dynamics simulations further reveal that the proposed vaccine candidate ensemble has a high interaction energy with the HLAs and TRL2/4 immunological receptors under study. Later, the vaccine sequence was used to generate an expression vector for the E. coli K12 strain. Further study uncovers that V5 was highly immunogenic because it produced robust primary, secondary, and tertiary immune responses. Eventually, the use of computer-aided vaccine designing may significantly reduce costs and speed up the process of developing vaccines. Although, the results of this research are promising, however, more research (experimental; in vivo, and in vitro studies) is needed to verify the biological efficacy of the proposed vaccine against MPXV.Communicated by Ramaswamy H. Sarma.},
}

@article {pmid37596715,
year = {2023},
author = {Sun, Y and Zheng, C and Zhou, J and Zhen, M and Wei, X and Yan, X and Guo, X and Zheng, L and Shao, M and Li, C and Qin, D and Zhang, J and Xiong, L and Xing, J and Huang, B and Dong, Z and Cheng, P and Yu, G},
title = {Pathogen Profile of Klebsiella variicola, the Causative Agent of Banana Sheath Rot.},
journal = {Plant disease},
volume = {},
number = {},
pages = {PDIS09222018RE},
doi = {10.1094/PDIS-09-22-2018-RE},
pmid = {37596715},
issn = {0191-2917},
abstract = {Banana (Musa spp.) is an important fruit and food crop worldwide. In recent years, banana sheath rot has become a major problem in banana cultivation, causing plant death and substantial economic losses. Nevertheless, the pathogen profile of this disease has not been fully characterized. Klebsiella variicola is a versatile bacterium capable of colonizing different hosts, such as plants, humans, insects, and animals, and is recognized as an emerging pathogen in various hosts. In this study, we obtained 12 bacterial isolates from 12 different banana samples showing banana sheath rot in Guangdong and Guangxi Provinces, China. Phylogenetic analysis based on 16S rRNA sequences confirmed that all 12 isolates were K. variicola strains. We sequenced the genomes of these strains, performed comparative genomic analysis with other sequenced K. variicola strains, and found a lack of consistency in accessory gene content among these K. variicola strains. However, prediction based on the pan-genome of K. variicola revealed 22 unique virulence factors carried by the 12 pathogenic K. variicola isolates. Microbiome and microbial interaction network analysis of endophytes between the healthy tissues of diseased plants and healthy plants of two cultivars showed that Methanobacterium negatively interacts with Klebsiella in banana plants and that Herbaspirillum might indirectly inhibit Methanobacterium to promote Klebsiella growth. These results suggest that banana sheath rot is caused by the imbalance of plant endophytes and opportunistic pathogenic bacteria, providing an important basis for research and control of this disease.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.},
}

@article {pmid37596178,
year = {2023},
author = {Mertz, P and Hentgen, V and Boursier, G and Delon, J and Georgin-Lavialle, S},
title = {[Monogenic auto-inflammatory diseases associated with actinopathies: A review of the literature].},
journal = {La Revue de medecine interne},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.revmed.2023.06.005},
pmid = {37596178},
issn = {1768-3122},
abstract = {Auto-inflammatory diseases (AIDs) are diseases resulting from an inappropriate activation of innate immunity in the absence of any infection. The field of monogenic AIDs is constantly expanding, with the discovery of new pathologies and pathophysiological mechanisms thanks to pangenomic sequencing. Actinopathies with auto-inflammatory manifestations are a new emerging group of AIDs, linked to defects in the regulation of the actin cytoskeleton dynamics. These diseases most often begin in the neonatal period and combine to varying degrees a more or less severe primary immune deficiency, cytopenias (especially thrombocytopenia), auto-inflammatory manifestations (especially cutaneous and digestive), atopic and auto-immune manifestations. The diagnosis is to be evoked essentially in front of a cutaneous-digestive auto-inflammation picture of early onset, associated with a primary immune deficiency and thrombocytopenia or a tendency to bleed. Some of these diseases have specificities, including a risk of macrophagic activation syndrome or a tendency to atopy or lymphoproliferation. We propose here a review of the literature on these new diseases, with a proposal for a practical approach according to the main associated biological abnormalities and some clinical particularities. However, the diagnosis remains genetic, and several differential diagnoses must be considered. The pathophysiology of these diseases is not yet fully elucidated, and studies are needed to better clarify the inherent mechanisms that can guide the choice of therapies. In most cases, the severity of the picture indicates allogeneic marrow transplantation.},
}

@article {pmid37594286,
year = {2023},
author = {Kim, M and Cha, IT and Lee, KE and Li, M and Park, SJ},
title = {Pangenome analysis provides insights into the genetic diversity, metabolic versatility, and evolution of the genus Flavobacterium.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0100323},
doi = {10.1128/spectrum.01003-23},
pmid = {37594286},
issn = {2165-0497},
abstract = {Members of the genus Flavobacterium are widely distributed and produce various polysaccharide-degrading enzymes. Many species in the genus have been isolated and characterized. However, few studies have focused on marine isolates or fish pathogens, and in-depth genomic analyses, particularly comparative analyses of isolates from different habitat types, are lacking. Here, we isolated 20 strains of the genus from various environments in South Korea and sequenced their full-length genomes. Combined with published sequence data, we examined genomic traits, evolution, environmental adaptation, and putative metabolic functions in total 187 genomes of isolated species in Flavobacterium categorized as marine, host-associated, and terrestrial including freshwater. A pangenome analysis revealed a correlation between genome size and coding or noncoding density. Flavobacterium spp. had high levels of diversity, allowing for novel gene repertories via recombination events. Defense-related genes only accounted for approximately 3% of predicted genes in all Flavobacterium genomes. While genes involved in metabolic pathways did not differ with respect to isolation source, there was substantial variation in genomic traits; in particular, the abundances of tRNAs and rRNAs were higher in the host-associdated group than in other groups. One genome in the host-associated group contained a Microviridae prophage closely related to an enterobacteria phage. The proteorhodopsin gene was only identified in four terrestrial strains isolated for this study. Furthermore, recombination events clearly influenced genomic diversity and may contribute to the response to environmental stress. These findings shed light on the high genetic variation in Flavobacterium and functional roles in diverse ecosystems as a result of their metabolic versatility. IMPORTANCE The genus Flavobacterium is a diverse group of bacteria that are found in a variety of environments. While most species of this genus are harmless and utilize organic substrates such as proteins and polysaccharides, some members may play a significant role in the cycling for organic substances within their environments. Nevertheless, little is known about the genomic dynamics and/or metabolic capacity of Flavobacterium. Here, we found that Flavobacterium species may have an open pangenome, containing a variety of diverse and novel gene repertoires. Intriguingly, we discovered that one genome (classified into host-associated group) contained a Microviridae prophage closely related to that of enterobacteria. Proteorhodopsin may be expressed under conditions of light or oxygen pressure in some strains isolated for this study. Our findings significantly contribute to the understanding of the members of the genus Flavobacterium diversity exploration and will provide a framework for the way for future ecological characterizations.},
}

@article {pmid37592233,
year = {2023},
author = {Zhang, X and Xiao, L and Liu, J and Tian, Q and Xie, J},
title = {Trade-off in genome turnover events leading to adaptive evolution of Microcystis aeruginosa species complex.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {462},
pmid = {37592233},
issn = {1471-2164},
support = {32101368//National Natural Science Foundation of China/ ; 2022YFE0119600//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Numerous studies in the past have expanded our understanding of the genetic differences of global distributed cyanobacteria that originated around billions of years ago, however, unraveling how gene gain and loss drive the genetic evolution of cyanobacterial species, and the trade-off of these evolutionary forces are still the central but poorly understood issues.

RESULTS: To delineate the contribution of gene flow in mediating the hereditary differentiation and shaping the microbial evolution, a global genome-wide study of bloom-forming cyanobacterium, Microcystis aeruginosa species complex, provided robust evidence for genetic diversity, reflected by enormous variation in gene repertoire among various strains. Mathematical extrapolation showed an 'open' microbial pan-genome of M. aeruginosa species, since novel genes were predicted to be introduced after new genomes were sequenced. Identification of numerous horizontal gene transfer's signatures in genome regions of interest suggested that genome expansion via transformation and phage-mediated transduction across bacterial lineage as an evolutionary route may contribute to the differentiation of Microcystis functions (e.g., carbohydrate metabolism, amino acid metabolism, and energy metabolism). Meanwhile, the selective loss of some dispensable genes at the cost of metabolic versatility is as a mean of adaptive evolution that has the potential to increase the biological fitness.

CONCLUSIONS: Now that the recruitment of novel genes was accompanied by a parallel loss of some other ones, a trade-off in gene content may drive the divergent differentiation of M. aeruginosa genomes. Our study provides a genetic framework for the evolution of M. aeruginosa species and illustrates their possible evolutionary patterns.},
}

@article {pmid37587248,
year = {2023},
author = {Pei, Z and Li, X and Cui, S and Yang, B and Lu, W and Zhao, J and Mao, B and Chen, W},
title = {Population genomics of Lacticaseibacillus paracasei: pan-genome, integrated prophage, antibiotic resistance, and carbohydrate utilization.},
journal = {World journal of microbiology & biotechnology},
volume = {39},
number = {10},
pages = {280},
pmid = {37587248},
issn = {1573-0972},
support = {32172173//National Natural Science Foundation of China/ ; 31972086//National Natural Science Foundation of China/ ; 2021YFD2100700//Key Technologies Research and Development Program/ ; },
abstract = {Lacticaseibacillus paracasei has beneficial effects on human health and holds promising potential as a probiotic for use in the development of functional foods, especially dairy products. This species can adapt to a variety of ecological niches and presents fundamental carbohydrate metabolism and tolerance to environmental stresses. However, the population structure, ecology, and antibiotic resistance of Lc. paracasei in diverse ecological niches are poorly understood. Reclassification of Lc. paracasei as a separate species of Lacticaseibacillus has stimulated renewed interest in its research, and a deeper interpretation of it will be important for screening strains beneficial to human health. Here, we collected 121 self-isolated and 268 publicly available Lc. paracasei genomes discussed how genomic approaches have advanced our understanding of its taxonomy, ecology, evolution, diversity, integrated prophage-related element distribution, antibiotic resistance, and carbohydrate utilization. Moreover, for the Lc. paracasei strains isolated in this study, we assessed the inducibility of integrated prophages in their genomes and determined the phenotypes that presented tolerance to multiple antibiotics to provide evidence for safety evaluations of Lc. paracasei during the fermentation processes.},
}

@article {pmid37580659,
year = {2023},
author = {Ma, C and Li, M and Peng, H and Lan, M and Tao, L and Li, C and Wu, C and Bai, H and Zhong, Y and Zhong, S and Qin, R and Li, F and Li, J and He, J},
title = {Mesomycoplasma ovipneumoniae from goats with respiratory infection: pathogenic characteristics, population structure, and genomic features.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {220},
pmid = {37580659},
issn = {1471-2180},
support = {AB16380106//Guangxi key research and development plan/ ; 19-50-40-A-04//Guangxi Key Laboratory of Veterinary Biotechnology Independent Research Topic/ ; },
abstract = {BACKGROUND: Mycoplasma ovipneumoniae is a critical pathogen that causes respiratory diseases that threaten Caprini health and cause economic damage. A genome-wide study of M. ovipneumoniae will help understand the pathogenic characteristics of this microorganism.

RESULTS: Toxicological pathology and whole-genome sequencing of nine M. ovipneumoniae strains isolated from goats were performed using an epidemiological survey. These strains exhibited anterior ventral lung consolidation, typical of bronchopneumonia in goats. Average nucleotide identity and phylogenetic analysis based on whole-genome sequences showed that all M. ovipneumoniae strains clustered into two clades, largely in accordance with their geographical origins. The pan-genome of the 23 M. ovipneumoniae strains contained 5,596 genes, including 385 core, 210 soft core, and 5,001 accessory genes. Among these genes, two protein-coding genes were annotated as cilium adhesion and eight as paralog surface adhesins when annotated to VFDB, and no antibiotic resistance-related genes were predicted. Additionally, 23 strains carried glucosidase-related genes (ycjT and group_1595) and glucosidase-related genes (atpD_2), indicating that M. ovipneumoniae possesses a wide range of glycoside hydrolase activities.

CONCLUSIONS: The population structure and genomic features identified in this study will facilitate further investigations into the pathogenesis of M. ovipneumoniae and lay the foundation for the development of preventive and therapeutic methods.},
}

@article {pmid37580306,
year = {2023},
author = {Alexandrov, N and Wang, T and Blair, L and Nadon, B and Sayer, D},
title = {HLA-OLI: A new MHC class I pseudogene and HLA-Y are located on a 60 kb indel in the human MHC between HLA-W and HLA-J.},
journal = {HLA},
volume = {},
number = {},
pages = {},
doi = {10.1111/tan.15180},
pmid = {37580306},
issn = {2059-2310},
abstract = {Analysis of publicly available whole-genome sequence data from the Human Pangenome Project and the 1000 Genomes Project has identified a DNA segment of approximately 60 kb in the major histocompatibility complex (MHC) between HLA-W and HLA-J that is present in some MHC haplotypes but not others. This DNA segment is largely repeat element-rich but includes the pseudogene HLA-Y, thus pinpointing the location of this pseudogene, and a new HLA class I sequence we have called HLA-OLI. HLA-OLI clusters phylogenetically with the HLA class I pseudogenes, HLA-P and HLA-W, and appears to have a similar genetic structure. The availability of whole-genome sequence data from diverse populations enables a detailed characterization of the MHC at the population level and will have implications for understanding MHC disease associations and the non-HLA MHC factors that impact unrelated hematopoietic cell transplant outcomes.},
}

@article {pmid37578072,
year = {2023},
author = {Khan, K and Burki, S and Alsaiari, AA and Alhuthali, HM and Alharthi, NS and Jalal, K},
title = {A therapeutic epitopes-based vaccine engineering against Salmonella enterica XDR strains for typhoid fever: a Pan-vaccinomics approach.},
journal = {Journal of biomolecular structure & dynamics},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/07391102.2023.2246587},
pmid = {37578072},
issn = {1538-0254},
abstract = {A prevalent food-borne pathogen, Salmonella enterica serotypes Typhi, is responsible for gastrointestinal and systemic infections globally. Salmonella vaccines are the most effective, however, producing a broad-spectrum vaccine remains challenging due to Salmonella's many serotypes. Efforts are urgently required to develop a novel vaccine candidate that can tackle all S. Typhi strains because of their high resistance to multiple kinds of antibiotics (particularly the XDR H58 strain). In this work, we used a computational pangenome-based vaccine design technique on all available (n = 119) S. Typhi reference genomes and identified one TonB-dependent siderophore receptor (WP_001034967.1) as highly conserved and prospective vaccine candidates from the predicted core genome (n = 3,351). The applied pan-proteomics and Immunoinformatic approaches help in the identification of four epitopes that may trigger adequate host body immune responses. Furthermore, the proposed vaccine ensemble demonstrates a stable binding conformation with the examined immunological receptor (HLAs and TRL2/4) and has large interaction energy determined via molecular docking and molecular dynamics simulation techniques. Eventually, an expression vector for the Escherichia. coli K12 strain was constructed from the vaccine sequence. Additional analysis revealed that the vaccine may help to elicit strong immune responses for typhoid infections, however, experimental analysis is required to verify the vaccine's effectiveness based on these results. Moreover, the applied computer-assisted vaccine design may considerably decrease vaccine development costs and speed up the process. The study's findings are intriguing, but they must be evaluated in the experimental labs to confirm the developed vaccine's biological efficiency against XDR S. Typhi.Communicated by Ramaswamy H. Sarma.},
}

@article {pmid37577683,
year = {2023},
author = {Yocca, AE and Platts, A and Alger, E and Teresi, S and Mengist, MF and Benevenuto, J and Felipe V Ferrão, L and Jacobs, M and Babinski, M and Magallanes-Lundback, M and Bayer, P and Golicz, A and Humann, JL and Main, D and Espley, RV and Chagné, D and Albert, NW and Montanari, S and Vorsa, N and Polashock, J and Díaz-Garcia, L and Zalapa, J and Bassil, NV and Munoz, PR and Iorizzo, M and Edger, PP},
title = {Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.07.31.551392},
pmid = {37577683},
abstract = {Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry continues to face a wide variety of production challenges (e.g. disease pressures) as well as a demand for higher-yielding cultivars with improved fruit quality characteristics. Unfortunately, molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops. Here, we describe the construction and analysis of the first pangenome for both blueberry and cranberry. Our analysis of these pangenomes revealed both crops exhibit great genetic diversity, including the presence-absence variation of 48.4% genes in highbush blueberry and 47.0% genes in cranberry. Auxiliary genes, those not shared by all cultivars, are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites, including compounds previously associated with improving fruit quality traits. The discovery of thousands of genes, not present in the previous reference genomes for blueberry and cranberry, will serve as the basis of future research and as potential targets for future breeding efforts. The pangenome, as a multiple-sequence alignment, as well as individual annotated genomes, are publicly available for analysis on the Genome Database for Vaccinium - a curated and integrated web-based relational database. Lastly, the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.},
}

@article {pmid37576785,
year = {2023},
author = {Qiu, J and Shi, Y and Zhao, F and Xu, Y and Xu, H and Dai, Y and Cao, Y},
title = {The Pan-Genomic Analysis of Corynebacterium striatum Revealed its Genetic Characteristics as an Emerging Multidrug-Resistant Pathogen.},
journal = {Evolutionary bioinformatics online},
volume = {19},
number = {},
pages = {11769343231191481},
pmid = {37576785},
issn = {1176-9343},
abstract = {Corynebacterium striatum is a Gram-positive bacterium that is straight or slightly curved and non-spore-forming. Although it was originally believed to be a part of the normal microbiome of human skin, a growing number of studies have identified it as a cause of various chronic diseases, bacteremia, and respiratory infections. However, despite its increasing importance as a pathogen, the genetic characteristics of the pathogen population, such as genomic characteristics and differences, the types of resistance genes and virulence factors carried by the pathogen and their distribution in the population are poorly understood. To address these knowledge gaps, we conducted a pan-genomic analysis of 314 strains of C. striatum isolated from various tissues and geographic locations. Our analysis revealed that C. striatum has an open pan-genome, comprising 5692 gene families, including 1845 core gene families, 2362 accessory gene families, and 1485 unique gene families. We also found that C. striatum exhibits a high degree of diversity across different sources, but strains isolated from skin tissue are more conserved. Furthermore, we identified 53 drug resistance genes and 42 virulence factors by comparing the strains to the drug resistance gene database (CARD) and the pathogen virulence factor database (VFDB), respectively. We found that these genes and factors are widely distributed among C. striatum, with 77.7% of strains carrying 2 or more resistance genes and displaying primary resistance to aminoglycosides, tetracyclines, lincomycin, macrolides, and streptomycin. The virulence factors are primarily associated with pathogen survival within the host, iron uptake, pili, and early biofilm formation. In summary, our study provides insights into the population diversity, resistance genes, and virulence factors ofC. striatum from different sources. Our findings could inform future research and clinical practices in the diagnosis, prevention, and treatment of C. striatum-associated diseases.},
}

@article {pmid37576287,
year = {2023},
author = {Liu, L and Yu, W and Cai, K and Ma, S and Wang, Y and Ma, Y and Zhao, H},
title = {Identification of vaccine candidates against rhodococcus equi by combining pangenome analysis with a reverse vaccinology approach.},
journal = {Heliyon},
volume = {9},
number = {8},
pages = {e18623},
pmid = {37576287},
issn = {2405-8440},
abstract = {Rhodococcus equi (R. equi) is a zoonotic opportunistic pathogen that can cause life-threatening infections. The rapid evolution of multidrug-resistant R. equi and the fact that there is no currently licensed effective vaccine against R. equi warrant the need for vaccine development. Reverse vaccinology (RV), which involves screening a pathogen's entire genome and proteome using various web-based prediction tools, is considered one of the most effective approaches for identifying vaccine candidates. Here, we performed a pangenome analysis to determine the core proteins of R. equi. We then used the RV approach to examine the subcellular localization, host and gut flora homology, antigenicity, transmembrane helices, physicochemical properties, and immunogenicity of the core proteins to select potential vaccine candidates. The vaccine candidates were then subjected to epitope mapping to predict the exposed antigenic epitopes that possess the ability to bind with major histocompatibility complex I/II (MHC I/II) molecules. These vaccine candidates and epitopes will form a library of elements for the development of a polyvalent or universal vaccine against R. equi. Sixteen R. equi complete proteomes were found to contain 6,238 protein families, and the core proteins consisted of 3,969 protein families (∼63.63% of the pangenome), reflecting a low degree of intraspecies genomic variability. From the pool of core proteins, 483 nonhost homologous membrane and extracellular proteins were screened, and 12 vaccine candidates were finally identified according to their antigenicity, physicochemical properties and other factors. These included four cell wall/membrane/envelope biogenesis proteins; four amino acid transport and metabolism proteins; one cell cycle control, cell division and chromosome partitioning protein; one carbohydrate transport and metabolism protein; one secondary metabolite biosynthesis, transport and catabolism protein; and one defense mechanism protein. All 12 vaccine candidates have an experimentally validated 3D structure available in the protein data bank (PDB). Epitope mapping of the candidates showed that 16 MHC I epitopes and 13 MHC II epitopes with the strongest immunogenicity were exposed on the protein surface, indicating that they could be used to develop a polypeptide vaccine. Thus, we utilized an analytical strategy that combines pangenome analysis and RV to generate a peptide antigen library that simplifies the development of multivalent or universal vaccines against R. equi and can be applied to the development of other vaccines.},
}

@article {pmid37575187,
year = {2023},
author = {Chao, KH and Chen, PW and Seshia, SA and Langmead, B},
title = {WGT: Tools and algorithms for recognizing, visualizing, and generating Wheeler graphs.},
journal = {iScience},
volume = {26},
number = {8},
pages = {107402},
pmid = {37575187},
issn = {2589-0042},
abstract = {A Wheeler graph represents a collection of strings in a way that is particularly easy to index and query. Such a graph is a practical choice for representing a graph-shaped pangenome, and it is the foundation for current graph-based pangenome indexes. However, there are no practical tools to visualize or to check graphs that may have the Wheeler properties. Here, we present Wheelie, an algorithm that combines a renaming heuristic with a permutation solver (Wheelie-PR) or a Satisfiability Modulo Theory (SMT) solver (Wheelie-SMT) to check whether a given graph has the Wheeler properties, a problem that is NP-complete in general. Wheelie can check a variety of random and real-world graphs in far less time than any algorithm proposed to date. It can check a graph with 1,000s of nodes in seconds. We implement these algorithms together with complementary visualization tools in the WGT toolkit, available as open source software at https://github.com/Kuanhao-Chao/Wheeler_Graph_Toolkit.},
}

@article {pmid37573136,
year = {2023},
author = {Kokate, PP and Bales, E and Joyner, D and Hazen, TC and Techtmann, SM},
title = {Biogeographic patterns in populations of marine pseudoalteromonas atlantica isolates.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnad081},
pmid = {37573136},
issn = {1574-6968},
abstract = {Intra-specific genomic diversity is well documented in microbes. The question, however, remains whether natural selection or neutral evolution is the major contributor to this diversity. We undertook this study to estimate genomic diversity in Pseudoalteromonas atlantica populations and whether the diversity, if present, could be attributed to environmental factors or distance effects. We isolated and sequenced twenty-three strains of P. atlantica from three geographically distant deep marine basins and performed comparative genomic analyses to study the genomic diversity of populations among these basins. Average nucleotide identity followed a strictly geographical pattern. In two out of three locations, the strains within the location exhibited > 99.5% identity, whereas, among locations, the strains showed < 98.11% identity. Phylogenetic and pangenome analysis also reflected the biogeographical separation of the strains. Strains from the same location shared many accessory genes and clustered closely on the phylogenetic tree. Phenotypic diversity between populations was studied in ten out of twenty-three strains testing carbon and nitrogen source utilization, and osmotolerance. A genetic basis for phenotypic diversity could be established in most cases but was apparently not influenced by local environmental conditions. Our study suggests that neutral evolution may have a substantial role in the biodiversity of P. atlantica.},
}

@article {pmid37571822,
year = {2023},
author = {Raza, A and Bohra, A and Garg, V and Varshney, RK},
title = {Back to wild relatives for future breeding through super-pangenome.},
journal = {Molecular plant},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molp.2023.08.005},
pmid = {37571822},
issn = {1752-9867},
}

@article {pmid37567624,
year = {2023},
author = {Rajput, A and Chauhan, SM and Mohite, OS and Hyun, JC and Ardalani, O and Jahn, LJ and Sommer, MO and Palsson, BO},
title = {Pangenome analysis reveals the genetic basis for taxonomic classification of the Lactobacillaceae family.},
journal = {Food microbiology},
volume = {115},
number = {},
pages = {104334},
doi = {10.1016/j.fm.2023.104334},
pmid = {37567624},
issn = {1095-9998},
abstract = {Lactobacillaceae represent a large family of important microbes that are foundational to the food industry. Many genome sequences of Lactobacillaceae strains are now available, enabling us to conduct a comprehensive pangenome analysis of this family. We collected 3591 high-quality genomes from public sources and found that: 1) they contained enough genomes for 26 species to perform a pangenomic analysis, 2) the normalized Heap's coefficient λ (a measure of pangenome openness) was found to have an average value of 0.27 (ranging from 0.07 to 0.37), 3) the pangenome openness was correlated with the abundance and genomic location of transposons and mobilomes, 4) the pangenome for each species was divided into core, accessory, and rare genomes, that highlight the species-specific properties (such as motility and restriction-modification systems), 5) the pangenome of Lactiplantibacillus plantarum (which contained the highest number of genomes found amongst the 26 species studied) contained nine distinct phylogroups, and 6) genome mining revealed a richness of detected biosynthetic gene clusters, with functions ranging from antimicrobial and probiotic to food preservation, but ∼93% were of unknown function. This study provides the first in-depth comparative pangenomics analysis of the Lactobacillaceae family.},
}

@article {pmid37556679,
year = {2023},
author = {Hill, H and Mitsi, E and Nikolaou, E and Blizard, A and Pojar, S and Howard, A and Hyder-Wright, A and Devin, J and Reiné, J and Robinson, R and Solórzano, C and Jochems, SP and Kenny-Nyazika, T and Ramos-Sevillano, E and Weight, CM and Myerscough, C and McLenaghan, D and Morton, B and Gibbons, E and Farrar, M and Randles, V and Burhan, H and Chen, T and Shandling, AD and Campo, JJ and Heyderman, RS and Gordon, SB and Brown, JS and Collins, AM and Ferreira, DM},
title = {A Randomised Controlled Trial of Nasal Immunisation with Live Virulence Attenuated Streptococcus pneumoniae Strains Using Human Infection Challenge.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1164/rccm.202302-0222OC},
pmid = {37556679},
issn = {1535-4970},
abstract = {RATIONALE: Pneumococcal pneumonia remains a global health problem. Pneumococcal colonisation increases local and systemic protective immunity, suggesting nasal administration of live attenuated S. pneumoniae strains could help prevent infections.

OBJECTIVES: We used a controlled human infection model to investigate whether nasopharyngeal colonisation with attenuated S. pneumoniae strains protected against re-colonisation with wild-type (WT) S. pneumoniae (Spn).

METHODS: Healthy adults aged 18-50 years were randomised (1:1:1:1) for nasal administration twice (two weeks interval) with saline, WT Spn6B (BHN418) or one of two genetically modified Spn6B strains - SpnA1 (∆fhs/piaA) or SpnA3 (∆proABC/piaA) (Stage I). After 6 months, participants were challenged with SpnWT to assess protection against the homologous serotype (Stage II).

MEASUREMENTS AND MAIN RESULTS: 125 participants completed both study stages as per intention to treat. No Serious Adverse Events were reported. In Stage I, colonisation rates were similar amongst groups: SpnWT 58.1% (18/31), SpnA1 60% (18/30) and SpnA3 59.4% (19/32). Anti-Spn nasal IgG levels post-colonisation were similar in all groups whilst serum IgG responses were higher in the SpnWT and SpnA1 groups than the SpnA3 group. In colonised individuals, increases in IgG responses were identified against 197 Spn protein antigens and serotype 6 capsular polysaccharide using a pangenome array. Participants given SpnWT or SpnA1 in stage 1 were partially protected against homologous challenge with SpnWT (29% and 30% recolonisation rates, respectively) at stage II, whereas those exposed to SpnA3 achieved recolonisation rate similar to control group group (50% vs 47%, respectively).

CONCLUSION: Nasal colonisation with genetically modified live attenuated Spn was safe and induced protection against recolonisation, suggesting nasal adminstration of live attenuated Spn could be an effective stategy for preventing pneumococcal infections.},
}

@article {pmid37555725,
year = {2023},
author = {Wei, F and Liang, X and Shi, JC and Luo, J and Qiu, LJ and Li, XX and Lu, LJ and Wen, Y and Feng, J},
title = {Pan-genomic Analysis Identifies the Chinese Strain as a New Subspecies of Xanthomonas fragariae.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-05-23-0933-SC},
pmid = {37555725},
issn = {0191-2917},
abstract = {Xanthomonas fragariae (X. fragariae) is classified as a quarantine pathogen by the European and Mediterranean Plant Protection Organization. It commonly induces typical angular leaf spot (ALS) symptoms in strawberry leaves. X. fragariae strains from China (YL19, SHAQP01, and YLX21) exhibit ALS symptoms in leaves and more severe symptoms of dry cavity rot in strawberry crowns. Conversely, strains from other countries do not cause severe dry cavity rot symptoms in strawberries. Employing multilocus sequence analysis (MLSA), average nucleotide identity (ANI), and amino acid identity (AAI), we determined that Chinese strains of X. fragariae are genetically distinct from other strains and can be considered a new subspecies. Subsequent analysis of 63 X. fragariae genomes published at NCBI using IPGA and EDGAR3.0 revealed the pan-genomic profile, with 1680 shared genes present in the all 63 strains, including 71 virulence-related genes. Additionally, we identified 123 genes exclusive to the of all Chinese strains, encompassing 12 virulence-related genes. The qRT-PCR analysis demonstrated that the expression of XopD, XopG1, CE8, GT2 and GH121, out of 12 virulence-related genes of Chinese strains (YL19) exhibited a constant increase in the early stages (6 hpi, 24 hpi, 54 hpi, and 96 hpi) of strawberry leaf infected by YL19. Hence, the presence of XopD, XopG1, CE8, GT2, and GH121 in Chinese strains may play important roles in the early infection process of Chinese strains. These findings offer novel insights into comprehending the population structure and variation in the pathogenic capacity of X. fragariae.},
}

@article {pmid37553643,
year = {2023},
author = {Hyun, JC and Palsson, BO},
title = {Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {183},
pmid = {37553643},
issn = {1474-760X},
support = {T32GM8806/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: Cumulative sequencing efforts have yielded enough genomes to construct pangenomes for dozens of bacterial species and elucidate intraspecies gene conservation. Given the diversity of organisms for which this is achievable, similar analyses for ancestral species are feasible through the integration of pangenomics and phylogenetics, promising deeper insights into the nature of ancient life.

RESULTS: We construct pangenomes for 183 bacterial species from 54,085 genomes and identify their core genomes using a novel statistical model to estimate genome-specific error rates and underlying gene frequencies. The core genomes are then integrated into a phylogenetic tree to reconstruct the core genome of the last bacterial common ancestor (LBCA), yielding three main results: First, the gene content of modern and ancestral core genomes are diverse at the level of individual genes but are similarly distributed by functional category and share several poorly characterized genes. Second, the LBCA core genome is distinct from any individual modern core genome but has many fundamental biological systems intact, especially those involving translation machinery and biosynthetic pathways to all major nucleotides and amino acids. Third, despite this metabolic versatility, the LBCA core genome likely requires additional non-core genes for viability, based on comparisons with the minimal organism, JCVI-Syn3A.

CONCLUSIONS: These results suggest that many cellular systems commonly conserved in modern bacteria were not just present in ancient bacteria but were nearly immutable with respect to short-term intraspecies variation. Extending this analysis to other domains of life will likely provide similar insights into more distant ancestral species.},
}

@article {pmid37546276,
year = {2023},
author = {Gao, Z and Bian, J and Lu, F and Jiao, Y and He, H},
title = {Triticeae crop genome biology: an endless frontier.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1222681},
pmid = {37546276},
issn = {1664-462X},
abstract = {Triticeae, the wheatgrass tribe, includes several major cereal crops and their wild relatives. Major crops within the Triticeae are wheat, barley, rye, and oat, which are important for human consumption, animal feed, and rangeland protection. Species within this tribe are known for their large genomes and complex genetic histories. Powered by recent advances in sequencing technology, researchers worldwide have made progress in elucidating the genomes of Triticeae crops. In addition to assemblies of high-quality reference genomes, pan-genome studies have just started to capture the genomic diversities of these species, shedding light on our understanding of the genetic basis of domestication and environmental adaptation of Triticeae crops. In this review, we focus on recent signs of progress in genome sequencing, pan-genome analyses, and resequencing analysis of Triticeae crops. We also propose future research avenues in Triticeae crop genomes, including identifying genome structure variations, the association of genomic regions with desired traits, mining functions of the non-coding area, introgression of high-quality genes from wild Triticeae resources, genome editing, and integration of genomic resources.},
}

@article {pmid37542576,
year = {2023},
author = {Hong, H and Yang, SM and Kim, E and Kim, HJ and Park, SH},
title = {Comprehensive metagenomic analysis of stress-resistant and -sensitive Listeria monocytogenes.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {37542576},
issn = {1432-0614},
support = {E0210702-01//Korea Food Research Institute/ ; },
abstract = {Listeria monocytogenes is a pathogenic bacterium which can live in adverse environments (low pH, high salinity, and low temperature). Even though there are various whole genome sequencing (WGS) data on L. monocytogenes, investigations on genetic differences between stress-resistant and -sensitive L. monocytogenes grown under stress environments have been not fully examined. This study aims to investigate and compare genetic characteristics between stress-resistant and -sensitive L. monocytogenes using whole genome sequencing (WGS). A total of 47 L. monocytogenes strains (43 stress-resistant and 4 stress-sensitive) were selected based on the stress-resistance tests under pH 3, 5% salt concentration, and 1 °C. The sequencing library for WGS was prepared and sequenced using an Illumina MiSeq. Genetic characteristics of two different L. monocytogenes groups were examined to analyze the pangenome, functionality, virulence, antibiotic resistance, core, and unique genes. The functionality of unique genes in the stress-resistant L. monocytogenes was distinct compared to the stress-sensitive L. monocytogenes, such as carbohydrate and nucleotide transport and metabolism. The lisR virulence gene was detected more in the stress-resistant L. monocytogenes than in the stress-sensitive group. Five stress-resistant L. monocytogenes strains possessed tet(M) antibiotic resistance gene. This is the first study suggesting that deep genomic characteristics of L. monocytogenes may have different resistance level under stress conditions. This new insight will aid in understanding the genetic relationship between stress-resistant and -sensitive L. monocytogenes strains isolated from diverse resources. KEY POINTS: • Whole genomes of L. monocytogenes isolated from three different sources were analyzed. • Differences in two L. monocytogenes groups were identified in functionality, virulence, and antibiotic resistance genes. • This study first examines the association between resistances and whole genomes of stress-resistant and -sensitive L. monocytogenes.},
}

@article {pmid37538845,
year = {2023},
author = {Morales-Olavarría, M and Nuñez-Belmar, J and González, D and Vicencio, E and Rivas-Pardo, JA and Cortez, C and Cárdenas, JP},
title = {Phylogenomic analysis of the Porphyromonas gingivalis - Porphyromonas gulae duo: approaches to the origin of periodontitis.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1226166},
pmid = {37538845},
issn = {1664-302X},
abstract = {Porphyromonas gingivalis is an oral human pathogen associated with the onset and progression of periodontitis, a chronic immune-inflammatory disease characterized by the destruction of the teeth-supporting tissue. P. gingivalis belongs to the genus Porphyromonas, which is characterized by being composed of Gram-negative, asaccharolytic, non-spore-forming, non-motile, obligatory anaerobic species, inhabiting niches such as the oral cavity, urogenital tract, gastrointestinal tract and infected wound from different mammals including humans. Among the Porphyromonas genus, P. gingivalis stands out for its specificity in colonizing the human oral cavity and its keystone pathogen role in periodontitis pathogenesis. To understand the evolutionary process behind P. gingivalis in the context of the Pophyoromonas genus, in this study, we performed a comparative genomics study with publicly available Porphyromonas genomes, focused on four main objectives: (A) to confirm the phylogenetic position of P. gingivalis in the Porphyromonas genus by phylogenomic analysis; (B) the definition and comparison of the pangenomes of P. gingivalis and its relative P. gulae; and (C) the evaluation of the gene family gain/loss events during the divergence of P. gingivalis and P. gulae; (D) the evaluation of the evolutionary pressure (represented by the calculation of Tajima-D values and dN/dS ratios) comparing gene families of P. gingivalis and P. gulae. Our analysis found 84 high-quality assemblies representing P. gingivalis and 14 P. gulae strains (from a total of 233 Porphyromonas genomes). Phylogenomic analysis confirmed that P. gingivalis and P. gulae are highly related lineages, close to P. loveana. Both organisms harbored open pangenomes, with a strong core-to-accessory ratio for housekeeping genes and a negative ratio for unknown function genes. Our analyses also characterized the gene set differentiating P. gulae from P. gingivalis, mainly associated with unknown functions. Relevant virulence factors, such as the FimA, Mfa1, and the hemagglutinins, are conserved in P. gulae, P. gingivalis, and P. loveana, suggesting that the origin of those factors occurred previous to the P. gulae - P. gingivalis divergence. These results suggest an unexpected evolutionary relationship between the P. gulae - P. gingivalis duo and P. loveana, showing more clues about the origin of the role of those organisms in periodontitis.},
}

@article {pmid37537691,
year = {2023},
author = {Wu, D and Xie, L and Sun, Y and Huang, Y and Jia, L and Dong, C and Shen, E and Ye, CY and Qian, Q and Fan, L},
title = {A syntelog-based pan-genome provides insights into rice domestication and de-domestication.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {179},
pmid = {37537691},
issn = {1474-760X},
mesh = {*Oryza/genetics ; Domestication ; Genome, Plant ; Genes, Plant ; Genomics ; Evolution, Molecular ; },
abstract = {BACKGROUND: Asian rice is one of the world's most widely cultivated crops. Large-scale resequencing analyses have been undertaken to explore the domestication and de-domestication genomic history of Asian rice, but the evolution of rice is still under debate.

RESULTS: Here, we construct a syntelog-based rice pan-genome by integrating and merging 74 high-accuracy genomes based on long-read sequencing, encompassing all ecotypes and taxa of Oryza sativa and Oryza rufipogon. Analyses of syntelog groups illustrate subspecies divergence in gene presence-and-absence and haplotype composition and identify massive genomic regions putatively introgressed from ancient Geng/japonica to ancient Xian/indica or its wild ancestor, including almost all well-known domestication genes and a 4.5-Mbp centromere-spanning block, supporting a single domestication event in main rice subspecies. Genomic comparisons between weedy and cultivated rice highlight the contribution from wild introgression to the emergence of de-domestication syndromes in weedy rice.

CONCLUSIONS: This work highlights the significance of inter-taxa introgression in shaping diversification and divergence in rice evolution and provides an exploratory attempt by utilizing the advantages of pan-genomes in evolutionary studies.},
}

*Oryza/genetics
Domestication
Genome, Plant
Genes, Plant
Genomics
Evolution, Molecular

@article {pmid37531401,
year = {2023},
author = {Burgaya, J and Marin, J and Royer, G and Condamine, B and Gachet, B and Clermont, O and Jaureguy, F and Burdet, C and Lefort, A and de Lastours, V and Denamur, E and Galardini, M and Blanquart, F and , },
title = {The bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans.},
journal = {PLoS genetics},
volume = {19},
number = {8},
pages = {e1010842},
pmid = {37531401},
issn = {1553-7404},
mesh = {Humans ; Escherichia coli ; *Escherichia coli Infections/genetics/microbiology ; Genes, Bacterial ; Virulence/genetics ; *Sepsis/genetics ; Phylogeny ; },
abstract = {Escherichia coli is both a highly prevalent commensal and a major opportunistic pathogen causing bloodstream infections (BSI). A systematic analysis characterizing the genomic determinants of extra-intestinal pathogenic vs. commensal isolates in human populations, which could inform mechanisms of pathogenesis, diagnostic, prevention and treatment is still lacking. We used a collection of 912 BSI and 370 commensal E. coli isolates collected in France over a 17-year period (2000-2017). We compared their pangenomes, genetic backgrounds (phylogroups, STs, O groups), presence of virulence-associated genes (VAGs) and antimicrobial resistance genes, finding significant differences in all comparisons between commensal and BSI isolates. A machine learning linear model trained on all the genetic variants derived from the pangenome and controlling for population structure reveals similar differences in VAGs, discovers new variants associated with pathogenicity (capacity to cause BSI), and accurately classifies BSI vs. commensal strains. Pathogenicity is a highly heritable trait, with up to 69% of the variance explained by bacterial genetic variants. Lastly, complementing our commensal collection with an older collection from 1980, we predict that pathogenicity continuously increased through 1980, 2000, to 2010. Together our findings imply that E. coli exhibit substantial genetic variation contributing to the transition between commensalism and pathogenicity and that this species evolved towards higher pathogenicity.},
}

Humans
Escherichia coli
*Escherichia coli Infections/genetics/microbiology
Genes, Bacterial
Virulence/genetics
*Sepsis/genetics
Phylogeny

@article {pmid37530223,
year = {2023},
author = {Sun, M and Yan, H and Zhang, A and Jin, Y and Lin, C and Luo, L and Wu, B and Fan, Y and Tian, S and Cao, X and Wang, Z and Luo, J and Yang, Y and Jia, J and Zhou, P and Tang, Q and Jones, CS and Varshney, RK and Srivastava, RK and He, M and Xie, Z and Wang, X and Feng, G and Nie, G and Huang, D and Zhang, X and Zhu, F and Huang, L},
title = {Milletdb: a multi-omics database to accelerate the research of functional genomics and molecular breeding of millets.},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/pbi.14136},
pmid = {37530223},
issn = {1467-7652},
support = {CARS-34//CARS/ ; SCCXTD-2021-16//Modern Agricultural Industry System Sichuan Forage Innovation Team/ ; 31771866//National Natural Science Foundation of China/ ; 32071867//National Natural Science Foundation of China/ ; 2021YFYZ0013//Sichuan Province Research Grant/ ; },
abstract = {Millets are a class of nutrient-rich coarse cereals with high resistance to abiotic stress; thus, they guarantee food security for people living in areas with extreme climatic conditions and provide stress-related genetic resources for other crops. However, no platform is available to provide a comprehensive and systematic multi-omics analysis for millets, which seriously hinders the mining of stress-related genes and the molecular breeding of millets. Here, a free, web-accessible, user-friendly millets multi-omics database platform (Milletdb, http://milletdb.novogene.com) has been developed. The Milletdb contains six millets and their one related species genomes, graph-based pan-genomics of pearl millet, and stress-related multi-omics data, which enable Milletdb to be the most complete millets multi-omics database available. We stored GWAS (genome-wide association study) results of 20 yield-related trait data obtained under three environmental conditions [field (no stress), early drought and late drought] for 2 years in the database, allowing users to identify stress-related genes that support yield improvement. Milletdb can simplify the functional genomics analysis of millets by providing users with 20 different tools (e.g., 'Gene mapping', 'Co-expression', 'KEGG/GO Enrichment' analysis, etc.). On the Milletdb platform, a gene PMA1G03779.1 was identified through 'GWAS', which has the potential to modulate yield and respond to different environmental stresses. Using the tools provided by Milletdb, we found that the stress-related PLATZs TFs (transcription factors) family expands in 87.5% of millet accessions and contributes to vegetative growth and abiotic stress responses. Milletdb can effectively serve researchers in the mining of key genes, genome editing and molecular breeding of millets.},
}

@article {pmid37529582,
year = {2023},
author = {Liang, J and Duan, R and Qin, S and Lv, D and He, Z and Zhang, H and Duan, Q and Xi, J and Chun, H and Fu, G and Zheng, X and Tang, D and Wu, W and Han, H and Jing, H and Wang, X},
title = {The complex genomic diversity of Yersinia pestis on the long-term plague foci in Qinghai-Tibet plateau.},
journal = {Ecology and evolution},
volume = {13},
number = {8},
pages = {e10387},
pmid = {37529582},
issn = {2045-7758},
abstract = {Plague is a typical natural focus disease that circulates in different ecology of vectors and reservoir hosts. We conducted genomic population and phylogenetic analyses of the Yersinia pestis collected from the 12 natural plague foci in China with more than 20 kinds of hosts and vectors. Different ecological landscapes with specific hosts, vectors, and habitat which shape various niches for Y. pestis. The phylogeographic diversity of Y. pestis in different kinds plague foci in China showed host niches adaptation. Most natural plague foci strains are region-and focus-specific, with one predominant subpopulation; but the isolates from the Qinghai-Tibet plateau harbor a higher genetic diversity than other foci. The Y. pestis from Marmota himalayana plague foci are defined as the ancestors of different populations at the root of the evolutionary tree, suggesting several different evolutionary paths to other foci. It has the largest pan-genome and widest SNP distances with most accessory genes enriched in mobilome functions (prophages, transposons). Geological barriers play an important role in the maintenance of local Y. pestis species and block the introduction of non-native strains. This study provides new insights into the control of plague outbreaks and epidemics, deepened the understanding of the evolutionary history of MHPF (M. himalayana plague focus) in China. The population structure and identify clades among different natural foci of China renewed the space cognition of the plague.},
}

@article {pmid37526693,
year = {2023},
author = {Campillo-Balderas, JA and Lazcano, A and Cottom-Salas, W and Jácome, R and Becerra, A},
title = {Pangenomic Analysis of Nucleo-Cytoplasmic Large DNA Viruses. I: The Phylogenetic Distribution of Conserved Oxygen-Dependent Enzymes Reveals a Capture-Gene Process.},
journal = {Journal of molecular evolution},
volume = {},
number = {},
pages = {},
pmid = {37526693},
issn = {1432-1432},
support = {IN214421//DGAPA-PAPIIT, UNAM/ ; },
abstract = {The Nucleo-Cytoplasmic Large DNA Viruses (NCLDVs) infect a wide range of eukaryotic species, including amoeba, algae, fish, amphibia, arthropods, birds, and mammals. This group of viruses has linear or circular double-stranded DNA genomes whose size spans approximately one order of magnitude, from 100 to 2500 kbp. The ultimate origin of this peculiar group of viruses remains an open issue. Some have argued that NCLDVs' origin may lie in a bacteriophage ancestor that increased its genome size by subsequent recruitment of eukaryotic and bacterial genes. Others have suggested that NCLDVs families originated from cells that underwent an irreversible process of genome reduction. However, the hypothesis that a number of NCLDVs sequences have been recruited from the host genomes has been largely ignored. In the present work, we have performed pangenomic analyses of each of the seven known NCLDVs families. We show that these families' core- and shell genes have cellular homologs, supporting possible escaping-gene events as part of its evolution. Furthermore, the detection of sequences that belong to two protein families (small chain ribonucleotide reductase and Erv1/Air) and to one superfamily [2OG-Fe(II) oxygenases] that are for distribution in all NCLDVs core and shell clusters encoding for oxygen-dependent enzymes suggests that the highly conserved core these viruses originated after the Proterozoic Great Oxidation Event that transformed the terrestrial atmosphere 2.4-2.3 Ga ago.},
}

@article {pmid37526649,
year = {2023},
author = {Rodrigues, JA and Blankenship, HM and Cha, W and Mukherjee, S and Sloup, RE and Rudrik, JT and Soehnlen, M and Manning, SD},
title = {Pangenomic analyses of antibiotic-resistant Campylobacter jejuni reveal unique lineage distributions and epidemiological associations.},
journal = {Microbial genomics},
volume = {9},
number = {8},
pages = {},
doi = {10.1099/mgen.0.001073},
pmid = {37526649},
issn = {2057-5858},
mesh = {Animals ; Cattle ; Anti-Bacterial Agents/pharmacology ; *Campylobacter jejuni/genetics ; *Campylobacter Infections/epidemiology ; Phylogeny ; Multilocus Sequence Typing ; },
abstract = {Application of whole-genome sequencing (WGS) to characterize foodborne pathogens has advanced our understanding of circulating genotypes and evolutionary relationships. Herein, we used WGS to investigate the genomic epidemiology of Campylobacter jejuni, a leading cause of foodborne disease. Among the 214 strains recovered from patients with gastroenteritis in Michigan, USA, 85 multilocus sequence types (STs) were represented and 135 (63.1 %) were phenotypically resistant to at least one antibiotic. Horizontally acquired antibiotic resistance genes were detected in 128 (59.8 %) strains and the genotypic resistance profiles were mostly consistent with the phenotypes. Core-gene phylogenetic reconstruction identified three sequence clusters that varied in frequency, while a neighbour-net tree detected significant recombination among the genotypes (pairwise homoplasy index P<0.01). Epidemiological analyses revealed that travel was a significant contributor to pangenomic and ST diversity of C. jejuni, while some lineages were unique to rural counties and more commonly possessed clinically important resistance determinants. Variation was also observed in the frequency of lineages over the 4 year period with chicken and cattle specialists predominating. Altogether, these findings highlight the importance of geographically specific factors, recombination and horizontal gene transfer in shaping the population structure of C. jejuni. They also illustrate the usefulness of WGS data for predicting antibiotic susceptibilities and surveillance, which are important for guiding treatment and prevention strategies.},
}

Animals
Cattle
Anti-Bacterial Agents/pharmacology
*Campylobacter jejuni/genetics
*Campylobacter Infections/epidemiology
Phylogeny
Multilocus Sequence Typing

@article {pmid37525145,
year = {2023},
author = {Safar, HA and Alatar, F and Nasser, K and Al-Ajmi, R and Alfouzan, W and Mustafa, AS},
title = {The impact of applying various de novo assembly and correction tools on the identification of genome characterization, drug resistance, and virulence factors of clinical isolates using ONT sequencing.},
journal = {BMC biotechnology},
volume = {23},
number = {1},
pages = {26},
pmid = {37525145},
issn = {1472-6750},
mesh = {*Virulence Factors/genetics ; Reproducibility of Results ; *Genomics ; Escherichia coli/genetics ; High-Throughput Nucleotide Sequencing ; Drug Resistance ; Sequence Analysis, DNA ; },
abstract = {Oxford Nanopore sequencing technology (ONT) is currently widely used due to its affordability, simplicity, and reliability. Despite the advantage ONT has over next-generation sequencing in detecting resistance genes in mobile genetic elements, its relatively high error rate (10-15%) is still a deterrent. Several bioinformatic tools are freely available for raw data processing and obtaining complete and more accurate genome assemblies. In this study, we evaluated the impact of using mix-and-matched read assembly (Flye, Canu, Wtdbg2, and NECAT) and read correction (Medaka, NextPolish, and Racon) tools in generating complete and accurate genome assemblies, and downstream genomic analysis of nine clinical Escherichia coli isolates. Flye and Canu assemblers were the most robust in genome assembly, and Medaka and Racon correction tools significantly improved assembly parameters. Flye functioned well in pan-genome analysis, while Medaka increased the number of core genes detected. Flye, Canu, and NECAT assembler functioned well in detecting antimicrobial resistance genes (AMR), while Wtdbg2 required correction tools for better detection. Flye was the best assembler for detecting and locating both virulence and AMR genes (i.e., chromosomal vs. plasmid). This study provides insight into the performance of several read assembly and read correction tools for analyzing ONT sequencing reads for clinical isolates.},
}

*Virulence Factors/genetics
Reproducibility of Results
*Genomics
Escherichia coli/genetics
High-Throughput Nucleotide Sequencing
Drug Resistance
Sequence Analysis, DNA

@article {pmid37524789,
year = {2023},
author = {O'Donnell, S and Yue, JX and Saada, OA and Agier, N and Caradec, C and Cokelaer, T and De Chiara, M and Delmas, S and Dutreux, F and Fournier, T and Friedrich, A and Kornobis, E and Li, J and Miao, Z and Tattini, L and Schacherer, J and Liti, G and Fischer, G},
title = {Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {37524789},
issn = {1546-1718},
support = {ANR-16-CE 12-0019//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-15-IDEX-01//Agence Nationale de la Recherche (French National Research Agency)/ ; 772505//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; },
abstract = {Pangenomes provide access to an accurate representation of the genetic diversity of species, both in terms of sequence polymorphisms and structural variants (SVs). Here we generated the Saccharomyces cerevisiae Reference Assembly Panel (ScRAP) comprising reference-quality genomes for 142 strains representing the species' phylogenetic and ecological diversity. The ScRAP includes phased haplotype assemblies for several heterozygous diploid and polyploid isolates. We identified circa (ca.) 4,800 nonredundant SVs that provide a broad view of the genomic diversity, including the dynamics of telomere length and transposable elements. We uncovered frequent cases of complex aneuploidies where large chromosomes underwent large deletions and translocations. We found that SVs can impact gene expression near the breakpoints and substantially contribute to gene repertoire evolution. We also discovered that horizontally acquired regions insert at chromosome ends and can generate new telomeres. Overall, the ScRAP demonstrates the benefit of a pangenome in understanding genome evolution at population scale.},
}

@article {pmid37512795,
year = {2023},
author = {Jaén-Luchoro, D and Kahnamouei, A and Yazdanshenas, S and Lindblom, A and Samuelsson, E and Åhrén, C and Karami, N},
title = {Comparative Genomic Analysis of ST131 Subclade C2 of ESBL-Producing E. coli Isolates from Patients with Recurrent and Sporadic Urinary Tract Infections.},
journal = {Microorganisms},
volume = {11},
number = {7},
pages = {},
pmid = {37512795},
issn = {2076-2607},
support = {ALFGBG-725361//Region Västra Götaland/ ; VGFOUREG-929979//Region Västra Götaland/ ; 2020-02518//Sahlgrenska University Hospital/ ; },
abstract = {The global emergence of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E. coli), mainly causing urinary tract infections (UTI), is a major threat to human health. ESBL-E. coli sequence type (ST) 131 is the dominating clone worldwide, especially its subclade C2. Patients developing recurrent UTI (RUTI) due to ST131 subclade C2 appear to have an increased risk of recurrent infections. We have thus compared the whole genome of ST131 subclade C2 isolates from 14 patients with RUTI to those from 14 patients with sporadic UTI (SUTI). We aimed to elucidate if isolates causing RUTI can be associated with specific genomic features. Paired isolates from patients with RUTI were identical, presenting 2-18 single nucleotide polymorphism (SNP) differences for all six patients investigated. Comparative genomic analyses, including virulence factors, antibiotic resistance, pangenome and SNP analyses did not find any pattern associated with isolates causing RUTI. Despite extensive whole genome analyses, an increased risk of recurrences seen in patients with UTI due to ST131 subclade C2 isolates could not be explained by bacterial genetic differences in the two groups of isolates. Hence, additional factors that could aid in identifying bacterial properties contributing to the increased risk of RUTI due to ESBL-E. coli ST131 subclade C2 remains to be explored.},
}

@article {pmid37511853,
year = {2023},
author = {Panova, VV and Dolinnaya, NG and Novoselov, KA and Savitskaya, VY and Chernykh, IS and Kubareva, EA and Alexeevski, AV and Zvereva, MI},
title = {Conserved G-Quadruplex-Forming Sequences in Mammalian TERT Promoters and Their Effect on Mutation Frequency.},
journal = {Life (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {37511853},
issn = {2075-1729},
support = {21-14-00161//Russian Science Foundation/ ; },
abstract = {Somatic mutations in the promoter region of the human telomerase reverse transcriptase (hTERT) gene have been identified in many types of cancer. The hTERT promoter is known to be enriched with sequences that enable the formation of G-quadruplex (G4) structures, whose presence is associated with elevated mutagenicity and genome instability. Here, we used a bioinformatics tool (QGRS mapper) to search for G4-forming sequences (G4 motifs) in the 1000 bp TERT promoter regions of 141 mammalian species belonging to 20 orders, 5 of which, including primates and predators, contain more than 10 species. Groups of conserved G4 motifs and single-nucleotide variants within these groups were discovered using a block alignment approach (based on the Nucleotide PanGenome explorer). It has been shown that: (i) G4 motifs are predominantly located in the region proximal to the transcription start site (up to 400 bp) and are over-represented on the non-coding strand of the TERT promoters, (ii) 11 to 22% of the G4 motifs found are evolutionarily conserved across the related organisms, and (iii) a statistically significant higher frequency of nucleotide substitutions in the conserved G4 motifs compared to the surrounding regions was confirmed only for the order Primates. These data support the assumption that G4s can interfere with the DNA repair process and affect the evolutionary adaptation of organisms and species.},
}

@article {pmid37510288,
year = {2023},
author = {Leszczyńska, K and Święcicka, I and Daniluk, T and Lebensztejn, D and Chmielewska-Deptuła, S and Leszczyńska, D and Gawor, J and Kliber, M},
title = {Escherichia albertii as a Potential Enteropathogen in the Light of Epidemiological and Genomic Studies.},
journal = {Genes},
volume = {14},
number = {7},
pages = {},
pmid = {37510288},
issn = {2073-4425},
mesh = {Humans ; Animals ; *Enterobacteriaceae Infections ; *Genome, Bacterial ; Polymorphism, Restriction Fragment Length ; Computational Biology ; Phylogeny ; },
abstract = {Escherichia albertii is a new enteropathogen of humans and animals. The aim of the study was to assess the prevalence and pathogenicity of E. albertii strains isolated in northeastern Poland using epidemiological and genomic studies. In 2015-2018, a total of 1154 fecal samples from children and adults, 497 bird droppings, 212 food samples, 92 water samples, and 500 lactose-negative E. coli strains were tested. A total of 42 E. albertii strains were isolated. The PCR method was suitable for their rapid identification. In total, 33.3% of E. albertii isolates were resistant to one antibiotic, and 16.7% to two. Isolates were sensitive to cefepime, imipenem, levofloxacin, gentamicin, trimethoprim/sulfamethoxazole, and did not produce ESBL β-lactamases. High genetic variability of E. albertii has been demonstrated. In the PFGE method, 90.5% of the strains had distinct pulsotypes. In MLST typing, 85.7% of strains were assigned distinct sequence types (STs), of which 64% were novel ST types. Cytolethal distending toxin (CDT) and Paa toxin genes were found in 100% of E. albertii isolates. Genes encoding toxins, IbeA, CdtB type 2, Tsh and Shiga (Stx2f), were found in 26.2%, 9.7%, 1.7%, and 0.4% of E. albertii isolates, respectively. The chromosome size of the tested strains ranged from 4,573,338 to 5,141,010 bp (average 4,784,003 bp), and at least one plasmid was present in all strains. The study contributes to a more accurate assessment of the genetic diversity of E. albertii and the potential threat it poses to public health.},
}

Humans
Animals
*Enterobacteriaceae Infections
*Genome, Bacterial
Polymorphism, Restriction Fragment Length
Computational Biology
Phylogeny

@article {pmid37503282,
year = {2023},
author = {Joglekar, P and Conlan, S and Lee-Lin, SQ and Deming, C and Kashaf, SS and , and Kong, HH and Segre, JA},
title = {Integrated genomic and functional analyses of human skin-associated Staphylococcus reveals extensive inter- and intra-species diversity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37503282},
abstract = {UNLABELLED: Human skin is stably colonized by a distinct microbiota that functions together with epidermal cells to maintain a protective physical barrier. Staphylococcus , a prominent genus of the skin microbiota, participates in colonization resistance, tissue repair, and host immune regulation in strain specific manners. To unlock the potential of engineering skin microbial communities, we aim to fully characterize the functional diversity of this genus within the context of the skin environment. We conducted metagenome and pan-genome analyses of isolates obtained from distinct body sites of healthy volunteers, providing a detailed biogeographic depiction of staphylococcal species that colonize our skin. S. epidermidis , S. capitis, and S. hominis were the most abundant species present in all volunteers and were detected at all body sites. Pan-genome analysis of these three species revealed that the genus-core was dominated by central metabolism genes. Species-specific core genes were enriched in host colonization functions. The majority (∼68%) of genes were detected only in a fraction of isolate genomes, underscoring the immense strain-specific gene diversity. Conspecific genomes grouped into phylogenetic clades, exhibiting body site preference. Each clade was enriched for distinct gene-sets that are potentially involved in site tropism. Finally, we conducted gene expression studies of select isolates showing variable growth phenotypes in skin-like medium. In vitro expression revealed extensive intra- and inter-species gene expression variation, substantially expanding the functional diversification within each species. Our study provides an important resource for future ecological and translational studies to examine the role of shared and strain-specific staphylococcal genes within the skin environment.

SIGNIFICANCE: The bacterial genus Staphylococcus is a prominent member of the human skin microbiome, performing important and diverse functions such as tuning immunity, driving tissue repair, and preventing pathogen colonization. Each of these functions is carried out by a subset of staphylococcal strains, displaying differences in gene content and regulation. Delineating the genomic and functional diversity of Staphylococcus will enable researchers to unlock the potential of engineering skin communities to promote health. Here, we present a comprehensive multi-omics analysis to characterize the inter- and intra-species diversity present in human skin-associated staphylococci. Our study is the first to conduct a detailed pan-genome comparison between prominent skin staphylococcal species giving a valuable insight into gene sharing and provides an important resource.},
}

@article {pmid37502876,
year = {2023},
author = {Ahmed, NM and Joglekar, P and Deming, C and , and Lemon, KP and Kong, HH and Segre, JA and Conlan, S},
title = {Genomic characterization of the C. tuberculostearicum species complex, a ubiquitous member of the human skin microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37502876},
abstract = {UNLABELLED: Corynebacterium is a predominant genus in the skin microbiome, yet its genetic diversity on skin is incompletely characterized and lacks a comprehensive set of reference genomes. Our work aims to investigate the distribution of Corynebacterium species on the skin, as well as to expand the existing genome reference catalog to enable more complete characterization of skin metagenomes. We used V1-V3 16S rRNA gene sequencing data from 14 body sites of 23 healthy volunteers to characterize Corynebacterium diversity and distribution across healthy human skin. Corynebacterium tuberculostearicum is the predominant species found on human skin and we identified two distinct C. tuberculostearicum ribotypes (A & B) that can be distinguished by variation in the 16S rRNA V1-V3 sequence. One is distributed across all body sites and the other found primarily on the feet. We performed whole genome sequencing of 40 C. tuberculostearicum isolates cultured from the skin of five healthy individuals across seven skin sites. We generated five closed genomes of diverse C. tuberculostearicum which revealed that C. tuberculostearicum isolates are largely syntenic and carry a diversity of methylation patterns, plasmids and CRISPR/Cas systems. The pangenome of C. tuberculostearicum is open with a core genome size of 1806 genes and a pangenome size of 5451 total genes. This expanded pangenome enabled the mapping of 24% more C. tuberculostearicum reads from shotgun metagenomic datasets derived from skin body sites. Finally, while the genomes from this study all fall within a C. tuberculostearicum species complex, the ribotype B isolates may constitute a new species.

IMPORTANCE: Amplicon sequencing data combined with isolate whole genome sequencing has expanded our understanding of Corynebacterium on the skin. Human skin is characterized by a diverse collection of Corynebacterium species but C. tuberculostearicum predominates many sites. Our work supports the emerging idea that C. tuberculostearicum is a species complex encompassing several distinct species. We produced a collection of genomes that help define this complex including a potentially new species which we are calling C. hallux based on a preference for sites on the feet, whole-genome average nucleotide identity, pangenomics and growth in skin-like media. This isolate collection and high-quality genome resource sets the stage for developing engineered strains for both basic and translational clinical studies. Microbiomes are shaped by taxa that are both characteristic to those sites and functionally important to that community. The genus Corynebacterium is one such taxa for the human skin and nares. Foundational studies using 16S rRNA gene sequencing and shotgun metagenomics by our lab (1, 2) and others (3) have established Corynebacterium as common members of the skin microbiome. While Corynebacterium have been positively correlated with the resolution of dysbiosis associated with eczema flares (4), the importance of the Corynebacterium spp. is less defined for skin disease severity in primary immune deficient patients (5, 6). Corynebacterium spp. are predominant members of the human aerodigestive tract microbiome (nares, oral cavity and respiratory tract) (3) and participate in microbe-microbe interactions with members of nasal microbiome (7, 8). Corynebacterium have been shown to engage with the host immune system, specifically C. accolens -promoted IL23-dependent inflammation in mice on a high-fat diet (9). C. bovis and C. mastiditis have been shown to predominate the microbiome of a ADAM10-deficient mouse model (10) as well as an ADAM17-deficient mouse model of eczema (11). Finally, C. tuberculostearicum has been shown to induce inflammation in human epidermal keratinocyte cell cultures (12). These studies establish Corynebacterium spp. as key members of the skin microbiome capable of both microbe-microbe and microbe-host interactions. A critical resource for understanding the biology of Corynebacterium on the skin is a robust collection of complete reference genomes, including isolates collected from a variety of individuals and body sites. Previously published genome collections from skin- or nares-resident species include Staphylococcus epidermidis (13), Cutibacterium acnes (14) and the recent comparative analysis of Dolosigranulum pigrum (15). Of note, while emerging bioinformatic methods and pipelines are now being employed to extract nearly-complete genomes (MAGs) from metagenomic assemblies of skin samples (16), MAGs are not yet a substitute for genomes from cultured isolates to understand strain level or pangenomic diversity. In addition to functional prediction, comparative genomics is increasingly being used to augment conventional microbiological methods to define or redefine taxonomic boundaries (17, 18), as well as describe the full extent of diversity within these boundaries (19). A pangenome, which encompasses the complete set of genes present within a set of genome sequences, enables the characterization of gene-level heterogeneity within a taxonomic group. The pangenome is commonly subdivided into the 'core' genome, referring to genes present in all strains, and the 'accessory' or 'dispensable' genome, referring to those present in only one or some isolates. (The accessory pangenome can be further subdivided to reflect a wider range of gene uniqueness, e.g. singletons.) Thorough characterization of taxa is limited by the availability of representative and high-quality genome assemblies. Unfortunately, with the exceptions of clinically relevant Corynebacterium spp. (e.g. , C. diphtheriae , C. striatum and C. pseudotuberculosis), the genus is inadequately sequenced, with 75% of species having fewer than six genomes. This includes common skin-associated species like C. tuberculostearicum with just five unique isolate genomes, only two of which are from skin. This work seeks first to characterize the distribution of Corynebacterium across 14 skin sites from 23 healthy volunteers. The second goal of this work focuses on what we identify as the predominant skin Corynebacterium species, C. tuberculostearicum . We have sequenced 23 distinct C. tuberculostearicum strains (n=40 genomes before dereplication), a five-fold increase in the number of publicly available, unique genomes (n=5). In addition to short-read assemblies, we generated five complete genomes which, along with the type strain (DSM44922), demonstrate that C. tuberculostearicum genomes are largely syntenic and carry a number of methylation systems as well as a CRISPR/Cas system. Genes from the C. tuberculostearicum genomes in our collection fall into 5451 gene clusters comprising the species pangenome. This expanded pangenome, as compared to existing public references, improved the mapping of C. tuberculostearicum metagenomic reads from unrelated healthy volunteers. In addition, we have identified a distinct C. tuberculostearicum clade that is highly enriched on the feet that may represent a new species, tentatively designated Corynebacterium hallux .},
}

@article {pmid37497030,
year = {2023},
author = {Price, C and Russell, JA},
title = {AMAnD: an automated metagenome anomaly detection methodology utilizing DeepSVDD neural networks.},
journal = {Frontiers in public health},
volume = {11},
number = {},
pages = {1181911},
pmid = {37497030},
issn = {2296-2565},
mesh = {Humans ; *Metagenome ; *COVID-19/genetics ; Neural Networks, Computer ; Genomics ; Metagenomics/methods ; },
abstract = {The composition of metagenomic communities within the human body often reflects localized medical conditions such as upper respiratory diseases and gastrointestinal diseases. Fast and accurate computational tools to flag anomalous metagenomic samples from typical samples are desirable to understand different phenotypes, especially in contexts where repeated, long-duration temporal sampling is done. Here, we present Automated Metagenome Anomaly Detection (AMAnD), which utilizes two types of Deep Support Vector Data Description (DeepSVDD) models; one trained on taxonomic feature space output by the Pan-Genomics for Infectious Agents (PanGIA) taxonomy classifier and one trained on kmer frequency counts. AMAnD's semi-supervised one-class approach makes no assumptions about what an anomaly may look like, allowing the flagging of potentially novel anomaly types. Three diverse datasets are profiled. The first dataset is hosted on the National Center for Biotechnology Information's (NCBI) Sequence Read Archive (SRA) and contains nasopharyngeal swabs from healthy and COVID-19-positive patients. The second dataset is also hosted on SRA and contains gut microbiome samples from normal controls and from patients with slow transit constipation (STC). AMAnD can learn a typical healthy nasopharyngeal or gut microbiome profile and reliably flag the anomalous COVID+ or STC samples in both feature spaces. The final dataset is a synthetic metagenome created by the Critical Assessment of Metagenome Annotation Simulator (CAMISIM). A control dataset of 50 well-characterized organisms was submitted to CAMISIM to generate 100 synthetic control class samples. The experimental conditions included 12 different spiked-in contaminants that are taxonomically similar to organisms present in the laboratory blank sample ranging from one strain tree branch taxonomic distance away to one family tree branch taxonomic distance away. This experiment was repeated in triplicate at three different coverage levels to probe the dependence on sample coverage. AMAnD was again able to flag the contaminant inserts as anomalous. AMAnD's assumption-free flagging of metagenomic anomalies, the real-time model training update potential of the deep learning approach, and the strong performance even with lightweight models of low sample cardinality would make AMAnD well-suited to a wide array of applied metagenomics biosurveillance use-cases, from environmental to clinical utility.},
}

Humans
*Metagenome
*COVID-19/genetics
Neural Networks, Computer
Genomics
Metagenomics/methods

@article {pmid37494467,
year = {2023},
author = {Ma, J and Cáceres, M and Salmela, L and Mäkinen, V and Tomescu, AI},
title = {Chaining for Accurate Alignment of Erroneous Long Reads to Acyclic Variation Graphs.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btad460},
pmid = {37494467},
issn = {1367-4811},
abstract = {MOTIVATION: Aligning reads to a variation graph is a standard task in pangenomics, with downstream applications such as improving variant calling. While the vg toolkit (Garrison et al., 2018) is a popular aligner of short reads, GraphAligner (Rautiainen and Marschall, 2020) is the state-of-the-art aligner of erroneous long reads. GraphAligner works by finding candidate read occurrences based on individually extending the best seeds of the read in the variation graph. However, a more principled approach recognized in the community is to co-linearly chain multiple seeds.

RESULTS: We present a new algorithm to co-linearly chain a set of seeds in a string labeled acyclic graph, together with the first efficient implementation of such a co-linear chaining algorithm into a new aligner of erroneous long reads to acyclic variation graphs, GraphChainer. We run experiments aligning real and simulated PacBio CLR reads with average error rates 15% and 5%. Compared to GraphAligner, GraphChainer aligns 12% to 17% more reads, and 21% to 28% more total read length, on real PacBio CLR reads from human chromosomes 1, 22 and the whole human pangenome. On both simulated and real data, GraphChainer aligns between 95% and 99% of all reads, and of total read length. We also show that minigraph (Li et al., 2020) and minichain (Chandra and Jain, 2023) obtain an accuracy of less than 60% on this setting.

AVAILABILITY: GraphChainer is freely available at https://github.com/algbio/GraphChainer. The datasets and evaluation pipeline can be reached from the previous address.

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

@article {pmid37492100,
year = {2023},
author = {Frazer, KA and Schork, NJ},
title = {The human pangenome reference anticipates equitable and fundamental genomic insights.},
journal = {Cell genomics},
volume = {3},
number = {7},
pages = {100360},
pmid = {37492100},
issn = {2666-979X},
abstract = {For the past few years, researchers in the Human Pangenome Reference Consortium (HPRC) have been working to catalog almost all human genomic diversity. Frazer and Schork preview an article recently published in Nature, "A draft human pangenome reference,"[1] which represents the initial release of 47 fully phased diploid assemblies of genomes of individuals with diverse ancestries.},
}

@article {pmid37491415,
year = {2023},
author = {Matrishin, CB and Haase, EM and Dewhirst, FE and Mark Welch, JL and Miranda-Sanchez, F and Chen, T and MacFarland, DC and Kauffman, KM},
title = {Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {161},
pmid = {37491415},
issn = {2049-2618},
support = {T32DE023526/DE/NIDCR NIH HHS/United States ; R01DE016937/DE/NIDCR NIH HHS/United States ; R03 DE030987/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; *Bacteriophages/genetics ; Porphyromonas gingivalis/genetics ; Prophages/genetics ; *Periodontal Diseases ; Base Sequence ; },
abstract = {BACKGROUND: Porphyromonas gingivalis (hereafter "Pg") is an oral pathogen that has been hypothesized to act as a keystone driver of inflammation and periodontal disease. Although Pg is most readily recovered from individuals with actively progressing periodontal disease, healthy individuals and those with stable non-progressing disease are also colonized by Pg. Insights into the factors shaping the striking strain-level variation in Pg, and its variable associations with disease, are needed to achieve a more mechanistic understanding of periodontal disease and its progression. One of the key forces often shaping strain-level diversity in microbial communities is infection of bacteria by their viral (phage) predators and symbionts. Surprisingly, although Pg has been the subject of study for over 40 years, essentially nothing is known of its phages, and the prevailing paradigm is that phages are not important in the ecology of Pg.

RESULTS: Here we systematically addressed the question of whether Pg are infected by phages-and we found that they are. We found that prophages are common in Pg, they are genomically diverse, and they encode genes that have the potential to alter Pg physiology and interactions. We found that phages represent unrecognized targets of the prevalent CRISPR-Cas defense systems in Pg, and that Pg strains encode numerous additional mechanistically diverse candidate anti-phage defense systems. We also found that phages and candidate anti-phage defense system elements together are major contributors to strain-level diversity and the species pangenome of this oral pathogen. Finally, we demonstrate that prophages harbored by a model Pg strain are active in culture, producing extracellular viral particles in broth cultures.

CONCLUSION: This work definitively establishes that phages are a major unrecognized force shaping the ecology and intra-species strain-level diversity of the well-studied oral pathogen Pg. The foundational phage sequence datasets and model systems that we establish here add to the rich context of all that is already known about Pg, and point to numerous avenues of future inquiry that promise to shed new light on fundamental features of phage impacts on human health and disease broadly. Video Abstract.},
}

Humans
*Bacteriophages/genetics
Porphyromonas gingivalis/genetics
Prophages/genetics
*Periodontal Diseases
Base Sequence

@article {pmid37491393,
year = {2023},
author = {Cho, MK and Fullerton, SM and Hammonds, EM and Lee, SS and Panofsky, A and Reardon, J},
title = {Pangenomics: prioritize diversity in collaborations.},
journal = {Nature},
volume = {619},
number = {7971},
pages = {698},
doi = {10.1038/d41586-023-02248-7},
pmid = {37491393},
issn = {1476-4687},
mesh = {Humans ; *Genomics/methods/trends ; *Health Equity ; *Intersectoral Collaboration ; },
}

Humans
*Genomics/methods/trends
*Health Equity
*Intersectoral Collaboration

@article {pmid37490004,
year = {2023},
author = {Wu, S and Sun, H and Gao, L and Branham, S and McGregor, C and Renner, SS and Xu, Y and Kousik, C and Wechter, WP and Levi, A and Fei, Z},
title = {A Citrullus genus super-pangenome reveals extensive variations in wild and cultivated watermelons and sheds light on watermelon evolution and domestication.},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/pbi.14120},
pmid = {37490004},
issn = {1467-7652},
support = {2015-51181-24285//National Institute of Food and Agriculture/ ; 2020-51181-32139//National Institute of Food and Agriculture/ ; 1855585//National Science Foundation/ ; },
}

@article {pmid37487084,
year = {2023},
author = {Bozan, I and Achakkagari, SR and Anglin, NL and Ellis, D and Tai, HH and Strömvik, MV},
title = {Pangenome analyses reveal impact of transposable elements and ploidy on the evolution of potato species.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {31},
pages = {e2211117120},
pmid = {37487084},
issn = {1091-6490},
mesh = {*Solanum tuberosum ; DNA Transposable Elements ; Phylogeny ; Ploidies ; *Solanum ; },
abstract = {Potato (Solanum sp., family Solanaceae) is the most important noncereal food crop globally. It has over 100 wild relatives in the Solanum section Petota, which features species with both sexual and asexual reproduction and varying ploidy levels. A pangenome of Solanum section Petota composed of 296 accessions was constructed including diploids and polyploids compared via presence/absence variation (PAV). The Petota core (genes shared by at least 97% of the accessions) and shell genomes (shared by 3 to 97%) are enriched in basic molecular and cellular functions, while the cloud genome (genes present in less than 3% of the member accessions) showed enrichment in transposable elements (TEs). Comparison of PAV in domesticated vs. wild accessions was made, and a phylogenetic tree was constructed based on PAVs, grouping accessions into different clades, similar to previous phylogenies produced using DNA markers. A cladewise pangenome approach identified abiotic stress response among the core genes in clade 1+2 and clade 3, and flowering/tuberization among the core genes in clade 4. The TE content differed between the clades, with clade 1+2, which is composed of species from North and Central America with reproductive isolation from species in other clades, having much lower TE content compared to other clades. In contrast, accessions with in vitro propagation history were identified and found to have high levels of TEs. Results indicate a role for TEs in adaptation to new environments, both natural and artificial, for Solanum section Petota.},
}

*Solanum tuberosum
DNA Transposable Elements
Phylogeny
Ploidies
*Solanum

@article {pmid37485508,
year = {2023},
author = {Liu, W and Ou, P and Tian, F and Liao, J and Ma, Y and Wang, J and Jin, X},
title = {Anti-Vibrio parahaemolyticus compounds from Streptomyces parvus based on Pan-genome and subtractive proteomics.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1218176},
pmid = {37485508},
issn = {1664-302X},
abstract = {INTRODUCTION: Vibrio parahaemolyticus is a foodborne pathogen commonly found in seafood, and drug resistance poses significant challenges to its control. This study aimed to identify novel drug targets for antibacterial drug discovery.

METHODS: To identify drug targets, we performed a pan-genome analysis on 58 strains of V. parahaemolyticus genomes to obtain core genes. Subsequently, subtractive proteomics and physiochemical checks were conducted on the core proteins to identify potential therapeutic targets. Molecular docking was then employed to screen for anti-V. parahaemolyticus compounds using a in-house compound library of Streptomyces parvus, chosen based on binding energy. The anti-V. parahaemolyticus efficacy of the identified compounds was further validated through a series of experimental tests.

RESULTS AND DISCUSSION: Pangenome analysis of 58 V. parahaemolyticus genomes revealed that there were 1,392 core genes. After Subtractive proteomics and physiochemical checks, Flagellar motor switch protein FliN was selected as a therapeutic target against V. parahaemolyticus. FliN was modeled and docked with Streptomyces parvus source compounds, and Actinomycin D was identified as a potential anti-V. parahaemolyticus agent with a strong binding energy. Experimental verification confirmed its effectiveness in killing V. parahaemolyticus and significantly inhibiting biofilm formation and motility. This study is the first to use pan-genome and subtractive proteomics to identify new antimicrobial targets for V. parahaemolyticus and to identify the anti-V. parahaemolyticus effect of Actinomycin D. These findings suggest potential avenues for the development of new antibacterial drugs to control V. parahaemolyticus infections.},
}

@article {pmid37480395,
year = {2023},
author = {Tanuku, SNR and Pinnaka, AK and Behera, S and Singh, A and Pydi, S and Vasudeva, G and Vaidya, B and Sharma, G and Ganta, SK and Garbhapu, NS},
title = {Marinobacterium lacunae sp. nov. isolated from estuarine sediment.},
journal = {Archives of microbiology},
volume = {205},
number = {8},
pages = {294},
pmid = {37480395},
issn = {1432-072X},
support = {GAP3195//Ministry of Earth Sciences/ ; },
mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; Agar ; *Alteromonadaceae ; Cardiolipins ; },
abstract = {A novel motile bacterium was isolated from a sediment sample collected in Kochi backwaters, Kerala, India. This bacterium is Gram negative, rod shaped, 1.0-1.5 µm wide, and 2.0-3.0 µm long. It was designated as strain AK27[T]. Colonies were grown on marine agar displayed circular, off-white, shiny, moist, translucent, flat, margin entire, 1-2 mm in diameter. The major fatty acids identified in this strain were C18:1 ω7c, C16:0, and summed in feature 3. The composition of polar lipids in the strain AK27[T] included phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, one unidentified amino lipid, two unidentified aminophospholipids, two unidentified phospholipids, and six unidentified lipids. The genomic DNA of strain AK27[T] exhibited a G+C content of 56.4 mol%. Based on the analysis of 16S rRNA gene sequence, strain AK27[T] showed sequence similarity to M. ramblicola D7[T] and M. zhoushanense WM3[T] as 98.99% and 98.58%, respectively. Compared to other type strains of the Marinobacterium genus, strain AK27[T] exhibited sequence similarities ranging from 91.7% to 96.4%. When compared to Marinobacterium zhoushanense WM3[T] and Marinobacterium ramblicola D7[T], strain AK27[T] exhibited average nucleotide identity values of 80.25% and 79.97%, and dDDH values of 22.9% and 22.6%, respectively. The genome size of the strain AK27[T] was 4.55 Mb, with 4,229 coding sequences. Based on the observed phenotypic and chemotaxonomic features, and the results of phylogenetic and phylogenomic analysis, this study proposes the classification of strain AK27[T] as a novel species within the genus Marinobacterium. The proposed name for this novel species is Marinobacterium lacunae sp. nov.},
}

Phylogeny
RNA, Ribosomal, 16S/genetics
Agar
*Alteromonadaceae
Cardiolipins

@article {pmid37477947,
year = {2023},
author = {Lyu, X and Xia, Y and Wang, C and Zhang, K and Deng, G and Shen, Q and Gao, W and Zhang, M and Liao, N and Ling, J and Bo, Y and Hu, Z and Yang, J and Zhang, M},
title = {Pan-genome analysis sheds light on structural variation-based dissection of agronomic traits in melon crops.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiad405},
pmid = {37477947},
issn = {1532-2548},
abstract = {Sweetness and appearance of fresh fruits are key palatable and preference attributes for consumers and are often controlled by multiple genes. However, fine-mapping the key loci or genes of interest by single genome-based genetic analysis is challenging. Herein, we present the chromosome-level genome assembly of one landrace melon accession (Cucumis melo ssp. agrestis) with wild morphologic features and thus construct a melon pan-genome atlas via integrating sequenced melon genome datasets. Our comparative genomic analysis reveals a total of 3.4 million genetic variations, of which the presence/absence variations (PAVs) are mainly involved in regulating the function of genes for sucrose metabolism during melon domestication and improvement. We further resolved several loci that are accountable for sucrose contents, flesh color, rind stripe and suture using a structural variation (SV)-based genome-wide association study (GWAS). Furthermore, via BSA-seq and map-based cloning, we uncovered that a single gene, (CmPIRL6), determines the edible or inedible characteristics of melon fruit exocarp. These findings provide important melon pan-genome information and provide a powerful toolkit for future pan-genome-informed cultivar breeding of melon.},
}

@article {pmid37476668,
year = {2023},
author = {Agarwal, V and Stubits, R and Nassrullah, Z and Dillon, MM},
title = {Pangenome insights into the diversification and disease specificity of worldwide Xanthomonas outbreaks.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1213261},
pmid = {37476668},
issn = {1664-302X},
abstract = {The bacterial genus Xanthomonas is responsible for disease outbreaks in several hundred plant species, many of them economically important crops. In the era of next-generation sequencing, thousands of strains from this genus have now been sequenced as part of isolated studies that focus on outbreak characterization, host range, diversity, and virulence factor identification. However, these data have not been synthesized and we lack a comprehensive phylogeny for the genus, with some species designations in public databases still relying on phenotypic similarities and representative sequence typing. The extent of genetic cohesiveness among Xanthomonas strains, the distribution of virulence factors across strains, and the impact of evolutionary history on host range across the genus are also poorly understood. In this study, we present a pangenome analysis of 1,910 diverse Xanthomonas genomes, highlighting their evolutionary relationships, the distribution of virulence-associated genes across strains, and rates of horizontal gene transfer. We find a number of broadly conserved classes of virulence factors and considerable diversity in the Type 3 Secretion Systems (T3SSs) and Type 3 Secreted Effector (T3SE) repertoires of different Xanthomonas species. We also use these data to re-assign incorrectly classified strains to phylogenetically informed species designations and find evidence of both monophyletic host specificity and convergent evolution of phylogenetically distant strains to the same host. Finally, we explore the role of recombination in maintaining genetic cohesion within the Xanthomonas genus as a result of both ancestral and recent recombination events. Understanding the evolutionary history of Xanthomonas species and the relationship of key virulence factors with host-specificity provides valuable insight into the mechanisms through which Xanthomonas species shift between hosts and will enable us to develop more robust resistance strategies against these highly virulent pathogens.},
}

@article {pmid37474912,
year = {2023},
author = {Ortega-Sanz, I and Barbero-Aparicio, JA and Canepa-Oneto, A and Rovira, J and Melero, B},
title = {CamPype: an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter.},
journal = {BMC bioinformatics},
volume = {24},
number = {1},
pages = {291},
pmid = {37474912},
issn = {1471-2105},
support = {LCF/PR/PR18/51130007//"la Caixa" Foundation/ ; },
mesh = {*Campylobacter/genetics ; Genome, Bacterial ; Workflow ; Bacteria/genetics ; Genomics ; },
abstract = {BACKGROUND: The rapid expansion of Whole-Genome Sequencing has revolutionized the fields of clinical and food microbiology. However, its implementation as a routine laboratory technique remains challenging due to the growth of data at a faster rate than can be effectively analyzed and critical gaps in bioinformatics knowledge.

RESULTS: To address both issues, CamPype was developed as a new bioinformatics workflow for the genomics analysis of sequencing data of bacteria, especially Campylobacter, which is the main cause of gastroenteritis worldwide making a negative impact on the economy of the public health systems. CamPype allows fully customization of stages to run and tools to use, including read quality control filtering, read contamination, reads extension and assembly, bacterial typing, genome annotation, searching for antibiotic resistance genes, virulence genes and plasmids, pangenome construction and identification of nucleotide variants. All results are processed and resumed in an interactive HTML report for best data visualization and interpretation.

CONCLUSIONS: The minimal user intervention of CamPype makes of this workflow an attractive resource for microbiology laboratories with no expertise in bioinformatics as a first line method for bacterial typing and epidemiological analyses, that would help to reduce the costs of disease outbreaks, or for comparative genomic analyses. CamPype is publicly available at https://github.com/JoseBarbero/CamPype .},
}

*Campylobacter/genetics
Genome, Bacterial
Workflow
Bacteria/genetics
Genomics

@article {pmid37474911,
year = {2023},
author = {Huff, M and Hulse-Kemp, AM and Scheffler, BE and Youngblood, RC and Simpson, SA and Babiker, E and Staton, M},
title = {Long-read, chromosome-scale assembly of Vitis rotundifolia cv. Carlos and its unique resistance to Xylella fastidiosa subsp. fastidiosa.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {409},
pmid = {37474911},
issn = {1471-2164},
support = {6062-21000-010-013//USDA-ARS/ ; 6062-21000-010-000-D//USDA-ARS/ ; 6062-21000-010-000-D//USDA-ARS/ ; 6062-21000-010-000-D//USDA-ARS/ ; 6062-21000-010-000-D//USDA-ARS/ ; 6062-21000-010-000-D//USDA-ARS/ ; 6062-21000-010-013//USDA-ARS/ ; },
mesh = {*Vitis/microbiology ; Disease Resistance/genetics ; *Xylella/genetics ; Chromosomes ; Plant Diseases/genetics/microbiology ; },
abstract = {BACKGROUND: Muscadine grape (Vitis rotundifolia) is resistant to many of the pathogens that negatively impact the production of common grape (V. vinifera), including the bacterial pathogen Xylella fastidiosa subsp. fastidiosa (Xfsf), which causes Pierce's Disease (PD). Previous studies in common grape have indicated Xfsf delays host immune response with a complex O-chain antigen produced by the wzy gene. Muscadine cultivars range from tolerant to completely resistant to Xfsf, but the mechanism is unknown.

RESULTS: We assembled and annotated a new, long-read genome assembly for 'Carlos', a cultivar of muscadine that exhibits tolerance, to build upon the existing genetic resources available for muscadine. We used these resources to construct an initial pan-genome for three cultivars of muscadine and one cultivar of common grape. This pan-genome contains a total of 34,970 synteny-constrained entries containing genes of similar structure. Comparison of resistance gene content between the 'Carlos' and common grape genomes indicates an expansion of resistance (R) genes in 'Carlos.' We further identified genes involved in Xfsf response by transcriptome sequencing 'Carlos' plants inoculated with Xfsf. We observed 234 differentially expressed genes with functions related to lipid catabolism, oxidation-reduction signaling, and abscisic acid (ABA) signaling as well as seven R genes. Leveraging public data from previous experiments of common grape inoculated with Xfsf, we determined that most differentially expressed genes in the muscadine response were not found in common grape, and three of the R genes identified as differentially expressed in muscadine do not have an ortholog in the common grape genome.

CONCLUSIONS: Our results support the utility of a pan-genome approach to identify candidate genes for traits of interest, particularly disease resistance to Xfsf, within and between muscadine and common grape.},
}

*Vitis/microbiology
Disease Resistance/genetics
*Xylella/genetics
Chromosomes
Plant Diseases/genetics/microbiology

@article {pmid37465028,
year = {2023},
author = {Thieringer, PH and Boyd, ES and Templeton, AS and Spear, JR},
title = {Metapangenomic investigation provides insight into niche differentiation of methanogenic populations from the subsurface serpentinizing environment, Samail Ophiolite, Oman.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1205558},
pmid = {37465028},
issn = {1664-302X},
abstract = {Serpentinization reactions produce highly reduced waters that have hyperalkaline pH and that can have high concentrations of H2 and CH4. Putatively autotrophic methanogenic archaea have been identified in the subsurface waters of the Samail Ophiolite, Sultanate of Oman, though the strategies to overcome hyperalkaline pH and dissolved inorganic carbon limitation remain to be fully understood. Here, we recovered metagenome assembled genomes (MAGs) and applied a metapangenomic approach to three different Methanobacterium populations to assess habitat-specific functional gene distribution. A Type I population was identified in the fluids with neutral pH, while a Type II and "Mixed" population were identified in the most hyperalkaline fluids (pH 11.63). The core genome of all Methanobacterium populations highlighted potential DNA scavenging techniques to overcome phosphate or nitrogen limitation induced by environmental conditions. With particular emphasis on the Mixed and Type II population found in the most hyperalkaline fluids, the accessory genomes unique to each population reflected adaptation mechanisms suggesting lifestyles that minimize niche overlap. In addition to previously reported metabolic capability to utilize formate as an electron donor and generate intracellular CO2, the Type II population possessed genes relevant to defense against antimicrobials and assimilating potential osmoprotectants to provide cellular stability. The accessory genome of the Mixed population was enriched in genes for multiple glycosyltransferases suggesting reduced energetic costs by adhering to mineral surfaces or to other microorganisms, and fostering a non-motile lifestyle. These results highlight the niche differentiation of distinct Methanobacterium populations to circumvent the challenges of serpentinization impacted fluids through coexistence strategies, supporting our ability to understand controls on methanogenic lifestyles and adaptations within the serpentinizing subsurface fluids of the Samail Ophiolite.},
}

@article {pmid37464310,
year = {2023},
author = {Singh, RP and Kumari, K and Sharma, PK and Ma, Y},
title = {Characterization and in-depth genome analysis of a halotolerant probiotic bacterium Paenibacillus sp. S-12, a multifarious bacterium isolated from Rauvolfia serpentina.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {192},
pmid = {37464310},
issn = {1471-2180},
mesh = {*Rauwolfia/genetics ; *Paenibacillus/genetics ; Base Composition ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Fatty Acids ; Soil Microbiology ; },
abstract = {BACKGROUND: Members of Paenibacillus genus from diverse habitats have attracted great attention due to their multifarious properties. Considering that members of this genus are mostly free-living in soil, we characterized the genome of a halotolerant environmental isolate belonging to the genus Paenibacillus. The genome mining unravelled the presence of CAZymes, probiotic, and stress-protected genes that suggested strain S-12 for industrial and agricultural purposes.

RESULTS: Molecular identification by 16 S rRNA gene sequencing showed its closest match to other Paenibacillus species. The complete genome size of S-12 was 5.69 Mb, with a GC-content 46.5%. The genome analysis of S-12 unravelled the presence of an open reading frame (ORF) encoding the functions related to environmental stress tolerance, adhesion processes, multidrug efflux systems, and heavy metal resistance. Genome annotation identified the various genes for chemotaxis, flagellar motility, and biofilm production, illustrating its strong colonization ability.

CONCLUSION: The current findings provides the in-depth investigation of a probiotic Paenibacillus bacterium that possessed various genome features that enable the bacterium to survive under diverse conditions. The strain shows the strong ability for probiotic application purposes.},
}

*Rauwolfia/genetics
*Paenibacillus/genetics
Base Composition
Phylogeny
RNA, Ribosomal, 16S/genetics
DNA, Bacterial/genetics
Sequence Analysis, DNA
Fatty Acids
Soil Microbiology

@article {pmid37461539,
year = {2023},
author = {Steenwyk, JL and Knowles, S and Bastos, RW and Balamurugan, C and Rinker, D and Mead, ME and Roberts, CD and Raja, HA and Li, Y and Colabardini, AC and de Castro, PA and Dos Reis, TF and Canóvas, D and Sanchez, RL and Lagrou, K and Torrado, E and Rodrigues, F and Oberlies, NH and Zhou, X and Goldman, GH and Rokas, A},
title = {Evolutionary origin, population diversity, and diagnostics for a cryptic hybrid pathogen.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37461539},
abstract = {Cryptic fungal pathogens pose significant identification and disease management challenges due to their morphological resemblance to known pathogenic species while harboring genetic and (often) infection-relevant trait differences. The cryptic fungal pathogen Aspergillus latus , an allodiploid hybrid originating from Aspergillus spinulosporus and an unknown close relative of Aspergillus quadrilineatus within section Nidulantes , remains poorly understood. The absence of accurate diagnostics for A. latus has led to misidentifications, hindering epidemiological studies and the design of effective treatment plans. We conducted an in-depth investigation of the genomes and phenotypes of 44 globally distributed isolates (41 clinical isolates and three type strains) from Aspergillus section Nidulantes . We found that 21 clinical isolates were A. latus ; notably, standard methods of pathogen identification misidentified all A. latus isolates. The remaining isolates were identified as A. spinulosporus (8), A. quadrilineatus (1), or A. nidulans (11). Phylogenomic analyses shed light on the origin of A. latus , indicating one or two hybridization events gave rise to the species during the Miocene, approximately 15.4 to 8.8 million years ago. Characterizing the A. latus pangenome uncovered substantial genetic diversity within gene families and biosynthetic gene clusters. Transcriptomic analysis revealed that both parental genomes are actively expressed in nearly equal proportions and respond to environmental stimuli. Further investigation into infection-relevant chemical and physiological traits, including drug resistance profiles, growth under oxidative stress conditions, and secondary metabolite biosynthesis, highlight distinct phenotypic profiles of the hybrid A. latus compared to its parental and closely related species. Leveraging our comprehensive genomic and phenotypic analyses, we propose five genomic and phenotypic markers as diagnostics for A. latus species identification. These findings provide valuable insights into the evolutionary origin, genomic outcome, and phenotypic implications of hybridization in a cryptic fungal pathogen, thus enhancing our understanding of the underlying processes contributing to fungal pathogenesis. Furthermore, our study underscores the effectiveness of extensive genomic and phenotypic analyses as a promising approach for developing diagnostics applicable to future investigations of cryptic and emerging pathogens.},
}

@article {pmid37460717,
year = {2023},
author = {Kumari, K and Sharma, PK and Shikha, S and Singh, RP},
title = {Molecular characterization and in-depth genome analysis of Enterobacter sp. S-16.},
journal = {Functional & integrative genomics},
volume = {23},
number = {3},
pages = {245},
pmid = {37460717},
issn = {1438-7948},
mesh = {Humans ; *Enterobacter/genetics ; RNA, Ribosomal, 16S ; *Genome, Bacterial ; Genomics ; Carbohydrates ; Phylogeny ; },
abstract = {Enterobacter species are considered to be an opportunistic human pathogen owing to the existence of antibiotic-resistant strains and drug resides; however, the detailed analysis of the antibiotic resistance and virulence features in environmental isolates is poorly characterized. Here, in the study, we characterized the biochemical characteristics, and genome, pan-genome, and comparative genome analyses of an environmental isolate Enterobacter sp. S-16. The strain was identified as Enterobacter spp. by using 16S rRNA gene sequencing. To unravel genomic features, whole genome of Enterobacter sp. S-16 was sequenced using a hybrid assembly approach and genome assembly was performed using the Unicycler tool. The assembled genome contained the single conting size 5.3 Mbp, GC content 55.43%, and 4500 protein-coding genes. The genome analysis revealed the various gene clusters associated with virulence, antibiotic resistance, type VI secretion system (T6SS), and many stress tolerant genes, which may provide important insight for adapting to changing environment conditions. Moreover, different metabolic pathways were identified that potentially contribute to environmental survival. Various hydrolytic enzymes and motility functions equipped the strain S-16 as an active colonizer. The genome analysis confirms the presence of carbohydrate-active enzymes (CAZymes), and non-enzymatic carbohydrate-binding modules (CBMs) involved in the hydrolysis of complex carbohydrate polymers. Moreover, the pan-genome analysis provides detailed information about the core genes and shared genes with the closest related Enterobacter species. The present study is the first report showing the presence of YdhE/NorM in Enterobacter spp. Thus, the elucidation of genome sequencing will increase our understanding of the pathogenic nature of environmental isolate, supporting the One Health Concept.},
}

Humans
*Enterobacter/genetics
RNA, Ribosomal, 16S
*Genome, Bacterial
Genomics
Carbohydrates
Phylogeny

@article {pmid37449094,
year = {2023},
author = {Buzzanca, D and Kerkhof, PJ and Alessandria, V and Rantsiou, K and Houf, K},
title = {Arcobacteraceae comparative genome analysis demonstrates genome heterogeneity and reduction in species isolated from animals and associated with human illness.},
journal = {Heliyon},
volume = {9},
number = {7},
pages = {e17652},
pmid = {37449094},
issn = {2405-8440},
abstract = {The Arcobacteraceae family groups Gram-negative bacterial species previously included in the family Campylobacteraceae. These species of which some are considered foodborne pathogens, have been isolated from different environmental niches and hosts. They have been isolated from various types of foods, though predominantly from food of animal origin, as well as from stool of humans with enteritis. Their different abilities to survive in different hosts and environments suggest an evolutionary pressure with consequent variation in their genome content. Moreover, their different physiological and genomic characteristics led to the recent proposal to create new genera within this family, which is however criticized due to the lack of discriminatory features and biological and clinical relevance. Aims of the present study were to assess the Arcobacteraceae pangenome, and to characterize existing similarities and differences in 20 validly described species. For this, analysis has been conducted on the genomes of the corresponding type strains obtained by Illumina sequencing, applying several bioinformatic tools. Results of the present study do not support the proposed division into different genera and revealed the presence of pangenome partitions with numbers comparable to other Gram-negative bacteria genera, such as Campylobacter. Different gene class compositions in animal and human-associated species are present, including a higher percentage of virulence-related gene classes such as cell motility genes. The adaptation to environmental and/or host conditions of some species was identified by the presence of specific genes. Furthermore, a division into pathogenic and non-pathogenic species is suggested, which can support future research on food safety and public health.},
}

@article {pmid37446042,
year = {2023},
author = {Arifuzzaman, M and Jost, M and Wang, M and Chen, X and Perovic, D and Park, RF and Rouse, M and Forrest, K and Hayden, M and Khan, GA and Dracatos, PM},
title = {Mining the Australian Grains Gene Bank for Rust Resistance in Barley.},
journal = {International journal of molecular sciences},
volume = {24},
number = {13},
pages = {},
pmid = {37446042},
issn = {1422-0067},
mesh = {Chromosome Mapping ; *Hordeum/genetics/microbiology ; Disease Resistance/genetics ; Australia ; Phenotype ; *Basidiomycota/genetics ; Plant Diseases/genetics/microbiology ; },
abstract = {Global barley production is threatened by plant pathogens, especially the rusts. In this study we used a targeted genotype-by-sequencing (GBS) assisted GWAS approach to identify rust resistance alleles in a collection of 287 genetically distinct diverse barley landraces and historical cultivars available in the Australian Grains Genebank (AGG) and originally sourced from Eastern Europe. The accessions were challenged with seven US-derived cereal rust pathogen races including Puccinia hordei (Ph-leaf rust) race 17VA12C, P. coronata var. hordei (Pch-crown rust) race 91NE9305 and five pathogenically diverse races of P. striiformis f. sp. hordei (Psh-stripe rust) (PSH-33, PSH-48, PSH-54, PSH-72 and PSH-100) and phenotyped quantitatively at the seedling stage. Novel resistance factors were identified on chromosomes 1H, 2H, 4H and 5H in response to Pch, whereas a race-specific QTL on 7HS was identified that was effective only to Psh isolates PSH-72 and PSH-100. A major effect QTL on chromosome 5HL conferred resistance to all Psh races including PSH-72, which is virulent on all 12 stripe rust differential tester lines. The same major effect QTL was also identified in response to leaf rust (17VA12C) suggesting this locus contains several pathogen specific rust resistance genes or the same gene is responsible for both leaf rust and stripe rust resistance. Twelve accessions were highly resistant to both leaf and stripe rust diseases and also carried the 5HL QTL. We subsequently surveyed the physical region at the 5HL locus for across the barley pan genome variation in the presence of known resistance gene candidates and identified a rich source of high confidence protein kinase and antifungal genes in the QTL region.},
}

Chromosome Mapping
*Hordeum/genetics/microbiology
Disease Resistance/genetics
Australia
Phenotype
*Basidiomycota/genetics
Plant Diseases/genetics/microbiology

@article {pmid37435610,
year = {2023},
author = {Deverka, P and Geary, J and Mathews, C and Cohen, M and Hooker, G and Majumder, M and Skvarkova, Z and Cook-Deegan, R},
title = {Payer reimbursement practices and incentives for improving interpretation of germline genetic testing.},
journal = {Journal of law and the biosciences},
volume = {10},
number = {2},
pages = {lsad020},
doi = {10.1093/jlb/lsad020},
pmid = {37435610},
issn = {2053-9711},
abstract = {Germline genetic testing for inherited cancer risk has shifted to multi-gene panel tests (MGPTs). While MGPTs detect more pathogenic variants, they also detect more variants of uncertain significance (VUSs) that increase the possibility of harms such as unnecessary surgery. Data sharing by laboratories is critical to addressing the VUS problem. However, barriers to sharing and an absence of incentives have limited laboratory contributions to the ClinVar database. Payers can play a crucial role in the expansion of knowledge and effectiveness of genetic testing. Current policies affecting MGPT reimbursement are complex and create perverse incentives. Trends in utilization and coverage for private payers and Medicare illustrate opportunities and challenges for data sharing to close knowledge gaps and improve clinical utility. Policy options include making data sharing (i) a condition of payment, and (ii) a metric of laboratory quality in payment contracts, yielding preferred coverage or enhanced reimbursement. Mandating data sharing sufficient to verify interpretations and resolve discordance among labs under Medicare and federal health programs is an option for the US Congress. Such policies can reduce the current waste of valuable data needed for precision oncology and improved patient outcomes, enabling a learning health system.},
}

@article {pmid37434713,
year = {2023},
author = {Batarseh, TN and Batarseh, SN and Morales-Cruz, A and Gaut, BS},
title = {Comparative genomics of the Liberibacter genus reveals widespread diversity in genomic content and positive selection history.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1206094},
pmid = {37434713},
issn = {1664-302X},
abstract = {'Candidatus Liberibacter' is a group of bacterial species that are obligate intracellular plant pathogens and cause Huanglongbing disease of citrus trees and Zebra Chip in potatoes. Here, we examined the extent of intra- and interspecific genetic diversity across the genus using comparative genomics. Our approach examined a wide set of Liberibacter genome sequences including five pathogenic species and one species not known to cause disease. By performing comparative genomics analyses, we sought to understand the evolutionary history of this genus and to identify genes or genome regions that may affect pathogenicity. With a set of 52 genomes, we performed comparative genomics, measured genome rearrangement, and completed statistical tests of positive selection. We explored markers of genetic diversity across the genus, such as average nucleotide identity across the whole genome. These analyses revealed the highest intraspecific diversity amongst the 'Ca. Liberibacter solanacearum' species, which also has the largest plant host range. We identified sets of core and accessory genes across the genus and within each species and measured the ratio of nonsynonymous to synonymous mutations (dN/dS) across genes. We identified ten genes with evidence of a history of positive selection in the Liberibacter genus, including genes in the Tad complex, which have been previously implicated as being highly divergent in the 'Ca. L. capsica' species based on high values of dN.},
}

@article {pmid37433982,
year = {2023},
author = {Attwaters, M},
title = {A diverse and inclusive human pangenome.},
journal = {Nature reviews. Genetics},
volume = {},
number = {},
pages = {},
pmid = {37433982},
issn = {1471-0064},
}

@article {pmid37431308,
year = {2023},
author = {Amas, JC and Bayer, PE and Hong Tan, W and Tirnaz, S and Thomas, WJW and Edwards, D and Batley, J},
title = {Comparative pangenome analyses provide insights into the evolution of Brassica rapa resistance gene analogues (RGAs).},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/pbi.14116},
pmid = {37431308},
issn = {1467-7652},
support = {DP200100762//Australian Research Council/ ; DP210100296//Australian Research Council/ ; UWA1905- 006RTX//Grains Research and Development Corporation/ ; },
abstract = {Brassica rapa is grown worldwide as economically important vegetable and oilseed crop. However, its production is challenged by yield-limiting pathogens. The sustainable control of these pathogens mainly relies on the deployment of genetic resistance primarily driven by resistance gene analogues (RGAs). While several studies have identified RGAs in B. rapa, these were mainly based on a single genome reference and do not represent the full range of RGA diversity in B. rapa. In this study, we utilized the B. rapa pangenome, constructed from 71 lines encompassing 12 morphotypes, to describe a comprehensive repertoire of RGAs in B. rapa. We show that 309 RGAs were affected by presence-absence variation (PAV) and 223 RGAs were missing from the reference genome. The transmembrane leucine-rich repeat (TM-LRR) RGA class had more core gene types than variable genes, while the opposite was observed for nucleotide-binding site leucine-rich repeats (NLRs). Comparative analysis with the B. napus pangenome revealed significant RGA conservation (93%) between the two species. We identified 138 candidate RGAs located within known B. rapa disease resistance QTL, of which the majority were under negative selection. Using blackleg gene homologues, we demonstrated how these genes in B. napus were derived from B. rapa. This further clarifies the genetic relationship of these loci, which may be useful in narrowing-down candidate blackleg resistance genes. This study provides a novel genomic resource towards the identification of candidate genes for breeding disease resistance in B. rapa and its relatives.},
}

@article {pmid37430957,
year = {2022},
author = {Rani, A and Dike, CC and Mantri, N and Ball, A},
title = {Point-of-Care Lateral Flow Detection of Viable Escherichia coli O157:H7 Using an Improved Propidium Monoazide-Recombinase Polymerase Amplification Method.},
journal = {Foods (Basel, Switzerland)},
volume = {11},
number = {20},
pages = {},
pmid = {37430957},
issn = {2304-8158},
abstract = {The detection of both viable and viable but non-culturable (VBNC) Escherichia coli O157:H7 is a crucial part of food safety. Traditional culture-dependent methods are lengthy, expensive, laborious, and unable to detect VBNC. Hence, there is a need to develop a rapid, simple, and cost-effective detection method to differentiate between viable/dead E. coli O157:H7 and detect VBNC cells. In this work, recombinase polymerase amplification (RPA) was developed for the detection of viable E. coli O157:H7 through integration with propidium monoazide (PMAxx). Initially, two primer sets, targeting two different genes (rfbE and stx) were selected, and DNA amplification by RPA combined with PMAxx treatment and the lateral flow assay (LFA) was carried out. Subsequently, the rfbE gene target was found to be more effective in inhibiting the amplification from dead cells and detecting only viable E. coli O157:H7. The assay's detection limit was found to be 10[2] CFU/mL for VBNC E. coli O157:H7 when applied to spiked commercial beverages including milk, apple juice, and drinking water. pH values from 3 to 11 showed no significant effect on the efficacy of the assay. The PMAxx-RPA-LFA was completed at 39 °C within 40 min. This study introduces a rapid, robust, reliable, and reproducible method for detecting viable bacterial counts. In conclusion, the optimised assay has the potential to be used by the food and beverage industry in quality assurance related to E. coli O157:H7.},
}

@article {pmid37429841,
year = {2023},
author = {Tisza, MJ and Smith, DDN and Clark, AE and Youn, JH and , and Khil, PP and Dekker, JP},
title = {Roving methyltransferases generate a mosaic epigenetic landscape and influence evolution in Bacteroides fragilis group.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {4082},
pmid = {37429841},
issn = {2041-1723},
mesh = {Humans ; *Methyltransferases/genetics ; Bacteroides fragilis/genetics ; Epigenomics ; DNA Methylation/genetics ; *Bacteriophages/genetics ; Bacteroides ; Epigenesis, Genetic ; },
abstract = {Three types of DNA methyl modifications have been detected in bacterial genomes, and mechanistic studies have demonstrated roles for DNA methylation in physiological functions ranging from phage defense to transcriptional control of virulence and host-pathogen interactions. Despite the ubiquity of methyltransferases and the immense variety of possible methylation patterns, epigenomic diversity remains unexplored for most bacterial species. Members of the Bacteroides fragilis group (BFG) reside in the human gastrointestinal tract as key players in symbiotic communities but also can establish anaerobic infections that are increasingly multi-drug resistant. In this work, we utilize long-read sequencing technologies to perform pangenomic (n = 383) and panepigenomic (n = 268) analysis of clinical BFG isolates cultured from infections seen at the NIH Clinical Center over four decades. Our analysis reveals that single BFG species harbor hundreds of DNA methylation motifs, with most individual motif combinations occurring uniquely in single isolates, implying immense unsampled methylation diversity within BFG epigenomes. Mining of BFG genomes identified more than 6000 methyltransferase genes, approximately 1000 of which were associated with intact prophages. Network analysis revealed substantial gene flow among disparate phage genomes, implying a role for genetic exchange between BFG phages as one of the ultimate sources driving BFG epigenome diversity.},
}

Humans
*Methyltransferases/genetics
Bacteroides fragilis/genetics
Epigenomics
DNA Methylation/genetics
*Bacteriophages/genetics
Bacteroides
Epigenesis, Genetic

@article {pmid37424551,
year = {2023},
author = {Narayanan, S and Couger, B and Bates, H and Gupta, SK and Malayer, J and Ramachandran, A},
title = {Characterization of three Francisella tularensis genomes from Oklahoma, USA.},
journal = {Access microbiology},
volume = {5},
number = {6},
pages = {acmi000451},
pmid = {37424551},
issn = {2516-8290},
abstract = {Francisella tularensis , the causative agent for tularaemia, is a Tier 1 select agent, and a pan-species pathogen of global significance due to its zoonotic potential. Consistent genome characterization of the pathogen is essential to identify novel genes, virulence factors, antimicrobial resistance genes, for studying phylogenetics and other features of interest. This study was conducted to understand the genetic variations among genomes of F. tularensis isolated from two felines and one human source. Pan-genome analysis revealed that 97.7 % of genes were part of the core genome. All three F. tularensis isolates were assigned to sequence type A based on single nucleotide polymorphisms (SNPs) in sdhA. Most of the virulence genes were part of the core genome. An antibiotic resistance gene coding for class A beta-lactamase was detected in all three isolates. Phylogenetic analysis showed that these isolates clustered with other isolates reported from Central and South-Central USA. Assessment of large sets of the F. tularensis genome sequences is essential in understanding pathogen dynamics, geographical distribution and potential zoonotic implications.},
}

@article {pmid37423939,
year = {2023},
author = {Priyamvada, P and Ramaiah, S},
title = {Pan-genome and reverse vaccinology approaches to design multi-epitope vaccine against Epstein-Barr virus associated with colorectal cancer.},
journal = {Immunologic research},
volume = {},
number = {},
pages = {},
pmid = {37423939},
issn = {1559-0755},
abstract = {Epstein-Barr virus (EBV) is a global lymphotropic virus and has been associated with various malignancies, among which colorectal cancer (CRC) is the prevalent one causing mortality worldwide. In the recent past, numerous research efforts have been made to develop a potential vaccine against this virus; however, none is effective possibly due to their low throughput, laboriousness, and lack of sensitivity. In this study, we designed a multi-epitope subunit vaccine that targets latent membrane protein (LMP-2B) of EBV using pan-genome and reverse vaccinology approaches. Twenty-three major histocompatibility complex (MHC) epitopes (five class-I and eighteen class-II) and eight B-cell epitopes, which have been found to be antigenic, immunogenic, and non-toxic, were selected for the vaccine construction. Furthermore, 24 vaccine constructs (VCs) were designed from the predicted epitopes and out of which VC1 was selected and finalized based on its structural parameters. The functionality of VC1 was validated through molecular docking with different immune receptors (MHC class-I, MHC class-II, and TLRs). The binding affinity, molecular and immune simulation revealed that the VC1 had more stable interaction and is believed to elicit good immune responses against EBV. HIGHLIGHTS: Pan-genome and reverse vaccinology approaches were used to design a multi-epitope subunit vaccine against LMP-2B protein of EBV. Epitopes were selected based on the antigenic, immunogenic, and non-toxic properties. Twenty-four vaccine constructs (VCs) were designed from the predicted epitopes. Designed vaccine VC1 has shown good binding affinity and molecular and immune simulation. VC1 was validated using molecular docking with different immune receptors.},
}

@article {pmid37409285,
year = {2023},
author = {Luo, M and Sarnowski, TJ and Libault, M and Ríos, G and Charron, JB and Mantri, N and Zhang, S},
title = {Editorial: New insights into mechanisms of epigenetic modifiers in plant growth and development, volume II.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1213511},
pmid = {37409285},
issn = {1664-462X},
}