Microbial Genomics最新文献

{"title":"Delineating bacterial genera based on gene content analysis: a case study of the <i>Mycoplasmatales-Entomoplasmatales</i> clade within the class <i>Mollicutes</i>.","authors":"Xiao-Hua Yan, Shen-Chian Pei, Hsi-Ching Yen, Alain Blanchard, Pascal Sirand-Pugnet, Vincent Baby, Gail E Gasparich, Chih-Horng Kuo","doi":"10.1099/mgen.0.001321","DOIUrl":"10.1099/mgen.0.001321","url":null,"abstract":"<p><p>Genome-based analysis allows for large-scale classification of diverse bacteria and has been widely adopted for delineating species. Unfortunately, for higher taxonomic ranks such as genus, establishing a generally accepted approach based on genome analysis is challenging. While core-genome phylogenies depict the evolutionary relationships among species, determining the correspondence between clades and genera may not be straightforward. For genotypic divergence, the percentage of conserved proteins and genome-wide average amino acid identity are commonly used, but often do not provide a clear threshold for classification. In this work, we investigated the utility of global comparisons and data visualization in identifying clusters of species based on their overall gene content and rationalized that such patterns can be integrated with phylogeny and other information such as phenotypes for improving taxonomy. As a proof of concept, we selected 177 representative genome sequences from the <i>Mycoplasmatales-Entomoplasmatales</i> clade within the class <i>Mollicutes</i> for a case study. We found that the clustering patterns corresponded to the current understanding of these organisms, namely the split into three above-genus groups: Hominis, Pneumoniae and <i>Spiroplasma-Entomoplasmataceae</i>-Mycoides. However, at the genus level, several important issues were found. For example, recent taxonomic revisions that split the Hominis group into three genera and <i>Entomoplasmataceae</i> into five genera are problematic, as those newly described or emended genera lack clear differentiations in gene content from one another. Moreover, several cases of misclassification were identified. These findings demonstrated the utility of this approach and its potential application to other bacteria.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 11","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11567158/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142639280","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pangenomic insights into <i>Dehalobacter</i> evolution and acquisition of functional genes for bioremediation.","authors":"Olivia Bulka, Radhakrishnan Mahadevan, Elizabeth A Edwards","doi":"10.1099/mgen.0.001324","DOIUrl":"10.1099/mgen.0.001324","url":null,"abstract":"<p><p><i>Dehalobacter</i> is a genus of organohalide-respiring bacteria that is recognized for its fastidious growth using reductive dehalogenases (RDases). In the SC05 culture, however, a <i>Dehalobacter</i> population also mineralizes dichloromethane (DCM) produced by chloroform dechlorination using the <i>mec</i> cassette, just downstream of its active RDase. A closed genome of this DCM-mineralizing lineage has previously evaded assembly. Here, we present the genomes of two novel <i>Dehalobacter</i> strains, each of which was assembled from the metagenome of a distinct subculture from SC05. A pangenomic analysis of the <i>Dehalobacter</i> genus, including RDase synteny and phylogenomics, reveals at least five species of <i>Dehalobacter</i> based on average nucleotide identity, RDase and core gene synteny, as well as differential functional genes. An integration hotspot is also pinpointed in the <i>Dehalobacter</i> genome, in which many recombinase islands have accumulated. This nested recombinase island encodes the active RDase and <i>mec</i> cassette in both SC05 <i>Dehalobacter</i> genomes, indicating the transfer of key functional genes between species of <i>Dehalobacter</i>. Horizontal gene transfer between these two novel <i>Dehalobacter</i> strains has implications for the evolutionary history within the SC05 subcultures and of the <i>Dehalobacter</i> genus as a whole, especially regarding adaptation to anthropogenic chemicals.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 11","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11578063/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142676028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of psychrotrophic and thermoduric bacteria in raw milk using a multi-omics approach.","authors":"Xue Qin, Jingqi Cheng, Yue Qiu, Ning Guan, Tanushree B Gupta, Shuyan Wu, Yujun Jiang, Xinyan Yang, Chaoxin Man","doi":"10.1099/mgen.0.001311","DOIUrl":"10.1099/mgen.0.001311","url":null,"abstract":"<p><p>Psychrotrophic and thermoduric bacteria are the main reasons for the spoilage of dairy products. This study aims to address the composition and function of psychrotrophic and thermoduric bacteria in eight groups of raw milk samples obtained from Heilongjiang Province and Inner Mongolia (China). Microbial enumeration showed an average total bacterial count of 4.63 log c.f.u. ml^-1 and psychrotrophic bacterial counts of 4.82 log c.f.u. ml^-1. The mean counts of mesophilic and thermophilic thermoduric bacteria were 3.68 log and 1.81 log c.f.u. ml^-1, respectively. Isolated psychrotrophic bacteria (26 genera and 50 species) and mesophilic thermoduric bacteria (20 genera and 32 species) showed high microbial diversity. Through metagenomic and proteomic analyses, significant disparities in the concentration and community structure of psychrotrophic and thermoduric bacteria were observed among different locations. A large number of peptidases were annotated by metagenomics, which may result in milk spoilage. They mainly come from some typical psychrotrophic and thermoduric bacteria, such as <i>Chryseobacterium</i>, <i>Epilithonimonas</i>, <i>Pseudomonas</i>, <i>Psychrobacter</i>, <i>Acinetobacter, Lactococcus, Escherichia</i> and <i>Bacillus</i>. However, the main proteins detected in fresh raw milk were associated with bacterial growth, reproduction and adaptation to cold environments. This investigation provides valuable insights into the microbial communities and protein profiles of raw milk, shedding light on the microbial factors contributing to milk deterioration.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 11","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11540130/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142583672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Matching excellence: Oxford Nanopore Technologies' rise to parity with Pacific Biosciences in genome reconstruction of non-model bacterium with high G+C content.","authors":"Axel Soto-Serrano, Wenwen Li, Farhad M Panah, Yan Hui, Pablo Atienza, Alexey Fomenkov, Richard J Roberts, Paulina Deptula, Lukasz Krych","doi":"10.1099/mgen.0.001316","DOIUrl":"10.1099/mgen.0.001316","url":null,"abstract":"<p><p>The reconstruction of complete bacterial genomes is essential for microbial research, offering insights into genetic content, ontology and regulation. While Pacific Biosciences (PacBio) provides high-quality genomes, its cost remains a limitation. Oxford Nanopore Technologies (ONT) offers long reads at a lower cost, yet its error rate raises scepticism. Recent ONT advancements, such as new Flow cells (R10.4.1), chemistry (V14) and duplex mode, improve data quality. Our study compares ONT with PacBio and Illumina, including hybrid data. We used <i>Propionibacterium freudenreichii</i>, a bacterium with a genome known for being difficult to reconstruct. By combining data from ONT's Native Barcoding and a custom-developed BARSEQ method, we achieved high-quality, near-perfect genome assemblies. Our findings demonstrate, for the first time, that the combination of nanopore-only long-native with shorter PCR DNA reads (~3 kb) results in high-quality genome reconstruction, comparable to hybrid data assembly from two sequencing platforms. This endorses ONT as a cost-effective, stand-alone strategy for bacterial genome reconstruction. Additionally, we compared methylated motif detection between PacBio and ONT R10.4.1 data, showing that results comparable to PacBio are achievable using ONT, especially when utilizing the advanced Nanomotif tool.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 11","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11649196/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142621736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pan-genomic characterization and structural variant analysis reveal insights into spore development and species diversity in <i>Ganoderma</i>.","authors":"Hang Yu, Shasha Wang, Lina Wang, Weixin Wu, Wei Xu, Shuisheng Wu, Xiaoyan Li, Wen Xu, Zehao Huang, Yu Lin, Haifeng Wang","doi":"10.1099/mgen.0.001328","DOIUrl":"https://doi.org/10.1099/mgen.0.001328","url":null,"abstract":"<p><p>Understanding the genomic diversity and functional implications of <i>Ganoderma</i> species is crucial for elucidating their evolutionary history and biotechnological potential. Here, we present the first pan-genomic analysis of <i>Ganoderma</i> spp., combining five newly sequenced genomes with ten publicly available genomes. Our comprehensive comparative study unveiled a rich genomic landscape, identifying core genes shared among all <i>Ganoderma</i> strains and species-specific gene sets. Additionally, we identified structural variants impacting the expression of key genes, including insights into the <i>MSH4</i> gene involved in DNA repair and recombination processes, which exhibits a 440 bp insertion in the promoter region and a leucine-to-serine mutation in the gene body, potentially increasing spore production in the S3 strain. Overall, our study provides valuable insights into the genomic architecture and functional diversity of <i>Ganoderma</i>, paving the way for further research on its evolutionary dynamics, biotechnological applications and pharmaceutical potential.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 11","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142676025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolution of the CRISPR-Cas9 defence system in <i>Mycoplasma gallisepticum</i> following colonization of a novel bird host.","authors":"Thomas Ipoutcha, Iason Tsarmpopoulos, Géraldine Gourgues, Vincent Baby, Paul Dubos, Geoffrey E Hill, Yonathan Arfi, Carole Lartigue, Patricia Thébault, Camille Bonneaud, Pascal Sirand-Pugnet","doi":"10.1099/mgen.0.001320","DOIUrl":"10.1099/mgen.0.001320","url":null,"abstract":"<p><p>Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems are bacterial defences that target bacteriophages and mobile genetic elements. How these defences evolve in novel host environments remains largely unknown. We studied the evolution of the CRISPR-Cas system in <i>Mycoplasma gallisepticum</i> (also named <i>Mycoplasmoides gallisepticum</i>), a bacterial pathogen of poultry that jumped into a passerine host ~30 years ago. Over the decade following the host shift, all isolates displaying a functional CRISPR-Cas system were found not only to harbour completely new sets of spacers, but the DNA protospacer adjacent motif recognized by the main effector <i>M. gallisepticum</i> Cas9 (MgCas9) was also different. These changes in CRISPR-Cas diversity and specificity are consistent with a change in the community of phages and mobile elements infecting <i>M. gallisepticum</i> as it colonized the novel host. In the years following the host shift, we also detected a gradual rise in isolates displaying non-functional MgCas9. After 12 years, all circulating isolates harboured inactive forms only. This loss of CRISPR-Cas function comes at a time when the passerine host is known to have evolved widespread resistance, which in turn drove the evolution of increasing <i>M. gallisepticum</i> virulence through antagonistic coevolution. Such striking concordance in the rise of inactivated forms of CRISPR-Cas and the evolution of host resistance suggests that the inactivation of the CRISPR-Cas system was necessary for enabling adaptive bacterial responses to host-driven selection. We highlight the need to consider both host and pathogen selection pressures on bacteria for understanding the evolution of CRISPR-Cas systems and the key factors driving the emergence of a pathogenic bacterium in a novel host.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 11","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142648679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic diversity of <i>Campylobacter jejuni</i> and <i>Campylobacter coli</i> isolates recovered from human and poultry in Australia and New Zealand, 2017 to 2019.","authors":"Danielle M Cribb, Patrick J Biggs, Angus T McLure, Rhiannon L Wallace, Nigel P French, Kathryn Glass, Martyn D Kirk","doi":"10.1099/mgen.0.001319","DOIUrl":"https://doi.org/10.1099/mgen.0.001319","url":null,"abstract":"<p><p>We used genomic and epidemiological data to assess and compare the population structure and origins of <i>Campylobacter,</i> a major foodborne pathogen, in two neighbouring countries with strong trade and cultural links, similar poultry production systems and frequent movement of people and food products. The most common sequence types (STs) differed between Australia and New Zealand, with many unique to each country. Over half of all STs were represented by a single isolate. Multidrug-resistant (MDR) genotypes were detected in 0.8% of all samples, with no MDR isolates detected in poultry. Quinolone and tetracycline resistant ST6964 was prevalent in New Zealand (10.6% of <i>C. jejuni</i>). Closely related isolates suggested some similar food sources or contacts. We have shown that there is little genetic overlap in human and poultry STs of <i>Campylobacter</i> between the countries, which highlights that this common foodborne pathogen has domestic origins in Australia and New Zealand.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 11","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142583675","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome and antibiotic resistance characteristics of <i>Shigella</i> clinical isolates in Fujian Province, Southeast China, 2005-2019.","authors":"Mengying Huang, Xiaoxuan Zhang, Chaochen Luo, Haibin Xu, Yufeng Qiu, Jinsong Yang","doi":"10.1099/mgen.0.001325","DOIUrl":"https://doi.org/10.1099/mgen.0.001325","url":null,"abstract":"<p><p>Shigellosis is a serious public health issue in many developing countries. The emergence of multidrug-resistant (MDR) <i>Shigella</i> isolates has deepened the treatment difficulty and health burden of shigellosis. China is the largest developing country in the world, but so far, the genome of MDR <i>Shigella</i> isolates has not been well characterized. In this study, 60 clinical isolates of <i>Shigella</i> spp. in Fujian Province, southeast China, from 2005 to 2019 were characterized for drug resistance phenotype, whole-genome sequencing and bioinformatics analysis. The results showed that the MDR rate of <i>Shigella</i> isolates was 100%, among which the resistance rates of cefotaxime, ciprofloxacin and azithromycin were 36.67, 21.67 and 10.00 %, respectively. The positive rate of extended-spectrum beta-lactamase (ESBL)-producing strains was 23.33%. The resistance profiles of <i>Shigella flexneri</i> and <i>Shigella sonnei</i> to some antimicrobials differed. The MDR isolates carried multiple antimicrobial resistance genes, among which <i>blaCTX-M-14</i> and <i>blaCTX-M-15</i> mediated ESBL resistance<i>.</i> '<i>ISEcp1 -blaCTX-M -IS903</i>' (type I) and '<i>ISEcp1 -blaCTX-M</i>' (type II) were the most common genetic environments around the <i>blaCTX-M</i> genes, and plasmids containing these structures included IncFII, IncI1, IncI2 and IncN. The double gene mutation pattern of <i>gyr</i>A and <i>par</i>C resulted in a significant decrease in the sensitivity of <i>S. flexneri</i> to ciprofloxacin. The overall resistance phenotype and genotype concordance rate was 88.50%, and the sensitivity and specificity of the genotype antimicrobial susceptibility test (AST) were 93.35 and 82.53 %, respectively. However, inconsistency occurred between phenotypic and genotype profiles for a few antibiotics. Phylogenomic investigation with core genome multi-locus sequence typing (cgMLST) and SNPs were used to characterize the endemic transmission of these infections in Fujian and their evolutionary origin within the global context. For <i>S. flexneri</i>, Fujian isolates were all limited to PG3 and could be divided into three phylogenetic clusters. The ciprofloxacin-resistant strains were mainly F2a and FXv and assigned to the three clusters with different quinolone resistance-determining region mutation patterns. For <i>S. sonnei</i>, most Fujian strains belonged to Lineage III with genotype 3.7.6, except three isolates of Lineage I with genotype 1.3. The strains carrying the <i>blaCTX-M</i> genes were dispersed, indicating different origins of gene acquisition. Most of the circulating isolates in Fujian Province were not related to major international outbreak lineages and were only endemic to the country. In conclusion, multi-drug resistance of <i>Shigella</i> isolates in Fujian Province was serious, and genome-based laboratory surveillance will be crucial to the clinical treatment and public health measures for shigellosis.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 11","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142676007","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Longitudinal genomic surveillance of a UK intensive care unit shows a lack of patient colonisation by multi-drug-resistant Gram-negative bacterial pathogens.","authors":"Ann E Snaith, Robert A Moran, Rebecca J Hall, Anna Casey, Liz Ratcliffe, Willem van Schaik, Tony Whitehouse, Alan McNally","doi":"10.1099/mgen.0.001314","DOIUrl":"10.1099/mgen.0.001314","url":null,"abstract":"<p><p>Vulnerable patients in an intensive care unit (ICU) setting are at high risk of infection from bacteria including gut-colonising <i>Escherichia coli</i> and <i>Klebsiella</i> species. Complex ICU procedures often depend on successful antimicrobial treatment, underscoring the importance of understanding the extent of patient colonisation by multi-drug-resistant organisms (MDROs) in large UK ICUs. Previous work on ICUs globally uncovered high rates of colonisation by transmission of MDROs, but the situation in UK ICUs is less understood. Here, we investigated the diversity and antibiotic resistance gene (ARG) carriage of bacteria present in one of the largest UK ICUs at the Queen Elizabeth Hospital Birmingham (QEHB), focusing primarily on <i>E. coli</i> as both a widespread commensal and a globally disseminated multi-drug-resistant pathogen. Samples were taken during highly restrictive coronavirus disease 2019 (COVID-19) control measures from May to December 2021. Whole-genome and metagenomic sequencing were used to detect and report strain-level colonisation of patients, focusing on <i>E. coli</i> sequence types (STs), their colonisation dynamics and antimicrobial resistance gene carriage. We found a lack of multi-drug resistance (MDR) in the QEHB. Only one carbapenemase-producing organism was isolated, a <i>Citrobacter</i> carrying <i>bla</i> _KPC-2. There was no evidence supporting the spread of this strain, and there was little evidence overall of nosocomial acquisition or circulation of colonising <i>E. coli</i>. Whilst 22 different <i>E. coli</i> STs were identified, only 1 strain of the pandemic ST131 lineage was isolated. This ST131 strain was non-MDR and was found to be a clade A strain, associated with low levels of antibiotic resistance. Overall, the QEHB ICU had very low levels of pandemic or MDR strains, a result that may be influenced in part by the strict COVID-19 control measures in place at the time. Employing some of these infection prevention and control measures where reasonable in all ICUs might therefore assist in maintaining low levels of nosocomial MDR.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 11","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533117/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142569126","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Population-level whole-genome sequencing of <i>Ascochyta rabiei</i> identifies genomic loci associated with isolate aggressiveness.","authors":"Niloofar Vaghefi, Ido Bar, Jonathan Wanderley Lawley, Prabhakaran Thanjavur Sambasivam, Melody Christie, Rebecca Ford","doi":"10.1099/mgen.0.001326","DOIUrl":"https://doi.org/10.1099/mgen.0.001326","url":null,"abstract":"<p><p>Ascochyta blight caused by the ascomycete <i>Ascochyta rabiei</i> poses a major biotic threat to chickpea (<i>Cicer arietinum</i>) industries worldwide and incurs substantial costs to the Australian multimillion-dollar chickpea industry in both disease control and yield loss. The fungus was introduced to Australia in the 1970s from an unknown source population and, within a few decades, successfully established in all Australian agroecological chickpea-growing regions. Although genetically highly clonal, a broad range of phenotypic variation in terms of aggressiveness exists among the Australian <i>A. rabiei</i> isolates. More recently, highly aggressive isolates capable of causing severe disease symptoms on moderate to highly resistant chickpea cultivars have increased in frequency. To identify genetic loci potentially associated with <i>A. rabiei</i> aggressiveness on Australian chickpea cultivars, we performed deep genome sequencing of 230 isolates collected from a range of agroecological chickpea-growing regions between 2013 and 2020. Population genetic analyses using genome-wide SNP data identified three main clusters of genetically closely related isolates in Australia. Phylogenetic analyses showed that highly aggressive phenotypes developed multiple times independently throughout the phylogeny. The results point to a minor contribution of multiple genetic regions and most likely epigenomic variations to aggressiveness of <i>A. rabiei</i> isolates on Australian chickpea cultivars.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 11","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142692751","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}