{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:20:23Z","timestamp":1787008823483,"version":"build-2736575974"},"reference-count":84,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,2,22]],"date-time":"2024-02-22T00:00:00Z","timestamp":1708560000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100007917","name":"Agricultural Research Service","doi-asserted-by":"publisher","award":["58-2040-9-011"],"award-info":[{"award-number":["58-2040-9-011"]}],"id":[{"id":"10.13039\/100007917","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"USDA NIFA","doi-asserted-by":"publisher","award":["HAW09706-G"],"award-info":[{"award-number":["HAW09706-G"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"USDA NIFA","doi-asserted-by":"publisher","award":["1030040"],"award-info":[{"award-number":["1030040"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"NIGMS","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P20GM125508"],"award-info":[{"award-number":["P20GM125508"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Homologous recombination is a major force mechanism driving bacterial evolution, host adaptability, and acquisition of novel virulence traits. Pectobacterium parmentieri is a plant bacterial pathogen distributed worldwide, primarily affecting potatoes, by causing soft rot and blackleg diseases. The goal of this investigation was to understand the impact of homologous recombination on the genomic evolution of P. parmentieri. Analysis of P. parmentieri genomes using Roary revealed a dynamic pan-genome with 3,742 core genes and over 55% accessory genome variability. Bayesian population structure analysis identified 7 lineages, indicating species heterogeneity. ClonalFrameML analysis displayed 5,125 recombination events, with the lineage 4 exhibiting the highest events. fastGEAR analysis identified 486 ancestral and 941 recent recombination events ranging from 43\u2005bp to 119\u2005kb and 36\u2005bp to 13.96\u2005kb, respectively, suggesting ongoing adaptation. Notably, 11% (412 genes) of the core genome underwent recent recombination, with lineage 1 as the main donor. The prevalence of recent recombination (double compared to ancient) events implies continuous adaptation, possibly driven by global potato trade. Recombination events were found in genes involved in vital cellular processes (DNA replication, DNA repair, RNA processing, homeostasis, and metabolism), pathogenicity determinants (type secretion systems, cell-wall degrading enzymes, iron scavengers, lipopolysaccharides (LPS), flagellum, etc.), antimicrobial compounds (phenazine and colicin) and even CRISPR-Cas genes. Overall, these results emphasize the potential role of homologous recombination in P. parmentieri's evolutionary dynamics, influencing host colonization, pathogenicity, adaptive immunity, and ecological fitness.<\/jats:p>","DOI":"10.1093\/gbe\/evae032","type":"journal-article","created":{"date-parts":[[2024,2,21]],"date-time":"2024-02-21T01:49:29Z","timestamp":1708480169000},"source":"Crossref","is-referenced-by-count":5,"title":["Impact of Homologous Recombination on Core Genome Evolution and Host Adaptation of\n                    <i>Pectobacterium parmentieri<\/i>"],"prefix":"10.1093","volume":"16","author":[{"given":"Dario","family":"Arizala","sequence":"first","affiliation":[{"name":"Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa , Honolulu, HI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5887-2050","authenticated-orcid":false,"given":"Mohammad","family":"Arif","sequence":"additional","affiliation":[{"name":"Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa , Honolulu, HI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,2,22]]},"reference":[{"key":"2024032920173927500_evae032-B1","doi-asserted-by":"crossref","first-page":"5575","DOI":"10.1099\/ijsem.0.001485","article-title":"Genome-based phylogeny and taxonomy of the \u2018enterobacteriales\u2019: proposal for enterobacterales ord. Nov. divided into the families Enterobacteriaceae, erwiniaceae fam. Nov., pectobacteriaceae fam. Nov., yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov","volume":"66","author":"Adeolu","year":"2016","journal-title":"Int J Syst Evol Microbiol"},{"key":"2024032920173927500_evae032-B2","doi-asserted-by":"crossref","first-page":"e02098-19","DOI":"10.1128\/AEM.02098-19","article-title":"Multiple introductions of tomato pathogen Clavibacter michiganensis subsp. michiganensis into Iran as revealed by a global-scale phylogeographic analysis","volume":"85","author":"Ansari","year":"2019","journal-title":"Appl Environ Microbiol"},{"key":"2024032920173927500_evae032-B3","doi-asserted-by":"crossref","first-page":"855262","DOI":"10.3389\/fpls.2022.855262","article-title":"Editorial: genome-wide analyses of Pectobacterium and Dickeya species","volume":"13","author":"Arif","year":"2022","journal-title":"Front Plant Sci"},{"key":"2024032920173927500_evae032-B4","doi-asserted-by":"crossref","first-page":"247","DOI":"10.3390\/pathogens8040247","article-title":"Genome-wide analyses revealed remarkable heterogeneity in pathogenicity determinants, antimicrobial compounds, and CRISPR-cas systems of complex phytopathogenic genus Pectobacterium","volume":"8","author":"Arizala","year":"2019","journal-title":"Pathogens"},{"key":"2024032920173927500_evae032-B5","doi-asserted-by":"crossref","first-page":"970","DOI":"10.1094\/PDIS-09-19-1894-PDN","article-title":"First report of bacterial soft rot and blackleg on potato caused by Pectobacterium parmentieri in Hawaii","volume":"104","author":"Arizala","year":"2019","journal-title":"Plant Dis"},{"key":"2024032920173927500_evae032-B6","doi-asserted-by":"crossref","first-page":"663851","DOI":"10.3389\/fpls.2021.663851","article-title":"Genomic and phenotypic biology of novel strains of Dickeya zeae isolated from pineapple and taro in Hawaii: insights into genome plasticity, pathogenicity, and virulence determinants","volume":"12","author":"Boluk","year":"2021","journal-title":"Front Plant Sci"},{"key":"2024032920173927500_evae032-B7","doi-asserted-by":"crossref","first-page":"8365","DOI":"10.1038\/srep08365","article-title":"RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes","volume":"5","author":"Brettin","year":"2015","journal-title":"Sci Rep"},{"key":"2024032920173927500_evae032-B8","doi-asserted-by":"crossref","first-page":"2237","DOI":"10.1094\/PDIS-11-20-2502-PDN","article-title":"First report of Pectobacterium parmentieri causing blackleg on potato in Inner Mongolia, China","volume":"105","author":"Cao","year":"2021","journal-title":"Plant Dis"},{"key":"2024032920173927500_evae032-B9","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"Trimal: a tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","author":"Capella-Guti\u00e9rrez","year":"2009","journal-title":"Bioinformatics"},{"key":"2024032920173927500_evae032-B10","doi-asserted-by":"crossref","first-page":"878","DOI":"10.1016\/j.ympev.2010.05.020","article-title":"Comparative network clustering of direct repeats (DRs) and cas genes confirms the possibility of the horizontal transfer of CRISPR locus among bacteria","volume":"56","author":"Chakraborty","year":"2010","journal-title":"Mol Phylogenet Evol"},{"key":"2024032920173927500_evae032-B11","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1146\/annurev-phyto-080417-045906","article-title":"The changing face of bacterial soft-rot diseases","volume":"56","author":"Charkowski","year":"2018","journal-title":"Annu Rev Phytopathol."},{"key":"2024032920173927500_evae032-B12","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1146\/annurev-phyto-081211-173013","article-title":"The role of secretion systems and small molecules in soft-rot Enterobacteriaceae pathogenicity","volume":"50","author":"Charkowski","year":"2012","journal-title":"Annu Rev Phytopathol"},{"key":"2024032920173927500_evae032-B13","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/j.micpath.2014.11.005","article-title":"The role of pgaC in Klebsiella pneumoniae virulence and biofilm formation","volume":"77","author":"Chen","year":"2014","journal-title":"Microb Pathog."},{"key":"2024032920173927500_evae032-B14","doi-asserted-by":"crossref","first-page":"606","DOI":"10.1186\/s12864-018-4975-4","article-title":"Horizontal gene transfer plays a major role in the pathological convergence of Xanthomonas lineages on common bean","volume":"19","author":"Chen","year":"2018","journal-title":"BMC Genomics"},{"key":"2024032920173927500_evae032-B15","doi-asserted-by":"crossref","first-page":"e991","DOI":"10.1002\/mbo3.991","article-title":"Type VI secretion system of Pseudomonas aeruginosa is associated with biofilm formation but not environmental adaptation","volume":"9","author":"Chen","year":"2020","journal-title":"MicrobiologyOpen"},{"key":"2024032920173927500_evae032-B16","doi-asserted-by":"crossref","first-page":"1224","DOI":"10.1093\/molbev\/mst028","article-title":"Hierarchical and spatially explicit clustering of DNA sequences with BAPS software","volume":"30","author":"Cheng","year":"2013","journal-title":"Mol Biol Evol"},{"key":"2024032920173927500_evae032-B17","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1094\/PHYTO-09-16-0321-R","article-title":"Homologous recombination and Xylella fastidiosa host\u2013pathogen associations in South America","volume":"107","author":"Coletta-Filho","year":"2017","journal-title":"Phytopathology"},{"key":"2024032920173927500_evae032-B18","doi-asserted-by":"crossref","first-page":"e1006855","DOI":"10.1371\/journal.pgen.1006855","article-title":"Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila","volume":"13","author":"David","year":"2017","journal-title":"PLoS Genet"},{"key":"2024032920173927500_evae032-B19","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1094\/PHYTO-04-12-0083-R","article-title":"Pectobacterium spp. Associated with bacterial stem rot syndrome of potato in Canada","volume":"102","author":"De Boer","year":"2012","journal-title":"Phytopathology"},{"key":"2024032920173927500_evae032-B20","doi-asserted-by":"crossref","first-page":"5222","DOI":"10.1099\/ijsem.0.002448","article-title":"Pectobacterium polaris sp. Nov., isolated from potato (Solanum tuberosum)","volume":"67","author":"Dees","year":"2017","journal-title":"Int J Syst Evol Microbiol"},{"key":"2024032920173927500_evae032-B21","first-page":"1","article-title":"Co-occurrence of latent Dickeya and Pectobacterium species in potato seed tuber samples from northern Finland","volume":"30","author":"Degefu","year":"2021","journal-title":"Agri Food Sci"},{"key":"2024032920173927500_evae032-B22","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1038\/nrmicro.2015.13","article-title":"Within-host evolution of bacterial pathogens","volume":"14","author":"Didelot","year":"2016","journal-title":"Nat Rev Microbiol"},{"key":"2024032920173927500_evae032-B23","doi-asserted-by":"crossref","first-page":"e1004041","DOI":"10.1371\/journal.pcbi.1004041","article-title":"ClonalFrameML: efficient inference of recombination in whole bacterial genomes","volume":"11","author":"Didelot","year":"2015","journal-title":"PLoS Comput Biol"},{"key":"2024032920173927500_evae032-B24","doi-asserted-by":"crossref","first-page":"9070","DOI":"10.1073\/pnas.1510839112","article-title":"Recombinant transfer in the basic genome of Escherichia coli","volume":"112","author":"Dixit","year":"2015","journal-title":"Proc. Natl. Acad. Sci. U S A"},{"key":"2024032920173927500_evae032-B25","doi-asserted-by":"crossref","first-page":"3956","DOI":"10.1038\/ncomms4956","article-title":"Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus","volume":"5","author":"Everitt","year":"2014","journal-title":"Nat Commun"},{"key":"2024032920173927500_evae032-B26","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1111\/mpp.12007","article-title":"Role of iron homeostasis in the virulence of phytopathogenic bacteria: an \u2018\u00e0 la carte\u2019 menu","volume":"14","author":"Franza","year":"2013","journal-title":"Molecu Plant Pathol"},{"key":"2024032920173927500_evae032-B27","doi-asserted-by":"crossref","first-page":"316","DOI":"10.3390\/microorganisms9020316","article-title":"Interaction between Dickeya dianthicola and Pectobacterium parmentieri in potato infection under field conditions","volume":"9","author":"Ge","year":"2021","journal-title":"Microorganisms"},{"key":"2024032920173927500_evae032-B28","doi-asserted-by":"crossref","first-page":"e02494-18","DOI":"10.1128\/mBio.02494-18","article-title":"Impact of homologous recombination on the evolution of prokaryotic core genomes","volume":"10","author":"Gonz\u00e1lez-Torres","year":"2019","journal-title":"mBio"},{"key":"2024032920173927500_evae032-B29","doi-asserted-by":"crossref","first-page":"9594","DOI":"10.3390\/ijms22179594","article-title":"The knockout of enterobactin-related gene in Pectobacterium atrosepticum results in reduced stress resistance and virulence towards the primed plants","volume":"22","author":"Gorshkov","year":"2021","journal-title":"IJMS"},{"key":"2024032920173927500_evae032-B30","doi-asserted-by":"crossref","first-page":"e33033","DOI":"10.1371\/journal.pone.0033033","article-title":"Ferredoxin containing bacteriocins suggest a novel mechanism of iron uptake in Pectobacterium spp","volume":"7","author":"Grinter","year":"2012","journal-title":"PLoS One"},{"key":"2024032920173927500_evae032-B31","doi-asserted-by":"crossref","first-page":"1431","DOI":"10.1094\/MPMI-21-11-1431","article-title":"The flagellar sigma factor FliA is required for Dickeya dadantii virulence","volume":"21","author":"Jahn","year":"2008","journal-title":"Mol Plant Microbe Interact"},{"key":"2024032920173927500_evae032-B32","doi-asserted-by":"crossref","first-page":"e00136-18","DOI":"10.1128\/AEM.00136-18","article-title":"Genomic inference of recombination-mediated evolution in Xanthomonas euvesicatoria and X. perforans","volume":"84","author":"Jibrin","year":"2018","journal-title":"Appl Environ Microbiol"},{"key":"2024032920173927500_evae032-B33","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/07060661.2020.1777465","article-title":"Systemic colonization of potato plants resulting from potato haulm inoculation with Dickeya solani or Pectobacterium parmentieri","volume":"43","author":"Kastelein","year":"2021","journal-title":"Can J Plant Pathol"},{"key":"2024032920173927500_evae032-B34","doi-asserted-by":"crossref","first-page":"5379","DOI":"10.1099\/ijsem.0.001524","article-title":"Transfer of the potato plant isolates of Pectobacterium wasabiae to Pectobacterium parmentieri sp. Nov","volume":"66","author":"Khayi","year":"2016","journal-title":"Int J Syst Evol Microbiol"},{"key":"2024032920173927500_evae032-B35","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1007\/s10709-014-9793-2","article-title":"Genomic overview of the phytopathogen Pectobacterium wasabiae strain RNS 08.42.1A suggests horizontal acquisition of quorum-sensing genes","volume":"143","author":"Khayi","year":"2015","journal-title":"Genetica"},{"key":"2024032920173927500_evae032-B36","doi-asserted-by":"crossref","first-page":"4539","DOI":"10.1128\/AEM.01336-08","article-title":"Phylogeny and virulence of naturally occurring type III secretion system-deficient Pectobacterium strains","volume":"75","author":"Kim","year":"2009","journal-title":"Appl Environ Microbiol"},{"key":"2024032920173927500_evae032-B37","doi-asserted-by":"crossref","first-page":"45133","DOI":"10.1038\/srep45133","article-title":"Sequential displacement of type VI secretion system effector genes leads to evolution of diverse immunity gene arrays in Vibrio cholerae","volume":"7","author":"Kirchberger","year":"2017","journal-title":"Sci Rep"},{"key":"2024032920173927500_evae032-B38","doi-asserted-by":"crossref","first-page":"679","DOI":"10.4161\/rna.24022","article-title":"CRISPR-Cas: evolution of an RNA-based adaptive immunity system in prokaryotes","volume":"10","author":"Koonin","year":"2013","journal-title":"RNA Biol"},{"key":"2024032920173927500_evae032-B39","doi-asserted-by":"crossref","first-page":"4453","DOI":"10.1093\/bioinformatics\/btz305","article-title":"RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference","volume":"35","author":"Kozlov","year":"2019","journal-title":"Bioinformatics"},{"key":"2024032920173927500_evae032-B40","doi-asserted-by":"crossref","DOI":"10.1128\/ecosalplus.7.2.6","article-title":"Homologous recombination\u2014experimental systems, analysis, and significance","volume":"4","author":"Kuzminov","year":"2011","journal-title":"EcoSal Plus"},{"key":"2024032920173927500_evae032-B41","doi-asserted-by":"crossref","first-page":"1487","DOI":"10.1099\/mic.0.067280-0","article-title":"Characterization of genes required for the pathogenicity of Pectobacterium carotovorum subsp. carotovorum Pcc21 in Chinese cabbage","volume":"159","author":"Lee","year":"2013","journal-title":"Microbiology"},{"key":"2024032920173927500_evae032-B42","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1038\/cr.2008.1","article-title":"Homologous recombination in DNA repair and DNA damage tolerance","volume":"18","author":"Li","year":"2008","journal-title":"Cell Res"},{"key":"2024032920173927500_evae032-B43","doi-asserted-by":"crossref","first-page":"e57794","DOI":"10.1371\/journal.pone.0057794","article-title":"Aerobactin synthesis genes iucA and iucC contribute to the pathogenicity of avian pathogenic Escherichia coli O2 strain E058","volume":"8","author":"Ling","year":"2013","journal-title":"PLoS One"},{"key":"2024032920173927500_evae032-B44","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1007\/978-1-62703-646-7_10","article-title":"Phylogeny-aware alignment with PRANK. In: multiple sequence alignment methods. Russell, DJ, editor","volume":"1079","author":"L\u00f6ytynoja","year":"2014","journal-title":"Methods Mol Biol"},{"key":"2024032920173927500_evae032-B45","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1038\/nrmicro3569","article-title":"An updated evolutionary classification of CRISPR\u2013cas systems","volume":"13","author":"Makarova","year":"2015","journal-title":"Nat Rev Microbiol"},{"key":"2024032920173927500_evae032-B46","doi-asserted-by":"crossref","first-page":"e22974","DOI":"10.1371\/journal.pone.0022974","article-title":"The 3-hydroxy-2-butanone pathway is required for Pectobacterium carotovorum pathogenesis","volume":"6","author":"Marquez-Villavicencio","year":"2011","journal-title":"PLoS One"},{"key":"2024032920173927500_evae032-B47","doi-asserted-by":"crossref","first-page":"3527","DOI":"10.1002\/pmic.200600759","article-title":"Host-extract induced changes in the secretome of the plant pathogenic bacterium Pectobacterium atrosepticum","volume":"7","author":"Mattinen","year":"2007","journal-title":"Proteomics"},{"key":"2024032920173927500_evae032-B48","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1007\/s10658-012-0084-4","article-title":"Characterisation of Pectobacterium wasabiae causing blackleg and soft rot diseases in South Africa","volume":"135","author":"Moleleki","year":"2013","journal-title":"Eur J Plant Pathol"},{"key":"2024032920173927500_evae032-B49","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1111\/mpp.12372","article-title":"A quorum sensing-defective mutant of Pectobacterium carotovorum ssp. brasiliense 1692 is attenuated in virulence and unable to occlude xylem tissue of susceptible potato plant stems","volume":"18","author":"Moleleki","year":"2017","journal-title":"Mol Plant Pathol"},{"key":"2024032920173927500_evae032-B50","doi-asserted-by":"crossref","first-page":"8249","DOI":"10.1038\/s41598-022-12382-3","article-title":"Diversity and distribution of type VI secretion system gene clusters in bacterial plasmids","volume":"12","author":"Morgado","year":"2022","journal-title":"Sci Rep"},{"key":"2024032920173927500_evae032-B51","doi-asserted-by":"crossref","first-page":"6840","DOI":"10.1073\/pnas.1800672115","article-title":"Bacterial iron acquisition mediated by outer membrane translocation and cleavage of a host protein","volume":"115","author":"Mosbahi","year":"2018","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2024032920173927500_evae032-B52","doi-asserted-by":"crossref","first-page":"1167","DOI":"10.1093\/molbev\/msx066","article-title":"Efficient inference of recent and ancestral recombination within bacterial populations","volume":"34","author":"Mostowy","year":"2017","journal-title":"Mol Biol Evol"},{"key":"2024032920173927500_evae032-B53","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1007\/s10658-012-0036-z","article-title":"Pectinolytic bacteria associated with potato soft rot and blackleg in South Africa and Zimbabwe","volume":"134","author":"Ngadze","year":"2012","journal-title":"Eur J Plant Pathol"},{"key":"2024032920173927500_evae032-B54","doi-asserted-by":"crossref","first-page":"e73718","DOI":"10.1371\/journal.pone.0073718","article-title":"Role and regulation of the flp\/tad pilus in the virulence of Pectobacterium atrosepticum SCRI1043 and Pectobacterium wasabiae SCC3193","volume":"8","author":"Nykyri","year":"2013","journal-title":"PLoS One"},{"key":"2024032920173927500_evae032-B55","doi-asserted-by":"crossref","first-page":"e1003013","DOI":"10.1371\/journal.ppat.1003013","article-title":"Revised phylogeny and novel horizontally acquired virulence determinants of the model soft rot phytopathogen Pectobacterium wasabiae SCC3193","volume":"8","author":"Nykyri","year":"2012","journal-title":"PLoS Pathog"},{"key":"2024032920173927500_evae032-B56","doi-asserted-by":"crossref","first-page":"2077","DOI":"10.3390\/ijms23042077","article-title":"Heterogenicity within the LPS structure in relation to the chosen genomic and physiological features of the plant pathogen Pectobacterium parmentieri","volume":"23","author":"Ossowska","year":"2022","journal-title":"IJMS"},{"key":"2024032920173927500_evae032-B57","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: rapid large-scale prokaryote pan genome analysis","volume":"31","author":"Page","year":"2015","journal-title":"Bioinformatics"},{"key":"2024032920173927500_evae032-B58","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1146\/annurev-genet-120215-035146","article-title":"Transition metals and virulence in bacteria","volume":"50","author":"Palmer","year":"2016","journal-title":"Annu Rev Genet"},{"key":"2024032920173927500_evae032-B59","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1111\/aab.12076","article-title":"Characterisation of Pectobacterium wasabiae and Pectobacterium carotovorum subsp. carotovorum isolates from diseased potato plants in Finland","volume":"163","author":"Pasanen","year":"2013","journal-title":"Ann Appl Biol"},{"key":"2024032920173927500_evae032-B60","doi-asserted-by":"crossref","first-page":"1659","DOI":"10.1007\/s00253-010-2509-3","article-title":"Metabolism and function of phenazines in bacteria: impacts on the behavior of bacteria in the environment and biotechnological processes","volume":"86","author":"Pierson","year":"2010","journal-title":"Appl Microbiol Biotechnol"},{"issue":"3","key":"2024032920173927500_evae032-B61","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1094\/MPMI-4-276","article-title":"Identification of pathogenicity determinants of Erwinia carotovora subsp. carotovora by transposon mutagenesis","volume":"4","author":"Pirhonen","year":"1991","journal-title":"Mol Plant Microbe Interact"},{"key":"2024032920173927500_evae032-B62","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1007\/s10658-009-9551-y","article-title":"Genetic characterisation of Pectobacterium wasabiae causing soft rot disease of potato in New Zealand","volume":"126","author":"Pitman","year":"2010","journal-title":"Eur J Plant Pathol"},{"key":"2024032920173927500_evae032-B63","doi-asserted-by":"crossref","first-page":"2319","DOI":"10.1038\/s41396-019-0423-y","article-title":"Patterns of inter- and intrasubspecific homologous recombination inform eco-evolutionary dynamics of Xylella fastidiosa","volume":"13","author":"Potnis","year":"2019","journal-title":"ISME J"},{"key":"2024032920173927500_evae032-B64","doi-asserted-by":"crossref","DOI":"10.1099\/mgen.0.000461","article-title":"Host adaptation and microbial competition drive Ralstonia solanacearum phylotype I evolution in the Republic of Korea","volume":"6","author":"Prokchorchik","year":"2020","journal-title":"Microbial Genomics"},{"key":"2024032920173927500_evae032-B65","doi-asserted-by":"crossref","first-page":"1528","DOI":"10.1073\/pnas.0510322103","article-title":"Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the dictyostelium host model system","volume":"103","author":"Pukatzki","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2024032920173927500_evae032-B66","doi-asserted-by":"crossref","first-page":"e01914-20","DOI":"10.1128\/mBio.01914-20","article-title":"Enterobacterial common antigen: synthesis and function of an enigmatic molecule","volume":"11","author":"Rai","year":"2020","journal-title":"mBio"},{"key":"2024032920173927500_evae032-B67","doi-asserted-by":"crossref","first-page":"7541","DOI":"10.1128\/AEM.03103-09","article-title":"Characterization of a new bacteriocin, carocin d, from Pectobacterium carotovorum subsp. carotovorum Pcc21","volume":"76","author":"Roh","year":"2010","journal-title":"Appl Environ Microbiol"},{"key":"2024032920173927500_evae032-B68","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1111\/j.1364-3703.2010.00644.x","article-title":"In silico analysis reveals multiple putative type VI secretion systems and effector proteins in Pseudomonas syringae pathovars","volume":"11","author":"Sarris","year":"2010","journal-title":"Mol Plant Pathol"},{"key":"2024032920173927500_evae032-B69","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"2024032920173927500_evae032-B70","doi-asserted-by":"crossref","first-page":"2379","DOI":"10.3389\/fmicb.2019.02379","article-title":"The impact of type VI secretion system, bacteriocins and antibiotics on bacterial competition of Pectobacterium carotovorum subsp. brasiliense and the regulation of carbapenem biosynthesis by iron and the ferric-uptake regulator","volume":"10","author":"Shyntum","year":"2019","journal-title":"Front Microbiol"},{"key":"2024032920173927500_evae032-B71","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1094\/PDIS-01-17-0013-PDN","article-title":"Pectobacterium parmentieri causing soft rot on potato tubers in Southern Europe","volume":"101","author":"Su\u00e1rez","year":"2017","journal-title":"Plant Disease"},{"issue":"11","key":"2024032920173927500_evae032-B72","doi-asserted-by":"crossref","first-page":"a016550","DOI":"10.1101\/cshperspect.a016550","article-title":"Recombination and replication","volume":"6","author":"Syeda","year":"2014","journal-title":"Cold Spring Harb Perspect Biol"},{"key":"2024032920173927500_evae032-B73","doi-asserted-by":"crossref","first-page":"1216","DOI":"10.1128\/JB.06521-11","article-title":"Nature and intensity of selection pressure on CRISPR-associated genes","volume":"194","author":"Takeuchi","year":"2012","journal-title":"J Bacteriol"},{"key":"2024032920173927500_evae032-B74","doi-asserted-by":"crossref","first-page":"786","DOI":"10.1094\/MPMI-06-17-0146-R","article-title":"Genomic analysis of Clavibacter michiganensis reveals insight into virulence strategies and genetic diversity of a gram-positive bacterial pathogen","volume":"30","author":"Thapa","year":"2017","journal-title":"Mol Plant Microbe Interact"},{"key":"2024032920173927500_evae032-B75","doi-asserted-by":"crossref","first-page":"93","DOI":"10.12688\/wellcomeopenres.14694.1","article-title":"RhierBAPS: an R implementation of the population clustering algorithm hierBAPS","volume":"3","author":"Tonkin-Hill","year":"2018","journal-title":"Wellcome Open Res"},{"key":"2024032920173927500_evae032-B76","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1146\/annurev.phyto.44.070505.143444","article-title":"Comparative genomics reveals what makes an enterobacterial plant pathogen","volume":"44","author":"Toth","year":"2006","journal-title":"Annu Rev Phytopathol"},{"key":"2024032920173927500_evae032-B77","doi-asserted-by":"crossref","first-page":"e11126","DOI":"10.1371\/journal.pone.0011126","article-title":"The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella","volume":"5","author":"Touchon","year":"2010","journal-title":"PLoS One"},{"key":"2024032920173927500_evae032-B78","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1111\/j.1462-2920.2007.01444.x","article-title":"Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses","volume":"10","author":"Tyson","year":"2008","journal-title":"Environ Microbiol"},{"key":"2024032920173927500_evae032-B79","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1094\/MPMI-21-5-0547","article-title":"Citrate uptake into Pectobacterium atrosepticum is critical for bacterial virulence","volume":"21","author":"Urbany","year":"2008","journal-title":"Mol Plant Microbe Interact"},{"key":"2024032920173927500_evae032-B80","doi-asserted-by":"crossref","first-page":"e02972-18","DOI":"10.1128\/AEM.02972-18","article-title":"Genomic diversity and recombination among Xylella fastidiosa subspecies","volume":"85","author":"Vanhove","year":"2019","journal-title":"Appl Environ Microbiol"},{"issue":"27","key":"2024032920173927500_evae032-B81","doi-asserted-by":"crossref","first-page":"10524","DOI":"10.1074\/jbc.TM118.000372","article-title":"Homologous recombination and the repair of DNA double-strand breaks","volume":"293","author":"Wright","year":"2018","journal-title":"J Biol Chem"},{"key":"2024032920173927500_evae032-B82","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1186\/s12864-018-5140-9","article-title":"High genomic variability in the plant pathogenic bacterium Pectobacterium parmentieri deciphered from de novo assembled complete genomes","volume":"19","author":"Zoledowska","year":"2018","journal-title":"BMC Genomics"},{"key":"2024032920173927500_evae032-B83","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1094\/PDIS-05-17-0761-RE","article-title":"Population structure and biodiversity of Pectobacterium parmentieri isolated from potato fields in temperate climate","volume":"102","author":"Zoledowska","year":"2018","journal-title":"Plant Dis"},{"key":"2024032920173927500_evae032-B84","doi-asserted-by":"crossref","first-page":"101","DOI":"10.3390\/microorganisms7040101","article-title":"Metabolic modeling of Pectobacterium parmentieri SCC3193 provides insights into metabolic pathways of plant pathogenic bacteria","volume":"7","author":"Zoledowska","year":"2019","journal-title":"Microorganisms"}],"container-title":["Genome Biology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/gbe\/advance-article-pdf\/doi\/10.1093\/gbe\/evae032\/56740699\/evae032.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gbe\/article-pdf\/16\/3\/evae032\/57080261\/evae032.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gbe\/article-pdf\/16\/3\/evae032\/57080261\/evae032.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,29]],"date-time":"2024-03-29T16:18:34Z","timestamp":1711729114000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gbe\/article\/doi\/10.1093\/gbe\/evae032\/7612553"}},"subtitle":[],"editor":[{"given":"Wenfeng","family":"Qian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024,2,22]]},"references-count":84,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2024,3,2]]}},"URL":"https:\/\/doi.org\/10.1093\/gbe\/evae032","relation":{},"ISSN":["1759-6653"],"issn-type":[{"value":"1759-6653","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,3]]},"published":{"date-parts":[[2024,2,22]]},"article-number":"evae032"}}