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Such genes with essential functions include those involved in resistance to antimicrobial compounds and virulence factors in pathogenic bacteria. Understanding gene turnover at microevolutionary scales is critical to assess the pace of this evolutionary process. Here, we characterized and quantified gene turnover for the epidemic lineage of a bacterial plant pathogen of major agricultural importance worldwide. Relying on a dense geographic sampling spanning 39\u00a0years of evolution, we estimated both the dynamics of single nucleotide polymorphism accumulation and gene content turnover. We identified extensive gene content variation among lineages even at the smallest phylogenetic and geographic scales. Gene turnover rate exceeded nucleotide substitution rate by three orders of magnitude. Accessory genes were found preferentially located on plasmids, but we identified a highly plastic chromosomal region hosting ecologically important genes such as transcription activator\u2010like effectors. Whereas most changes in the gene content are probably transient, the rapid spread of a mobile element conferring resistance to copper compounds widely used for the management of plant bacterial pathogens illustrates how some accessory genes can become ubiquitous within a population over short timeframes.<\/jats:p>","DOI":"10.1111\/mec.15770","type":"journal-article","created":{"date-parts":[[2020,12,11]],"date-time":"2020-12-11T04:01:36Z","timestamp":1607659296000},"page":"1823-1835","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Time\u2010calibrated genomic evolution of a monomorphic bacterium during its establishment as an endemic crop pathogen"],"prefix":"10.1111","volume":"30","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9179-7315","authenticated-orcid":false,"given":"Damien","family":"Richard","sequence":"first","affiliation":[{"name":"Cirad, UMR PVBMT R\u00e9union France"},{"name":"ANSES, Plant Health Laboratory R\u00e9union France"},{"name":"Universit\u00e9 de la R\u00e9union UMR PVBMT R\u00e9union France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3175-9795","authenticated-orcid":false,"given":"Olivier","family":"Pruvost","sequence":"additional","affiliation":[{"name":"Cirad, UMR PVBMT R\u00e9union France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1978-7715","authenticated-orcid":false,"given":"Fran\u00e7ois","family":"Balloux","sequence":"additional","affiliation":[{"name":"UCL Genetics Institute University College London London UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claudine","family":"Boyer","sequence":"additional","affiliation":[{"name":"Cirad, UMR PVBMT R\u00e9union France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7221-0010","authenticated-orcid":false,"given":"Adrien","family":"Rieux","sequence":"additional","affiliation":[{"name":"Cirad, UMR PVBMT R\u00e9union France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierre","family":"Lefeuvre","sequence":"additional","affiliation":[{"name":"Cirad, UMR PVBMT R\u00e9union France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2020,12,31]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1098\/rstb.2011.0303"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tree.2004.07.021"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2017.36"},{"key":"e_1_2_10_5_1","first-page":"111","volume-title":"Hommes et fruits en pays du Sud","author":"Aubert B.","year":"2014"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-phyto-080508-081803"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.1094\/PHYTO-06-12-0134-R"},{"key":"e_1_2_10_9_1","first-page":"71","article-title":"Genome plasticity: insertion sequence elements, transposons and integrons, and DNA rearrangement","volume":"266","author":"Bennett P. 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