Time-calibrated genomic evolution of a monomorphic bacterium during its establishment as an endemic crop pathogen
Horizontal gene transfer is of major evolutionary importance as it allows for the redistribution of phenotypically important genes among lineages. 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 years 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-like 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.
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dig-cirad-fr-5986112024-01-29T05:43:33Z http://agritrop.cirad.fr/598611/ http://agritrop.cirad.fr/598611/ Time-calibrated genomic evolution of a monomorphic bacterium during its establishment as an endemic crop pathogen. Richard Damien, Pruvost Olivier, Balloux François, Boyer Claudine, Rieux Adrien, Lefeuvre Pierre. 2021. Molecular Ecology, 30 (8) : 1823-1835.https://doi.org/10.1111/mec.15770 <https://doi.org/10.1111/mec.15770> Time-calibrated genomic evolution of a monomorphic bacterium during its establishment as an endemic crop pathogen Richard, Damien Pruvost, Olivier Balloux, François Boyer, Claudine Rieux, Adrien Lefeuvre, Pierre eng 2021 Molecular Ecology Xanthomonas campestris citri génome phylogénie transfert de gène gène pathologie végétale Xanthomonas épidémiologie Citrus Résistance aux antibiotiques évolution surveillance épidémiologique http://aims.fao.org/aos/agrovoc/c_36120 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_24846 http://aims.fao.org/aos/agrovoc/c_3214 http://aims.fao.org/aos/agrovoc/c_5974 http://aims.fao.org/aos/agrovoc/c_8455 http://aims.fao.org/aos/agrovoc/c_2615 http://aims.fao.org/aos/agrovoc/c_1637 http://aims.fao.org/aos/agrovoc/c_8848 http://aims.fao.org/aos/agrovoc/c_2745 http://aims.fao.org/aos/agrovoc/c_16411 La Réunion France Martinique http://aims.fao.org/aos/agrovoc/c_6543 http://aims.fao.org/aos/agrovoc/c_3081 http://aims.fao.org/aos/agrovoc/c_4635 Horizontal gene transfer is of major evolutionary importance as it allows for the redistribution of phenotypically important genes among lineages. 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 years 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-like 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. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/598611/1/mec21.pdf text Cirad license info:eu-repo/semantics/restrictedAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1111/mec.15770 10.1111/mec.15770 info:eu-repo/semantics/altIdentifier/doi/10.1111/mec.15770 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1111/mec.15770 info:eu-repo/grantAgreement/ERDF///// |
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Xanthomonas campestris citri génome phylogénie transfert de gène gène pathologie végétale Xanthomonas épidémiologie Citrus Résistance aux antibiotiques évolution surveillance épidémiologique http://aims.fao.org/aos/agrovoc/c_36120 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_24846 http://aims.fao.org/aos/agrovoc/c_3214 http://aims.fao.org/aos/agrovoc/c_5974 http://aims.fao.org/aos/agrovoc/c_8455 http://aims.fao.org/aos/agrovoc/c_2615 http://aims.fao.org/aos/agrovoc/c_1637 http://aims.fao.org/aos/agrovoc/c_8848 http://aims.fao.org/aos/agrovoc/c_2745 http://aims.fao.org/aos/agrovoc/c_16411 http://aims.fao.org/aos/agrovoc/c_6543 http://aims.fao.org/aos/agrovoc/c_3081 http://aims.fao.org/aos/agrovoc/c_4635 Xanthomonas campestris citri génome phylogénie transfert de gène gène pathologie végétale Xanthomonas épidémiologie Citrus Résistance aux antibiotiques évolution surveillance épidémiologique http://aims.fao.org/aos/agrovoc/c_36120 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_24846 http://aims.fao.org/aos/agrovoc/c_3214 http://aims.fao.org/aos/agrovoc/c_5974 http://aims.fao.org/aos/agrovoc/c_8455 http://aims.fao.org/aos/agrovoc/c_2615 http://aims.fao.org/aos/agrovoc/c_1637 http://aims.fao.org/aos/agrovoc/c_8848 http://aims.fao.org/aos/agrovoc/c_2745 http://aims.fao.org/aos/agrovoc/c_16411 http://aims.fao.org/aos/agrovoc/c_6543 http://aims.fao.org/aos/agrovoc/c_3081 http://aims.fao.org/aos/agrovoc/c_4635 |
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Xanthomonas campestris citri génome phylogénie transfert de gène gène pathologie végétale Xanthomonas épidémiologie Citrus Résistance aux antibiotiques évolution surveillance épidémiologique http://aims.fao.org/aos/agrovoc/c_36120 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_24846 http://aims.fao.org/aos/agrovoc/c_3214 http://aims.fao.org/aos/agrovoc/c_5974 http://aims.fao.org/aos/agrovoc/c_8455 http://aims.fao.org/aos/agrovoc/c_2615 http://aims.fao.org/aos/agrovoc/c_1637 http://aims.fao.org/aos/agrovoc/c_8848 http://aims.fao.org/aos/agrovoc/c_2745 http://aims.fao.org/aos/agrovoc/c_16411 http://aims.fao.org/aos/agrovoc/c_6543 http://aims.fao.org/aos/agrovoc/c_3081 http://aims.fao.org/aos/agrovoc/c_4635 Xanthomonas campestris citri génome phylogénie transfert de gène gène pathologie végétale Xanthomonas épidémiologie Citrus Résistance aux antibiotiques évolution surveillance épidémiologique http://aims.fao.org/aos/agrovoc/c_36120 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_24846 http://aims.fao.org/aos/agrovoc/c_3214 http://aims.fao.org/aos/agrovoc/c_5974 http://aims.fao.org/aos/agrovoc/c_8455 http://aims.fao.org/aos/agrovoc/c_2615 http://aims.fao.org/aos/agrovoc/c_1637 http://aims.fao.org/aos/agrovoc/c_8848 http://aims.fao.org/aos/agrovoc/c_2745 http://aims.fao.org/aos/agrovoc/c_16411 http://aims.fao.org/aos/agrovoc/c_6543 http://aims.fao.org/aos/agrovoc/c_3081 http://aims.fao.org/aos/agrovoc/c_4635 Richard, Damien Pruvost, Olivier Balloux, François Boyer, Claudine Rieux, Adrien Lefeuvre, Pierre Time-calibrated genomic evolution of a monomorphic bacterium during its establishment as an endemic crop pathogen |
description |
Horizontal gene transfer is of major evolutionary importance as it allows for the redistribution of phenotypically important genes among lineages. 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 years 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-like 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. |
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article |
topic_facet |
Xanthomonas campestris citri génome phylogénie transfert de gène gène pathologie végétale Xanthomonas épidémiologie Citrus Résistance aux antibiotiques évolution surveillance épidémiologique http://aims.fao.org/aos/agrovoc/c_36120 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_24846 http://aims.fao.org/aos/agrovoc/c_3214 http://aims.fao.org/aos/agrovoc/c_5974 http://aims.fao.org/aos/agrovoc/c_8455 http://aims.fao.org/aos/agrovoc/c_2615 http://aims.fao.org/aos/agrovoc/c_1637 http://aims.fao.org/aos/agrovoc/c_8848 http://aims.fao.org/aos/agrovoc/c_2745 http://aims.fao.org/aos/agrovoc/c_16411 http://aims.fao.org/aos/agrovoc/c_6543 http://aims.fao.org/aos/agrovoc/c_3081 http://aims.fao.org/aos/agrovoc/c_4635 |
author |
Richard, Damien Pruvost, Olivier Balloux, François Boyer, Claudine Rieux, Adrien Lefeuvre, Pierre |
author_facet |
Richard, Damien Pruvost, Olivier Balloux, François Boyer, Claudine Rieux, Adrien Lefeuvre, Pierre |
author_sort |
Richard, Damien |
title |
Time-calibrated genomic evolution of a monomorphic bacterium during its establishment as an endemic crop pathogen |
title_short |
Time-calibrated genomic evolution of a monomorphic bacterium during its establishment as an endemic crop pathogen |
title_full |
Time-calibrated genomic evolution of a monomorphic bacterium during its establishment as an endemic crop pathogen |
title_fullStr |
Time-calibrated genomic evolution of a monomorphic bacterium during its establishment as an endemic crop pathogen |
title_full_unstemmed |
Time-calibrated genomic evolution of a monomorphic bacterium during its establishment as an endemic crop pathogen |
title_sort |
time-calibrated genomic evolution of a monomorphic bacterium during its establishment as an endemic crop pathogen |
url |
http://agritrop.cirad.fr/598611/ http://agritrop.cirad.fr/598611/1/mec21.pdf |
work_keys_str_mv |
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