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Time‐calibrated genomic evolution of a monomorphic bacterium during its establishment as an endemic crop pathogen
Molecular Ecology ( IF 4.5 ) Pub Date : 2020-12-11 , DOI: 10.1111/mec.15770
Damien Richard 1, 2, 3 , Olivier Pruvost 1 , François Balloux 4 , Claudine Boyer 1 , Adrien Rieux 1 , Pierre Lefeuvre 1
Affiliation  

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.

中文翻译:

单态细菌作为地方性作物病原体建立期间的时间校准基因组进化

水平基因转移具有重要的进化重要性,因为它允许在谱系之间​​重新分配表型重要基因。这些具有基本功能的基因包括那些与病原菌对抗菌化合物和毒力因子的抗性有关的基因。了解微进化尺度的基因更新对于评估这一进化过程的速度至关重要。在这里,我们对全球具有重要农业意义的细菌植物病原体的流行谱系进行了表征和量化的基因转换。依靠跨越 39 年进化的密集地理采样,我们估计了单核苷酸多态性积累和基因内容周转的动态。即使在最小的系统发育和地理尺度上,我们也确定了谱系之间广泛的基因含量变异。基因周转率超过核苷酸替代率三个数量级。发现辅助基因优先位于质粒上,但我们发现了一个高度可塑性的染色体区域,该区域承载着生态学上重要的基因,例如转录激活因子样效应子。尽管基因含量的大多数变化可能是短暂的,但赋予对广泛用于管理植物细菌病原体的铜化合物的抗性的移动元素的快速传播说明了一些辅助基因如何在短时间内在人群中变得无处不在。但我们发现了一个高度可塑性的染色体区域,它承载着重要的生态基因,例如转录激活因子样效应子。尽管基因含量的大多数变化可能是短暂的,但赋予对广泛用于管理植物细菌病原体的铜化合物的抗性的移动元素的快速传播说明了一些辅助基因如何在短时间内在人群中变得无处不在。但我们发现了一个高度可塑性的染色体区域,它承载着重要的生态基因,例如转录激活因子样效应子。尽管基因含量的大多数变化可能是短暂的,但赋予对广泛用于管理植物细菌病原体的铜化合物的抗性的移动元素的快速传播说明了一些辅助基因如何在短时间内在人群中变得无处不在。
更新日期:2020-12-11
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