The reconstruction of the evolutionary histories of pathogen populations in space and time has greatly improved our understanding of their epidemiology. However, analyses are usually restricted to the non-recombining genomic regions and, thus, fail to inform on the dynamics of the accessory genome. Yet, horizontal gene transfer is of striking importance to the evolution of bacteria as it can redistribute phenotypically important genes. For bacterial pathogens, those include resistance to antimicrobial compounds and virulence factors. Understanding the gene turnover in genomes at microevolutionary scales is key to apprehend the pace of this evolutionary process. Here we addressed this question for the epidemic lineage of a major bacterial plant pathogen, relying on a dense geographic sampling spanning 39 years of evolution. Gene turnover rate exceeded SNP mutation rates by three orders of magnitude. Accessory genes were preferentially plasmid-encoded, but we evidenced a highly plastic chromosomal region hosting ecologically important genes such as transcription activator-like effectors. We argue that turnover of accessory genes provides a potent evolutionary force in monomorphic bacteria, and exemplify this statement retracing the history of a mobile element conferring resistance to copper compounds widely used for the management of plant bacterial pathogens.

中文翻译：

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建立为流行作物病原体的单态细菌的时间校准基因组进化

病原菌种群的时空演化历史的重建极大地增进了我们对病原菌流行病学的理解。但是，分析通常限于非重组基因组区域，因此无法告知辅助基因组的动态。然而，水平基因转移对于细菌的进化至关重要，因为它可以重新分配表型上重要的基因。对于细菌病原体，那些包括对抗菌化合物的抵抗力和毒力因子。了解微进化规模的基因组中的基因更新是理解这一进化过程步伐的关键。在这里，我们针对主要细菌植物病原体的流行谱系解决了这个问题，它依赖于跨越39年演变的密集地理采样。基因更新率比SNP突变率高三个数量级。辅助基因优先被质粒编码，但是我们证明了一个具有可塑性的染色体区域，该区域托管着具有生态学意义的重要基因，例如转录激活因子样效应子。我们认为，辅助基因的更新在单态细菌中提供了强大的进化力，并例证了该陈述，追溯了赋予对广泛用于植物细菌病原体管理的铜化合物具有抗性的移动元件的历史。