The pan-genome is defined as the combined set of all genes in the gene pool of a species. Pan-genome analyses have been very useful in helping to understand different evolutionary dynamics of bacterial species: an open pan-genome often indicates a free-living lifestyle with metabolic versatility, while closed pan-genomes are linked to host-restricted, ecologically specialized bacteria. A detailed understanding of the species pan-genome has also been instrumental in tracking the phylodynamics of emerging drug resistance mechanisms and drug-resistant pathogens. However, current approaches to analyse a species’ pan-genome do not take the species population structure into account, nor do they account for the uneven sampling of different lineages, as is commonplace due to over-sampling of clinically relevant representatives. Here we present the application of a population structure-aware approach for classifying genes in a pan-genome based on within-species distribution. We demonstrate our approach on a collection of 7500 Escherichia coli genomes, one of the most-studied bacterial species and used as a model for an open pan-genome. We reveal clearly distinct groups of genes, clustered by different underlying evolutionary dynamics, and provide a more biologically informed and accurate description of the species’ pan-genome.

中文翻译：

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不同进化趋势形成细菌泛基因组的暮光区

泛基因组被定义为一个物种基因库中所有基因的组合。泛基因组分析在帮助理解细菌物种的不同进化动态方面非常有用：开放的泛基因组通常表明具有代谢多功能性的自由生活生活方式，而封闭的泛基因组与宿主受限的生态特化细菌有关. 对物种泛基因组的详细了解也有助于追踪新兴耐药机制和耐药病原体的系统动力学。然而，目前分析物种泛基因组的方法没有考虑物种种群结构，也没有考虑不同谱系的不均匀抽样，因为临床相关代表的过度抽样很常见。在这里，我们展示了基于种内分布对泛基因组中基因进行分类的群体结构感知方法的应用。我们在 7500 个集合上展示了我们的方法 大肠杆菌 基因组，研究最多的细菌物种之一，用作开放泛基因组的模型。我们清楚地揭示了不同的基因组，由不同的潜在进化动力学聚集在一起，并提供了对该物种泛基因组的更生物学和准确的描述。