The pangenome contains all genes encoded by a species, with the core genome present in all strains and the accessory genome in only a subset. Coincident gene relationships are expected within the accessory genome, where the presence or absence of one gene is influenced by the presence or absence of another. Here, we analysed the accessory genome of an Escherichia coli pangenome consisting of 400 genomes from 20 sequence types to identify genes that display significant co-occurrence or avoidance patterns with one another. We present a complex network of genes that are either found together or that avoid one another more often than would be expected by chance, and show that these relationships vary by lineage. We demonstrate that genes co-occur by function, and that several highly connected gene relationships are linked to mobile genetic elements. We find that genes are more likely to co-occur with, rather than avoid, another gene in the accessory genome. This work furthers our understanding of the dynamic nature of prokaryote pangenomes and implicates both function and mobility as drivers of gene relationships.

中文翻译：

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大肠杆菌辅助基因组中的基因-基因关系与功能和流动性有关

泛基因组包含一个物种编码的所有基因，核心基因组存在于所有菌株中，辅助基因组仅存在于一个子集中。预计在辅助基因组中存在重合基因关系，其中一个基因的存在或不存在受另一个基因的存在或不存在的影响。在这里，我们分析了大肠杆菌的附属基因组 pangenome 由来自 20 种序列类型的 400 个基因组组成，用于识别显示出显着的共现或回避模式的基因。我们提出了一个复杂的基因网络，这些基因要么一起发现，要么比偶然预期的更频繁地相互避开，并表明这些关系因谱系而异。我们证明基因通过功能共同发生，并且几个高度相关的基因关系与移动遗传元件相关联。我们发现基因更有可能与辅助基因组中的另一个基因同时出现，而不是避免。这项工作进一步加深了我们对原核生物泛基因组动态特性的理解，并将功能和流动性作为基因关系的驱动因素。