Data from: The Chlamydiales pangenome revisited: structural stability and functional coherence

The entire publicly available set of 37 genome sequences from the bacterial order Chlamydiales has been subjected to comparative analysis in order to reveal the salient features of this pangenome and its evolutionary history. Over 2,000 protein families are detected across multiple species, with a distribution consistent to other studied pangenomes. Of these, there are 180 protein families with multiple members, 312 families with exactly 37 members corresponding to core genes, 428 families with peripheral genes with varying taxonomic distribution and finally 1,125 smaller families. The fact that, even for smaller genomes of Chlamydiales, core genes represent over a quarter of the average protein complement, signifies a certain degree of structural stability, given the wide range of phylogenetic relationships within the group. In addition, the propagation of a corpus of manually curated annotations within the discovered core families reveals key functional properties, reflecting a coherent repertoire of cellular capabilities for Chlamydiales. We further investigate over 2,000 genes without homologs in the pangenome and discover two new protein sequence domains. Our results, supported by the genome-based phylogeny for this group, are fully consistent with previous analyses and current knowledge, and point to future research directions towards a better understanding of the structural and functional properties of Chlamydiales.

本研究针对已公开的全部37条衣原体目（Chlamydiales）细菌基因组序列开展比较分析，旨在揭示该泛基因组（pangenome）的显著特征及其演化历程。本次分析在多个物种中总计检测到超过2000个蛋白质家族（protein families），其分布模式与其他已被研究的泛基因组保持一致。其中包含180个含多成员的蛋白质家族、312个恰好包含37个成员的核心基因（core genes）家族、428个分类分布各异的外围基因（peripheral genes）家族，以及1125个小型蛋白质家族。考虑到该类群内部存在广泛的系统发育关系（phylogenetic relationships）差异，即便对于基因组较小的衣原体目类群，核心基因仍占其平均蛋白质组的四分之一以上，这体现出该类群具备一定的结构稳定性。此外，针对已发现的核心家族所对应的人工手工注释数据集进行梳理分析，揭示了多项关键功能特性，反映出衣原体目拥有一套统一协调的细胞功能组合。我们进一步对泛基因组中超过2000个无同源基因（homologs）的基因展开分析，并发现了两个全新的蛋白质序列结构域（protein sequence domains）。本研究结果得到了该类群基于基因组的系统发育分析（genome-based phylogeny）的支持，与既往研究及现有学术认知完全一致，可为后续更深入解析衣原体目结构与功能特性的研究指明方向。