Wolbachia are widespread intracellular bacteria that mediate many important biological processes in arthropod species. In this study, we identified 210 conserved single-copy genes in 33 genome-sequenced Wolbachia strains in the A–F supergroups. Phylogenomic analyses with these core genes indicate that all 33 Wolbachia strains maintain the supergroup relationship, which was classified previously based on the multilocus sequence typing (MLST) genes. Using an interclade recombination screening method, 14 inter-supergroup recombination events were discovered in six genes (2.9%) among 210 single-copy orthologs. This finding suggests a relatively low frequency of intergroup recombination. Interestingly, they have occurred not only between A and B supergroups (nine events) but also between A and E supergroups (five events). Maintenance of such transfers suggests possible roles in Wolbachia infection-related functions. Comparisons of strain divergence using the five genes of the MLST system show a high correlation (Pearson correlation coefficient r = 0.98) between MLST and whole-genome divergences, indicating that MLST is a reliable method for identifying related strains when whole-genome data are not available. The phylogenomic analysis and the identified core gene set in our study will serve as a valuable foundation for strain identification and the investigation of recombination and genome evolution in Wolbachia.

中文翻译：

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Wolbachia 菌株的系统发育分析揭示了基因组进化和重组的模式

Wolbachia是广泛存在的细胞内细菌，在节肢动物物种中介导许多重要的生物过程。在这项研究中，我们在 A-F 超群的33 个基因组测序的Wolbachia菌株中鉴定了 210 个保守的单拷贝基因。对这些核心基因的系统发育分析表明，所有 33 种Wolbachia菌株保持超群关系，之前根据多位点序列分型 (MLST) 基因对其进行分类。使用进化枝间重组筛选方法，在 210 个单拷贝直向同源物中的 6 个基因 (2.9%) 中发现了 14 个超群间重组事件。这一发现表明组间重组的频率相对较低。有趣的是，它们不仅发生在 A 和 B 超群之间（九个事件），而且还发生在 A 和 E 超群之间（五个事件）。这种转移的维持表明可能在沃尔巴克氏菌感染相关功能中发挥作用。使用 MLST 系统的五个基因的菌株差异比较显示出高度相关性（Pearson 相关系数r = 0.98) 在 MLST 和全基因组差异之间，表明当全基因组数据不可用时，MLST 是识别相关菌株的可靠方法。我们研究中的系统发育分析和鉴定的核心基因组将为沃尔巴克氏菌菌株鉴定和重组和基因组进化研究提供有价值的基础。