Data from: Phylogenomics and analysis of shared genes suggest a single transition to mutualism in Wolbachia of nematodes

Wolbachia, endosymbiotic bacteria of the order Rickettsiales, are widespread in arthropods but also present in nematodes. In arthropods, A and B supergroup Wolbachia are generally associated with distortion of host reproduction. In filarial nematodes, including some human parasites, multiple lines of experimental evidence indicate that C and D supergroup Wolbachia are essential for the survival of the host, and here the symbiotic relationship is considered mutualistic. The origin of this mutualistic endosymbiosis is of interest for both basic and applied reasons: How does a parasite become a mutualist? Could intervention in the mutualism aid in treatment of human disease? Correct rooting and high-quality resolution of Wolbachia relationships are required to resolve this question. However, because of the large genetic distance between Wolbachia and the nearest outgroups, and the limited number of genomes so far available for large-scale analyses, current phylogenies do not provide robust answers. We therefore sequenced the genome of the D supergroup Wolbachia endosymbiont of Litomosoides sigmodontis, revisited the selection of loci for phylogenomic analyses, and performed a phylogenomic analysis including available complete genomes (from isolates in supergroups A, B, C and D). Using ninety orthologous genes with reliable phylogenetic signals, we obtained a robust phylogenetic reconstruction, including a highly supported root to the Wolbachia phylogeny between an (A+B) clade and a (C+D) clade. While we currently lack data from several Wolbachia supergroups, notably F, our analysis supports a model wherein the putatively mutualist endosymbiotic relationship between Wolbachia and nematodes originated from a single transition event.

立克次体目（Rickettsiales）的内共生细菌沃尔巴克氏体属（Wolbachia）广泛分布于节肢动物中，同时也可在线虫体内检出。在节肢动物体内，A、B超群沃尔巴克氏体通常会引发宿主生殖畸变。在包括部分人体寄生虫在内的丝虫线虫中，多项实验证据表明C、D超群沃尔巴克氏体对宿主存活不可或缺，二者的共生关系属于互利共生。这种互利共生关系的起源兼具基础研究与应用研究价值：寄生虫如何演变为互利共生生物？干预该共生关系能否为人类疾病治疗提供新策略？要解答上述问题，需对沃尔巴克氏体的演化关系进行准确定根与高质量解析。然而，由于沃尔巴克氏体与其最近缘外类群之间遗传距离较大，且当前可用于大规模分析的基因组数量有限，现有系统发育研究尚未得出可靠结论。为此，我们对烟鼠丝虫（Litomosoides sigmodontis）的D超群沃尔巴克氏体内共生体基因组进行了测序，重新筛选了系统基因组学分析所用的基因位点，并针对包含已发布的A、B、C、D超群分离株完整基因组的数据集开展了系统基因组学分析。通过90个携带可靠系统发育信号的直系同源基因，我们构建了稳健的系统发育树，其中沃尔巴克氏体系统发育树在（A+B）演化支与（C+D）演化支之间的定根得到了高度支持。尽管目前我们仍缺少包括F超群在内的多个沃尔巴克氏体超群的相关数据，但本分析支持如下模型：沃尔巴克氏体与线虫之间的推定互利共生关系起源于单次演化转变事件。