Comparative Genomics of Wolbachia and the Bacterial Species Concept

The importance of host-specialization to speciation processes in obligate host-associated bacteria is well known, as is also the ability of recombination to generate cohesion in bacterial populations. However, whether divergent strains of highly recombining intracellular bacteria, such as Wolbachia, can maintain their genetic distinctness when infecting the same host is not known. We first developed a protocol for the genome sequencing of uncultivable endosymbionts. Using this method, we have sequenced the complete genomes of the Wolbachia strains wHa and wNo, which occur as natural double infections in Drosophila simulans populations on the Seychelles and in New Caledonia. Taxonomically, wHa belong to supergroup A and wNo to supergroup B. A comparative genomics study including additional strains supported the supergroup classification scheme and revealed 24 and 33 group-specific genes, putatively involved in host-adaptation processes. Recombination frequencies were high for strains of the same supergroup despite different host-preference patterns, leading to genomic cohesion. The inferred recombination fragments for strains of different supergroups were of short sizes, and the genomes of the co-infecting Wolbachia strains wHa and wNo were not more similar to each other and did not share more genes than other A- and B-group strains that infect different hosts. We conclude that Wolbachia strains of supergroup A and B represent genetically distinct clades, and that strains of different supergroups can co-exist in the same arthropod host without converging into the same species. This suggests that the supergroups are irreversibly separated and that barriers other than host-specialization are able to maintain distinct clades in recombining endosymbiont populations. Acquiring a good knowledge of the barriers to genetic exchange in Wolbachia will advance our understanding of how endosymbiont communities are constructed from vertically and horizontally transmitted genes.

专性宿主相关细菌的宿主特化对物种形成过程的重要性已得到广泛认知，重组在细菌种群中维持基因组凝聚力的能力亦然。然而，对于高重组率的胞内细菌（如沃尔巴克氏体属（Wolbachia））而言，其分化菌株在感染同一宿主时能否维持遗传差异性，目前仍未明确。本研究首先建立了针对不可培养内共生体的基因组测序方案。利用该方案，我们完成了沃尔巴克氏体菌株wHa与wNo的全基因组测序——这两株菌在塞舌尔及新喀里多尼亚的拟果蝇（Drosophila simulans）种群中以自然双重感染的形式存在。分类学上，wHa隶属于超群（supergroup）A，wNo隶属于超群（supergroup）B。纳入更多菌株的比较基因组学分析验证了该超群分类体系，并分别鉴定出24个和33个与宿主适应过程潜在相关的超群特异性基因。尽管同一超群的菌株存在不同的宿主偏好，但其重组频率仍较高，进而维持了基因组凝聚力。不同超群菌株的推断重组片段长度较短；共感染的wHa与wNo菌株基因组间的相似性并未高于感染不同宿主的其他A、B超群菌株，二者共享的基因数量也未多于该类菌株。本研究结论认为，A、B超群的沃尔巴克氏体菌株属于遗传上相互独立的演化支；不同超群的菌株可在同一节肢动物宿主中共存，并不会趋同为同一物种。这表明各超群之间已发生不可逆的分化，且除宿主特化之外的其他遗传交换障碍，可在重组型内共生体种群中维持相互独立的演化支。深入解析沃尔巴克氏体属的遗传交换障碍，将有助于我们理解内共生体群落如何通过垂直传递与水平传递的基因构建而成。