Phylogenomic Analysis of Wolbachia Strains Reveals Patterns of Genome Evolution and Recombination

Abstract

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, B, C, D, E and 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 (9 events), but also between A and E supergroups (5 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.

Complete de novo assembly of Wolbachia endosymbiont of Diaphorina citri Kuwayama (Hemiptera: Liviidae) using long-read genome sequencing

“…The single copy genes were utilized instead of multilocus sequence typing loci ( gatB , coxA , hcpA , fbpA , and ftsZ ) 58 which are problematic in phylogenetic analyses and may not accurately represent the properties of different Wolbachia strains 59 . The advent of sequencing technology and availability of complete and draft genomes of Wolbachia , recent phylogenetic studies have been done utilizing single copy gene sets 53 , 59 , 60 rather than whole-genome sequence typing 61 . Although comparisons of whole Wolbachia genome sequences is useful for strain differentiation, diversity estimates, and phylogenetic analyses, the size is cumbersome and not necessary to answer specific questions that can be addressed using genetic marker loci 59 .…”

Genetic Diversity of Tamarixia radiata Populations and Their Associated Endosymbiont Wolbachia Species from China

“…However, it has been proposed that supergroup G be decommissioned, as it is based primarily on recombinant wsp sequences and clusters with A supergroup based on five multilocus sequence typing genes [72,73], and eight supergroups (A-H) are still widely used in the research community. An MLST system based on five house-keeping genes (coxA, gatB, hcpA, ftsZ, and fbpA) has been developed for Wolbachia [72] and is widely used for strain typing and to characterize strain variation within Wolbachia [74]. With the differentiation of Wolbachia from T. radiata and D. citri within the B subdivision, the idea of recent and rapid expansion of the B-clade Wolbachia could result from more frequent transfers of Wolbachia between host and parasitoid.…”

Are ecological communities the seat of endosymbiont horizontal transfer and diversification? A case study with soil arthropod community

“…The above two instances testify to the utility of a MLST‐based approach to understand Wolbachia diversity and spread across global arthropod communities (Wang et al., 2020). Moreover, these cases also highlight the importance of collecting community‐wide data to understand the probable chain of transfer of these bacteria.…”

“…This level of recombination is extensive enough to render single‐gene phylogenies unable to properly reflect the evolutionary history of an endosymbiont strain and, therefore, has necessitated the development of multilocus strain typing (MLST) systems (Maiden et al., 1998). Such MLST studies (Hou et al., 2020), as well as whole‐genome analysis of endosymbionts (Wang et al., 2020), indicate extensive recombination within them. However, for recombination to happen, at least two endosymbiont strains must be present in the same cytoplasm of a particular host.…”