Genome assembly of the A-group Wolbachia in Nasonia oneida and phylogenomic analysis of Wolbachia strains revealed genome evolution and lateral gene transfer

Wolbachia are obligate intracellular bacteria which commonly infect various nematode and arthropod species. Based on average depth and GC-content differences, we assembled the genome of Wolbachia in the parasitoid jewel wasp species Nasonia oneida ( w One), using 10X Genomics Chromium linked read technology. The final draft assembly of the w One genome consists of 938,765 bp in 254 scaffolds and it contains 948 coding genes. Comparative analysis of sequenced Wolbachia genomes and phylogenetic analysis of five genes ( coxA , gatB , hcpA , ftsZ and fbpA ) revealed that w One belongs to the A1 supergroup. Pyrosequencing experiments validated the lack of A2 or B strains, which were likely lost during laboratory culturing. 68 polymorphisms were identified in the w One genome, suggesting heteroplasmy and/or gene duplications. These polymorphisms are enriched in nonsynonymous changes in 37 coding genes, with biological functions related to bacterial infection, such as transporter activity related genes. Phylogenomic analysis of 34 sequenced Wolbachia genomes revealed that w One is more closely grouped with A- Wolbachia in the Drosophila simulans fruitfly ( w Ha) instead of A- Wolbachia in wasps ( w VitA and w Uni). Phylogenetic analysis of 211 single ortholog genes in these 34 Wolbachia genomes discovered six discordant trees, indicating lateral gene transfer or recombination events not only between A and B supergroups, but also between A and E strains. Assembling bacterial genomes from host genome projects can provide an effective method for characterizing Wolbachia genome diversity, as well as the assembling microbial genomes in the insect gut microbiota.