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

Wolbachia are obligate intracellular bacteria which commonly infect various nematode and arthropod species. Based on depth differences, we assembled the genome of Wolbachia in the parasitoid jewel wasp species Nasonia oneida (wOne), using 10X Genomics Chromium linked-read technology. The final draft assembly consists of 1,293,406 bp in 47 scaffolds with 1,114 coding genes and 97.01% genome completeness assessed by checkM. wOne is the A1 strain previously reported in N. oneida, and pyrosequencing confirms that the wasp strain lacks A2 and B types, which were likely lost during laboratory culturing. Polymorphisms identified in the wOneA1 genome have elevated read depths, indicating recent gene duplications rather that strain variation. These polymorphisms are enriched in nonsynonymous changes in 27 coding genes, including phase baseplate assembly proteins and transporter activity related genes. wOneA1 is more closely grouped with A-Wolbachia in the Drosophila simulans (wHa) than A-Wolbachia found in wasps. Genome variation was next evaluated in 34 published Wolbachia genomes for 211 single ortholog genes, and revealed six supergroup discordant trees, indicating recombination events not only between A and B supergroups, but also between A and E supergroups. Comparisons of strain divergence using the five genes of the Multi Locus Strain Typing (MLST) system show a high correlation (rho=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. Assembling bacterial genomes from host genome projects can provide an effective method for sequencing Wolbachia genomes and characterizing their diversity.\n\nAuthor SummaryMore than half of the arthropod species are infected by the obligated intracellular bacteria Wolbachia. As one of the most widespread parasitic microbes, Wolbachia mediate important biological processes such as cytoplasmic incompatibility and lateral gene transfer in insects. Their evolutionary relationship has been characterize using five protein-coding and 16S rRNA genes. In this work, we identified 211 conserved single copies genes in 34 genome sequenced Wolbachia strains, and we discovered that they maintain the supergroup relationship classified previously based on selected genes. We constructed phylogenetic trees for individual genes and found only six genes display discordant tree structure between supergroups, due to lateral gene transfer and homologous recombination events. But these events are not common (3%) in Wolbachia genomes, at least in these conserved single copy genes. In addition to known lateral gene transfer events between A and B supergroups, we identified transfers between A and E supergroups for the first time. Selective maintenance of such transfers suggests possible roles in Wolbachia infection related functions. We also found enriched nonsynonymous polymorphisms in Nasonia oneida Wobachia genome, and their differences are more likely to result from gene duplications within the strain, rather than strain variation within the parasitoid.