Genome assembly of the A-groupWolbachiainNasonia oneidaand phylogenomic analysis ofWolbachiastrains reveals patterns of genome evolution and lateral gene transfer
Authors: Wang Xiaozhu , Xiong Xiao , Cao Wenqi , Zhang Chao , Werren John H. , Wang Xu 
Published: December 2018

Wolbachiaare obligate intracellular bacteria which commonly infect various nematode and arthropod species. Based on depth differences, we assembled the genome ofWolbachiain the parasitoid jewel wasp speciesNasonia 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 inN. oneida, and pyrosequencing confirms that the wasp strain lacks A2 and B types, which were likely lost during laboratory culturing. Polymorphisms identified in thewOneA1 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-Wolbachiain theDrosophila simulans(wHa) than A-Wolbachiafound in wasps. Genome variation was next evaluated in 34 publishedWolbachiagenomes 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 sequencingWolbachiagenomes and characterizing their diversity.

Author Summary

More than half of the arthropod species are infected by the obligated intracellular bacteriaWolbachia. As one of the most widespread parasitic microbes,Wolbachiamediate 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 sequencedWolbachiastrains, 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%) inWolbachiagenomes, 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 inWolbachiainfection related functions. We also found enriched nonsynonymous polymorphisms inNasonia oneida Wobachiagenome, and their differences are more likely to result from gene duplications within the strain, rather than strain variation within the parasitoid.