Large scale reconstruction of over a thousand Wolbachia genomes sheds light on its co-evolution

Wolbachia is an iconic example of a successful intracellular bacterium. Despite its importance as a manipulator of invertebrate biology, its evolutionary dynamics and population biology have been poorly studied from a genomic viewpoint, mainly because of a paucity of available genomes. To expand the number of Wolbachia genomes across host phylogenies, we screened over 30,000 publicly available shotgun sequencing samples (>70TB of data) from more than 500 arthropods and nematodes species using metagenomic and phylogenomic approaches. By assembling over a thousand of high quality genomes, we provide the largest collection of Wolbachia genomes to date and a substantial increase in host representation. Our Wolbachia phylogenies based on both core-genome alignment and gene content provide a robust reference for future studies, support new strains in model organisms like Drosophila and economically relevant pest species, and reveal novel affinities including recent horizontal transfers amongst distantly related hosts. We found various instances of gene function gains and losses in different super-groups, particularly in Cytoplasmic Incompatibility inducing strains. Our intra-specific Wolbachia-host cophylogenies indicate striking heterogeneity of coevolutionary dynamics and show that horizontal transfer is widespread not only at the intraspecific, but also population interspecific level. Our work reveals new patterns of Wolbachia evolution and indicates that our strain-level metagenomic analysis of host sequencing projects is an effective method to recover endosymbiont genomes for downstream analyses.