Wolbachia are widespread bacterial endosymbionts that infect a large proportion of insect species. While some strains of this bacteria do not cause observable host phenotypes, many strains of Wolbachia have some striking effects on their hosts. In some cases, these symbionts manipulate host reproduction to increase the fitness of infected, transmitting females. Here we examine the genome and population genomics of a male-killing Wolbachia strain, w Inn, that infects Drosophila innubila mushroom-feeding flies. We compared w Inn to other closely-related Wolbachia genomes to understand the evolutionary dynamics of specific genes. The w Inn genome is similar in overall gene content to w Mel, but also contains many unique genes and repetitive elements that indicate distinct gene transfers between w Inn and non- Drosophila hosts. We also find that genes in the Wolbachia prophage and Octomom regions are particularly rapidly evolving, including those putatively or empirically confirmed to be involved in host pathogenicity. Of the genes that rapidly evolve, many also show evidence of recent horizontal transfer among Wolbachia symbiont genomes, suggesting frequent movement of rapidly evolving regions among individuals. These dynamics of rapid evolution and horizontal gene transfer across the genomes of several Wolbachia strains and divergent host species may be important underlying factors in the global success of Wolbachia as a symbiont. ### Competing Interest Statement The authors have declared no competing interest.
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