Extensive genomic diversity of closely related Wolbachia strains

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Abstract
Using microarray-based comparative genome hybridization (mCGH), the genomic content ofWolbachia pipientis wMel fromDrosophila melanogasterwas compared to the closely relatedWolbachiafromD. innubila(wInn),D. santomea(wSan), and three strains fromD. simulans(wAu,wRi,wSim). A large number of auxiliary genes are identified in these five strains, with most absent/divergent genes being unique to a given strain. Each strain caused an average of ∼60 genes to be removed from the core genome. As such, these organisms do not appear to have the streamlined genomes expected of obligate intracellular bacteria. Prophage, hypothetical and ankyrin repeat genes are over-represented in the absent/divergent genes, with 21–87 % of absent/divergent genes coming from prophage regions. The onlywMel region absent/divergent in all five query strains is that containing WD_0509 to WD_0511, including a DNA mismatch repair protein MutL-2, a degenerate RNase, and a conserved hypothetical protein. A region flanked by the two portions of the WO-B prophage inwMel is found in four of the fiveWolbachiastrains as well as on a plasmid of a rickettsial endosymbiont ofIxodes scapularis, suggesting lateral gene transfer between these two obligate intracellular species. Overall, these insect-associatedWolbachiahave highly mosaic genomes, with lateral gene transfer playing an important role in their diversity and evolution.