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Extensive genomic diversity of closely related Wolbachia strains

Nadeeza Ishmael^1,2,,

Julie C. Dunning Hotopp^1,2,

Sarah Biber^4,

¹ J. Craig Venter Institute, 9708 Medical Center Dr., Rockville, MD 20850, USA
² Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD 21201, USA
³ Department of Environmental and Natural Resources Management, University of Ioannina, 30100 Agrinio, Greece
⁴ Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, The Marine Biological Laboratory, Woods Hole, MA 02543, USA
⁵ Biology Department, University of Rochester, Rochester, NY 14627, USA
⁶ Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA

Using microarray-based comparative genome hybridization (mCGH), the genomic content of Wolbachia pipientis wMel from Drosophila melanogaster was compared to the closely related Wolbachia from D. innubila (wInn), D. santomea (wSan), and three strains from D. 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 only wMel 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 in wMel is found in four of the five Wolbachia strains as well as on a plasmid of a rickettsial endosymbiont of Ixodes scapularis, suggesting lateral gene transfer between these two obligate intracellular species. Overall, these insect-associated Wolbachia have highly mosaic genomes, with lateral gene transfer playing an important role in their diversity and evolution.

Correspondence
Julie C. Dunning Hotopp
jdhotopp{at}som.umaryland.edu

These authors contributed equally to this paper.

Present address: Centre for Structural and Functional Genomics, Concordia University, Montréal, QC H4B 1R6, Canada.

Present address: Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA 02454, USA.

||Present address: International Livestock Research Institute, PO Box 30709, Nairobi 00100, Kenya.

The GEO series accession number for the microarray data of this study is GSE13825.