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International Team Sequences Genome of Sex-Altering Insect Parasite

NEW YORK (GenomeWeb News) – A bacterial strain that infects Drosophila simulans — and uses reproduction manipulating tactics to alter sex-ratios in the fly — has a patchwork genome cobbled together from bits of DNA nabbed from their hosts and other bacteria, according to an international research team who sequenced the strain.

Researchers from Sweden, Greece, Denmark, and the UK sequenced the 1.4 million base pair genome of a strain of Wolbachia pipientis called wRi and part of the genome sequence of another W. pipientis strain infecting a parasitic wasp species. When they compared these genomes to one another and to previously sequenced strains, the researchers found that Wolbachia are capable both of stealing genes from their hosts and swapping genes with other Wolbachia strains. The research appeared online this week in the Proceedings of the National Academy of Sciences.

"With the help of viruses, these bacteria exchange genes with each other, which leads to a rapid dissemination of genes that are thought to be important for sex manipulation," co-lead author Lisa Klasson, a molecular evolution researcher at Uppsala University's Evolutionary Biology Centre, said in a statement.

Roughly a fifth of insects are infected with W. pipientis, a species of intracellular bacteria that are passed along to the next generation through host female eggs. The bacteria, which also infect spiders, scorpions, mites, and nematodes and frequently employ reproductive strategies that alter the ratio of male and female hosts — for instance, killing or feminizing male embryos or using parthenogenesis or cytoplasmic incompatibility to exert control over the proportion of males and females in their host population.

Although they all belong to one species, W. pipientis strains have been sub-classified into a set of so-called "supergroups." So far, three W. pipientis genomes have been sequenced: the 1.27 million base pair genome of the wMel strain, which infects D. melanogaster, the 1.48 million base pair genome of the wPip strain, which infects the Culex quinquefasciatus mosquito, and the 1.08 base pair genome of the wBm strain, which has a mutualistic relationship with the nematode Brugia malayi.

For this study, the researchers focused mainly on a group A strain called W. pipientis wRi, which infects Drosophila simulans causing cytoplasmic incompatibility — a situation in which W. pipientis infected females can mate with either infected or uninfected males while uninfected females can't mate with W. pipientis infected males.

To sequence the 1,445,873 base pair W. pipientis wRi genome to more than eight times coverage, the researchers constructed a W. pipientis wRi genetic library using DNA extracted from D. simulans embryos and then sequenced this library using tens of thousands of reads.

The genome, which is housed in one circular chromosome, contains roughly 1,150 protein-coding sequences and 114 pseudogenes.

Based on the sequence they obtained, the researchers concluded that the genome contains DNA from four different bacteria-infecting viruses. Nearly a quarter of the genome, about 22 percent, contained repeated sequences.

The genome also contained nearly three dozen genes containing ankyrin repeat domains — protein-protein interaction motifs usually found in eukaryotic cells. Viruses and bacteria can snatch up these domains via horizontal gene transfer with eukaryotes but aren't believed to carry ankyrin repeats otherwise. Previous studies suggest the D. melanogaster-infecting strain wMel, for its part, carries 23 ankyrin repeat domain-containing genes.

The team's subsequent comparisons suggest both wRi and wMel carry a slew of gene-disrupting mobile elements as well as genes coding for viral proteins. For instance, both harbored 35 breakpoints that appear to have resulted from gene insertions by repeats called IS-elements, viral sequences or long repeats. Based on such results, the researchers suggested that "mobile genetic elements and repeated sequences are hot spots for rearrangement in Wolbachia."

Next, the team sequenced 450 genes from W. pipientis wUni, which infects a parasitic wasp called Muscidifurax uniraptor, and compared divergence patterns for 450 orthologous genes found in wRi, wMel, and wUni, finding evidence for widespread recombination within the genes. In addition, they identified 177,000 bases of DNA in FlyBase that matched sequences in wRi, though the D. simulans genome itself did not harbor any of these sequences.

Because recombination is so prevalent in Wolbachia strains — particularly those in the A group — the researchers argued that it may be difficult to discern genotypes between these strains without sequencing each complete genome. "Pervasive recombination in parasitic Wolbachia destroys the anticipated correlation between gene history, genome history, and strain phenotype," Klasson and her co-authors wrote.

Even so, they noted, since selection likely influences traits involved in interactions with each host, understanding such interactions may provide new insights into genes exploited for reproductive manipulation. And, the researchers speculated that if they can determine which genes are responsible for altering host sex ratios, they may eventually be able to develop environmentally friendly pesticides based on a similar mechanism.

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