Sifting Through Fruitfly Sequences, Scientists Discover New Wolbachias

Finding the genomic equivalent of gold nuggets in the rough ore of a much larger set of data, TIGR scientists and collaborators have discovered the genomes of three new types of the microbe Wolbachia in fruitfly sequence data.

March 2, 2005

Rockville, MD — Finding the genomic equivalent of gold nuggets in the rough ore of a much larger set of data, a group of TIGR scientists and collaborators have discovered the genomes of three new types of the microbe Wolbachia in fruitfly sequence data.

The three previously-unknown Wolbachia, one-celled organisms which live as endosymbionts within fruitflies, were found by means of a search and analysis of Trace Archive data — open-source sets of raw sequence data that had been generated in the DNA sequencing of three different species of fruitfly: Drosophila ananassae, D. simulans, and D. mojavensis.

A team led by TIGR's senior director of bioinformatics, Steven Salzberg, used TIGR's data from the first Wolbachia to be sequenced (W. pipientis wMel) as a probe to analyze fruitfly Trace Archive data for other strains of the endosymbiont.

From the fruitfly species D. ananassae, they retrieved an estimated 98 percent of the genome of a new Wolbachia species, which they identified as Wolbachia wAna. In a similar fashion, they identified Wolbachia wSim in the genome of D. simulans and Wolbachia wMoj in the genome of D. mojavensis.

The results of the research, published in February in the journal Genome Biology, show "how powerful the public release of raw sequencing data can be," the scientists report. The work was supported in part by grants from the National Institutes of Health and the National Science Foundation.

"Even though the fruit fly genome projects did not have the goal of finding bacterial endosymbionts, our analysis of the Trace Archive data has yielded three partial genomes — one nearly complete — of this biologically important species," says Salzberg.

Salzberg had been approached to do the project by Michael Eisen, a University of California-Berkeley assistant professor of molecular and cell biology and a faculty scientist at Lawrence Berkeley National Laboratory. Eisen had found evidence of a Wolbachia in sequence traces from D. ananassae.

"TIGR took it from there," says Salzberg, "pulling out all the data from the Trace Archive and then searching all the other fly genomes. We found two more Wolbachia, which was a striking result."

TIGR's Mihai Pop and Art Delcher helped with the genome assemblies and Bill Nelson helped with annotation of the Wolbachia. Julie Dunning-Hotopp, a Wolbachia genomics expert, helped with analysis of the data.

When the TIGR team compared the new Wolbachia genomes with the known genome of the wMel strain of W. pipientis, they found new genes — as many as 464 new genes in wAna - as well as indications of extensive rearrangements between wMel and wAna. Those rearrangements indicate that the two strains have diverged significantly since they first infected the two Drosophila species.

The two most closely related strains are wAna and wSim, which have nearly identical genomes. A bit more distant from one another are wMel and wMoj, even through they share about 97% of their genomes with wAna and wSim, the researchers found.

The first complete genome of a Wolbachia species was published by TIGR and collaborators in the March 2004 issue of PLoS Biology. The investigators, led by TIGR Investigator Jonathan Eisen — brother of Michael Eisen — found that composition of the genome was very different from that of other intracellular bacteria. The wMel genome has accumulated more repetitive and so-called "junk" DNA (DNA for which a function cannot be identified) than any other intracellular bacteria.

Living inside the gonad cells of more than a million species of insects, spiders, crustaceans and worms, most members of the Wolbachia family of intracellular bacteria manipulate the reproduction of their host to help ensure their own survival.

The losers in that manipulation are always the males of the host organism. Depending on the specific pair of Wolbachia and host species involved, the host males are either killed, converted into females, or prevented from successfully fertilizing the eggs of uninfected females.