Three bacterial genomes found lurking inside recently sequenced fruit fly genomes

When scientists finished sequencing the genomes of seven species of fruit fly last year, little did they know that they had also sequenced the genes of several bacteria that dwell undetected inside fruit fly embryos.

The genes of these bacteria, from a genus Wolbachia that infects many insects, have been sitting in the fruit fly gene database since then, unnoticed, according to Michael B. Eisen, a UC Berkeley assistant professor of molecular and cell biology and a faculty scientist at Lawrence Berkeley National Laboratory. But Eisen, a geneticist who mines the fruit fly and other genomes for clues to how genes shape the organism, had an inkling they were there, and in a quick search of the genome database late last year, turned up a slew of bacterial genes.

Because he’s a fruit fly geneticist and not an expert on bacteria, Eisen contacted bacterial geneticists at The Institute for Genomic Research (TIGR) in Maryland, and together they pulled out genes from three species of Wolbachia – all of them new to science. “The sequencers who did the Drosophila species didn’t even notice this because this is just a very small fraction of the total sequence and it was sort of tossed into the garbage,” he said. “In every genome there is always stuff that doesn’t make sense, and people weren’t looking for it. We thought this was interesting as much for the novelty of the way the bacterial genomes were sequenced than what we learned about the bacteria themselves.”

A team led by Steven L. Salzberg of TIGR and including Eisen of UC Berkeley’s Center for Integrative Genomics published their discovery in the most recent issue of the open access journal Genome Biology, published this week. Eisen, a member of the California Institute for Quantitative Biomedical Research (QB3) at UC Berkeley, is a vocal advocate of open access publishing, which makes the results of all research and research data freely available on the Internet. “The discovery of these three new genomes demonstrates how powerful the public release of raw sequencing data can be,” wrote the authors, who have deposited their findings in Genbank, an open repository of genomic sequences.

The existence of these bacterial species inside the fruit fly genome database is an artifact of the way the fly was sequenced, Eisen said. Embryos were ground up and the DNA extracted, meaning that any endosymbionts – organisms that live their entire lives inside another organism and have developed a mutual dependence with the host – would have had their DNA intermixed with fly DNA before sequencing.

The sequencers of other genomes, especially the human genome, were more careful to eliminate any endosymbionts or parasites, he said, but secrets may still lie hidden inside these other genomes. “There is a lot of unexplored stuff out there in the genome databases – it’s certainly not out of the question that other genomes have these lurking endosymbionts,” Eisen said. “After all, there are more bacterial cells in a human body than there are human cells.”

These findings might help shed light on the evolution of bacterial endosymbionts and on the mechanisms these organisms use to alter the cell cycle of the host in order to reproduce. “There are a lot of interesting questions one could ask if one started to get endosymbiont species along with their host species – questions about the evolution of the host-symbiont relationship,” Eisen said. “Endosymbiosis was a crucial evolutionary event in the history of all eukaryotic organisms. Mitochondria in animals and chloroplasts in plants are relic symbionts – captured bacteria that slowly lost their ability to live freely. It’s clearly something that happens a lot in nature and has been very poorly characterized.”

Wolbachia made headlines a year ago with the publication of the genome sequence of the species Wolbachia pipientis, which lives inside the reproductive cells of the laboratory fruit fly Drosophila melanogaster. The bacteria were maligned as “male killers” because they sometimes kill developing males, and occasionally convert male embryos to female. But species of Wolbachia live inside a wide variety of insects, spiders, and crustaceans and have beneficial as well as deleterious effects, Eisen said.

Given the Wolbachia genome and the likelihood that W. pipientis had been sequenced along with the fruit fly genome, Eisen performed a quick look for Wolbachia in the Trace Archive, an open source for raw genome data. In his words, “I found a whole bunch of stuff.”

Salzburg and his TIGR colleagues took over and searched not only the D. melanogaster genome but also the genomes of six other fruit flies so far sequenced. They found Wolbachia DNA in three species. They were able to reconstruct 95 percent (1,440,650 base pairs) of the genome of one new species from D. ananassae, which they called Wolbachia wAna. Using the same technique, they identified Wolbachia wSim in the genome of D. simulans and Wolbachia wMoj in the genome of D. mojavensis.

The team compared the new Wolbachia genomes with the known genome of the wMel strain of W. pipientis and found a number of new genes – up to 464 new genes in wAna – as well as a sign of extensive rearrangement between wMel and wAna, indicating 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. wMel and wMoj share about 97% of their genomes with wAna and wSim but are a bit more distant from one another, they found.