New species from old data

Researchers have discovered three previously unknown species of a bacterium by scanning a publicly available data bank, reveals a study published today in the journal Genome Biology. The finding highlights the value of making unanalysed data from large-scale genome sequencing projects openly available online.

Steven Salzberg from The Institute for Genomic Research in Maryland and colleagues identified three new species of the bacterium Wolbachia from the genome sequences of the fruit fly Drosophila that are stored in the Trace Archive.

The Trace Archive is a public repository of raw genomic data from sequencing projects. When the genome of an organism is sequenced, the genome of endosymbiotic bacteria that live inside the organism can get incorporated into the data, contaminating the final genomic sequence of the host organism. Scanning raw sequences can therefore lead to the identification of previously unknown endosymbionts.

Salzberg and colleagues scanned through the newly sequenced genomes of seven different Drosophila species, using the genome of the bacterium Wolbachia pipientis wMel as a probe. From D. ananassae, they retrieved 32,720 sequences that matched the wMel strain. This yielded a new genome of 1,440,650 bp, which they identified as the new species 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 discovery of these three new genomes demonstrates how powerful the public release of raw sequencing data can be" write the authors, who have deposited their findings in Genbank, another open repository of genomic sequences.

The team compared the new Wolbachia genomes with the wMel genome 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.

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.

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Serendipitous discovery of Wolbachia genomes in multiple Drosophila species
Steven L. Salzberg, Julie C. Dunning Hotopp, Arthur L. Delcher, Mihai
Pop, Douglas R. Smith, Michael B. Eisen, and William C. Nelson
Genome Biology 6: R23

Source: BioMed Central