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PMID: 15774024 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.

Genome biology ·Vol. 6 ·No. 3 ·2005-00-00 ·Pages R23

Salzberg SL, Dunning Hotopp JC, Delcher AL, Pop M, Smith DR, Eisen MB, Nelson WC

Abstract

The Trace Archive is a repository for the raw, unanalyzed data generated by large-scale genome sequencing projects. The existence of this data offers scientists the possibility of discovering additional genomic sequences beyond those originally sequenced. In particular, if the source DNA for a sequencing project came from a species that was colonized by another organism, then the project may yield substantial amounts of genomic DNA, including near-complete genomes, from the symbiotic or parasitic organism. By searching the publicly available repository of DNA sequencing trace data, we discovered three new species of the bacterial endosymbiont Wolbachia pipientis in three different species of fruit fly: Drosophila ananassae, D. simulans, and D. mojavensis. We extracted all sequences with partial matches to a previously sequenced Wolbachia strain and assembled those sequences using customized software. For one of the three new species, the data recovered were sufficient to produce an assembly that covers more than 95% of the genome; for a second species the data produce the equivalent of a 'light shotgun' sampling of the genome, covering an estimated 75-80% of the genome; and for the third species the data cover approximately 6-7% of the genome. The results of this study reveal an unexpected benefit of depositing raw data in a central genome sequence repository: new species can be discovered within this data. The differences between these three new Wolbachia genomes and the previously sequenced strain revealed numerous rearrangements and insertions within each lineage and hundreds of novel genes. The three new genomes, with annotation, have been deposited in GenBank.

MeSH Terms
Animals Base Sequence Drosophila/microbiology Gene Transfer, Horizontal Genome, Bacterial Genomics Molecular Sequence Data Phylogeny Sequence Alignment Sequence Analysis, DNA Wolbachia/classification,genetics
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Salzberg Steven L
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. [email protected]
Dunning Hotopp Julie C
Delcher Arthur L
Pop Mihai
Smith Douglas R
Eisen Michael B
Nelson William C
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Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
DOI
10.1186/gb-2005-6-3-r23
Email
[email protected]
Published
2005-00-00
Epub
2005-00-22
Pages
R23
Language
English
Region
England
NLM ID
100960660
PMCID
PMC1088942
Subset
IM
Grants
NLM NIH HHS · R01 LM006845 · United States
NLM NIH HHS · R01 LM007938 · United States
NLM NIH HHS · R01-LM007938 · United States
NLM NIH HHS · R01-LM06845 · United States
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Corrections
CommentIn
PMID: 15998462
ErratumIn
PMID: 15998463
External Links
PubMed source DOI: 10.1186/gb-2005-6-3-r23 PMC Full Text View journal details
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