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Finishing a whole-genome shotgun: Release 3 of the Drosophila melanogaster euchromatic genome sequence

Susan E Celniker1*, David A Wheeler2, Brent Kronmiller1, Joseph W Carlson1, Aaron Halpern3, Sandeep Patel1, Mark Adams3, Mark Champe1, Shannon P Dugan4, Erwin Frise1, Ann Hodgson4, Reed A George1, Roger A Hoskins1, Todd Laverty5, Donna M Muzny4, Catherine R Nelson1, Joanne M Pacleb1, Soo Park1, Barret D Pfeiffer1, Stephen Richards14, Erica J Sodergren4, Robert Svirskas6, Paul E Tabor4, Kenneth Wan1, Mark Stapleton1, Granger G Sutton3, Craig Venter3, George Weinstock4, Steven E Scherer4, Eugene W Myers3, Richard A Gibbs4 and Gerald M Rubin15

Author affiliations

1 Berkeley Drosophila Genome Project, Department of Genome Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

2 Human Genome Sequencing Center, and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA

3 Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA

4 Drosophila Sequencing Team, Human Genome Sequencing Center, and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA

5 Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, USA

6 Amersham Biosciences, 2100 East Elliot Road, Tempe, AZ 85284, USA

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Citation and License

Genome Biology 2002, 3:research0079-0079.14  doi:10.1186/gb-2002-3-12-research0079

This article is part of a series of refereed research articles from Berkeley Drosophila Genome Project, FlyBase and colleagues, describing Release 3 of the Drosophila genome, which are freely available at

Published: 23 December 2002



The Drosophila melanogaster genome was the first metazoan genome to have been sequenced by the whole-genome shotgun (WGS) method. Two issues relating to this achievement were widely debated in the genomics community: how correct is the sequence with respect to base-pair (bp) accuracy and frequency of assembly errors? And, how difficult is it to bring a WGS sequence to the accepted standard for finished sequence? We are now in a position to answer these questions.


Our finishing process was designed to close gaps, improve sequence quality and validate the assembly. Sequence traces derived from the WGS and draft sequencing of individual bacterial artificial chromosomes (BACs) were assembled into BAC-sized segments. These segments were brought to high quality, and then joined to constitute the sequence of each chromosome arm. Overall assembly was verified by comparison to a physical map of fingerprinted BAC clones. In the current version of the 116.9 Mb euchromatic genome, called Release 3, the six euchromatic chromosome arms are represented by 13 scaffolds with a total of 37 sequence gaps. We compared Release 3 to Release 2; in autosomal regions of unique sequence, the error rate of Release 2 was one in 20,000 bp.


The WGS strategy can efficiently produce a high-quality sequence of a metazoan genome while generating the reagents required for sequence finishing. However, the initial method of repeat assembly was flawed. The sequence we report here, Release 3, is a reliable resource for molecular genetic experimentation and computational analysis.