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

S Celniker(Lawrence Berkeley National Laboratory), David A. Wheeler(Baylor College of Medicine), Brent A. Kronmiller(Lawrence Berkeley National Laboratory), Joseph W. Carlson(Lawrence Berkeley National Laboratory), Aaron L. Halpern, Sandeep Patel(Lawrence Berkeley National Laboratory), Mark D. Adams, Mark Champe(Lawrence Berkeley National Laboratory), Shannon Dugan(Baylor College of Medicine), Erwin Frise(Lawrence Berkeley National Laboratory), Ann Hodgson(Baylor College of Medicine), Reed George(Lawrence Berkeley National Laboratory), Roger A. Hoskins(Lawrence Berkeley National Laboratory), Todd Laverty(University of California, Berkeley), Donna M. Muzny(Baylor Genetics), Catherine R. Nelson(Lawrence Berkeley National Laboratory), Joanne Pacleb(Lawrence Berkeley National Laboratory), Soo Hyung Park(Lawrence Berkeley National Laboratory), Barret D. Pfeiffer(Lawrence Berkeley National Laboratory), Stephen M. Richards(Baylor College of Medicine), Erica Sodergren(Baylor College of Medicine), Robert Svirskas, Paul E. Tabor(Baylor College of Medicine), Kenneth H. Wan(Lawrence Berkeley National Laboratory), Mark Stapleton(Lawrence Berkeley National Laboratory), Granger G. Sutton, Craig Venter, George M. Weinstock(Baylor Genetics), Steven E. Scherer(Baylor Genetics), Eugene W. Myers, Richard A. Gibbs(Baylor College of Medicine), Gerald M. Rubin(Howard Hughes Medical Institute)
Genome biology
December 23, 2002
10.1186/gb-2002-3-12-research0079
Cited by 397Open Access
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Abstract

BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.

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