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 Richards¹^,4, 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 Rubin¹^,5

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

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

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

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

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

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

author email corresponding author email

Genome Biology 2002, 3:research0079.1-0079.14doi:10.1186/gb-2002-3-12-research0079


Published:	23 December 2002

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 http://genomebiology.com/drosophila/.

Subject areas: Model organisms, Bioinformatics, Methods, Molecular biology

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.