title: Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence.
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.
authors.affiliation: Berkeley Drosophila Genome Project, Department of Genome Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. celniker@bdgp.lbl.gov
authors.forename: Susan E
authors.initials: SE
authors.lastname: Celniker
authors.forename: David A
authors.initials: DA
authors.lastname: Wheeler
authors.forename: Brent
authors.initials: B
authors.lastname: Kronmiller
authors.forename: Joseph W
authors.initials: JW
authors.lastname: Carlson
authors.forename: Aaron
authors.initials: A
authors.lastname: Halpern
authors.forename: Sandeep
authors.initials: S
authors.lastname: Patel
authors.forename: Mark
authors.initials: M
authors.lastname: Adams
authors.forename: Mark
authors.initials: M
authors.lastname: Champe
authors.forename: Shannon P
authors.initials: SP
authors.lastname: Dugan
authors.forename: Erwin
authors.initials: E
authors.lastname: Frise
authors.forename: Ann
authors.initials: A
authors.lastname: Hodgson
authors.forename: Reed A
authors.initials: RA
authors.lastname: George
authors.forename: Roger A
authors.initials: RA
authors.lastname: Hoskins
authors.forename: Todd
authors.initials: T
authors.lastname: Laverty
authors.forename: Donna M
authors.initials: DM
authors.lastname: Muzny
authors.forename: Catherine R
authors.initials: CR
authors.lastname: Nelson
authors.forename: Joanne M
authors.initials: JM
authors.lastname: Pacleb
authors.forename: Soo
authors.initials: S
authors.lastname: Park
authors.forename: Barret D
authors.initials: BD
authors.lastname: Pfeiffer
authors.forename: Stephen
authors.initials: S
authors.lastname: Richards
authors.forename: Erica J
authors.initials: EJ
authors.lastname: Sodergren
authors.forename: Robert
authors.initials: R
authors.lastname: Svirskas
authors.forename: Paul E
authors.initials: PE
authors.lastname: Tabor
authors.forename: Kenneth
authors.initials: K
authors.lastname: Wan
authors.forename: Mark
authors.initials: M
authors.lastname: Stapleton
authors.forename: Granger G
authors.initials: GG
authors.lastname: Sutton
authors.forename: Craig
authors.initials: C
authors.lastname: Venter
authors.forename: George
authors.initials: G
authors.lastname: Weinstock
authors.forename: Steven E
authors.initials: SE
authors.lastname: Scherer
authors.forename: Eugene W
authors.initials: EW
authors.lastname: Myers
authors.forename: Richard A
authors.initials: RA
authors.lastname: Gibbs
authors.forename: Gerald M
authors.initials: GM
authors.lastname: Rubin
mesh_terms: D000818:Animals; D004331:Drosophila melanogaster / Q000235:genetics*; D022041:Euchromatin / Q000235:genetics*; D016678:Genome; D020161:Physical Chromosome Mapping / Q000379:methods; D012107:Research Design; D017422:Sequence Analysis, DNA / Q000379:methods*; D014960:X Chromosome / Q000235:genetics
chemical_list: D022041:Euchromatin