Reference
Citation
Celniker, S.E., Wheeler, D.A., Kronmiller, B., Carlson, J.W., Halpern, A., Patel, S., Adams, M., Champe, M., Dugan, S.P., Frise, E., Hodgson, A., George, R.A., Hoskins, R.A., Laverty, T., Muzny, D.M., Nelson, C.R., Pacleb, J.M., Park, S., Pfeiffer, B.D., Richards, S., Sodergren, E.J., Svirskas, R., Tabor, P.E., Wan, K., Stapleton, M., Sutton, G.G., Venter, C., Weinstock, G., Scherer, S.E., Myers, E.W., Gibbs, R.A., Rubin, G.M. (2002). Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence.  Genome Biol. 3(12): RESEARCH0079.
FlyBase ID
FBrf0155823
Publication Type
Research paper
Abstract
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.
PubMed ID
PubMed Central ID
PMC151181 (PMC) (EuropePMC)
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Secondary IDs
    Language of Publication
    English
    Additional Languages of Abstract
    Parent Publication
    Publication Type
    Journal
    Abbreviation
    Genome Biol.
    Title
    Genome Biology
    Publication Year
    2000-
    ISBN/ISSN
    1465-6906 1474-7596 1474-760X
    Data From Reference
    Genes (11)
    Strains (1)
    Natural transposons (10)