title: A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome.
abstract: Five years after the completion of the sequence of the Drosophila melanogaster genome, the number of protein-coding genes it contains remains a matter of debate; the number of computational gene predictions greatly exceeds the number of validated gene annotations. We have assembled a collection of >10,000 gene predictions that do not overlap existing gene annotations and have developed a process for their validation that allows us to efficiently prioritize and experimentally validate predictions from various sources by sequencing RT-PCR products to confirm gene structures. Our data provide experimental evidence for 122 protein-coding genes. Our analyses suggest that the entire collection of predictions contains only approximately 700 additional protein-coding genes. Although we cannot rule out the discovery of genes with unusual features that make them refractory to existing methods, our results suggest that the D. melanogaster genome contains approximately 14,000 protein-coding genes.
authors.affiliation: Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Life Sciences Addition, Berkeley, CA 94720-3200, USA. myandell@fruitfly.org
authors.forename: Mark
authors.initials: M
authors.lastname: Yandell
authors.forename: Adina M
authors.initials: AM
authors.lastname: Bailey
authors.forename: Sima
authors.initials: S
authors.lastname: Misra
authors.forename: ShengQiang
authors.initials: S
authors.lastname: Shu
authors.forename: Colin
authors.initials: C
authors.lastname: Wiel
authors.forename: Martha
authors.initials: M
authors.lastname: Evans-Holm
authors.forename: Susan E
authors.initials: SE
authors.lastname: Celniker
authors.forename: Gerald M
authors.initials: GM
authors.lastname: Rubin
mesh_terms: D000818:Animals; D017931:DNA Primers; D029721:Drosophila Proteins / Q000235:genetics*; D004331:Drosophila melanogaster / Q000235:genetics*; D016678:Genome; D008957:Models, Genetic; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods
chemical_list: D017931:DNA Primers; D029721:Drosophila Proteins