title: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.
abstract: The availability of sequenced genomes from 12 Drosophila species has enabled the use of comparative genomics for the systematic discovery of functional elements conserved within this genus. We have developed quantitative metrics for the evolutionary signatures specific to protein-coding regions and applied them genome-wide, resulting in 1193 candidate new protein-coding exons in the D. melanogaster genome. We have reviewed these predictions by manual curation and validated a subset by directed cDNA screening and sequencing, revealing both new genes and new alternative splice forms of known genes. We also used these evolutionary signatures to evaluate existing gene annotations, resulting in the validation of 87% of genes lacking descriptive names and identifying 414 poorly conserved genes that are likely to be spurious predictions, noncoding, or species-specific genes. Furthermore, our methods suggest a variety of refinements to hundreds of existing gene models, such as modifications to translation start codons and exon splice boundaries. Finally, we performed directed genome-wide searches for unusual protein-coding structures, discovering 149 possible examples of stop codon readthrough, 125 new candidate ORFs of polycistronic mRNAs, and several candidate translational frameshifts. These results affect >10% of annotated fly genes and demonstrate the power of comparative genomics to enhance our understanding of genome organization, even in a model organism as intensively studied as Drosophila melanogaster.
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA.
authors.forename: Michael F
authors.initials: MF
authors.lastname: Lin
authors.forename: Joseph W
authors.initials: JW
authors.lastname: Carlson
authors.forename: Madeline A
authors.initials: MA
authors.lastname: Crosby
authors.forename: Beverley B
authors.initials: BB
authors.lastname: Matthews
authors.forename: Charles
authors.initials: C
authors.lastname: Yu
authors.forename: Soo
authors.initials: S
authors.lastname: Park
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Wan
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Schroeder
authors.forename: L Sian
authors.initials: LS
authors.lastname: Gramates
authors.forename: Susan E
authors.initials: SE
authors.lastname: St Pierre
authors.forename: Margaret
authors.initials: M
authors.lastname: Roark
authors.forename: Kenneth L
authors.initials: KL
authors.lastname: Wiley
authors.forename: Rob J
authors.initials: RJ
authors.lastname: Kulathinal
authors.forename: Peili
authors.initials: P
authors.lastname: Zhang
authors.forename: Kyl V
authors.initials: KV
authors.lastname: Myrick
authors.forename: Jerry V
authors.initials: JV
authors.lastname: Antone
authors.forename: Susan E
authors.initials: SE
authors.lastname: Celniker
authors.forename: William M
authors.initials: WM
authors.lastname: Gelbart
authors.forename: Manolis
authors.initials: M
authors.lastname: Kellis
mesh_terms: D000818:Animals; D001483:Base Sequence; D003062:Codon / Q000235:genetics; D017124:Conserved Sequence; D029721:Drosophila Proteins / Q000737:chemistry / Q000235:genetics*; D004331:Drosophila melanogaster / Q000235:genetics*; D019143:Evolution, Molecular; D017344:Genes, Insect; D049750:Genome, Insect; D008969:Molecular Sequence Data; D016364:Reading Frames; D016415:Sequence Alignment
chemical_list: D003062:Codon; D029721:Drosophila Proteins