Home LiteratureArticle Details
PMID: 17989253 Published · ppublish English Comparative Study Journal Article

Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.

Genome research ·Vol. 17 ·No. 12 ·2007-12-00 ·Pages 1823-36

Lin MF, Carlson JW, Crosby MA, Matthews BB, Yu C, Park S, Wan KH, Schroeder AJ, Gramates LS, St Pierre SE, Roark M, Wiley KL, Kulathinal RJ, Zhang P, Myrick KV, Antone JV, Celniker SE, Gelbart WM, Kellis M

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.

MeSH Terms
Animals Base Sequence Codon/genetics Conserved Sequence Drosophila Proteins/chemistry,genetics Drosophila melanogaster/genetics Evolution, Molecular Genes, Insect Genome, Insect Molecular Sequence Data Reading Frames Sequence Alignment
Chemicals
Codon Drosophila Proteins
Authors & Affiliations
19 authors, click to expand affiliations / ORCID
Lin Michael F
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA.
Carlson Joseph W
Crosby Madeline A
Matthews Beverley B
Yu Charles
Park Soo
Wan Kenneth H
Schroeder Andrew J
Gramates L Sian
St Pierre Susan E
Roark Margaret
Wiley Kenneth L
Kulathinal Rob J
Zhang Peili
Myrick Kyl V
Antone Jerry V
Celniker Susan E
Gelbart William M
Kellis Manolis
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.6679507
Published
2007-12-00
Epub
2007-00-07
Pages
1823-36
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC2099591
Subset
IM
Databases
GENBANK
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PubMed source DOI: 10.1101/gr.6679507 PMC Full Text View journal details
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