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

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

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

Michael F Lin,Joseph W Carlson,Madeline A Crosby,Beverley B Matthews,Charles Yu,Soo Park,Kenneth H Wan,Andrew J Schroeder,L Sian Gramates,Susan E St Pierre,Margaret Roark,Kenneth L Wiley,Rob J Kulathinal,Peili Zhang,Kyl V Myrick,Jerry V Antone,Susan E Celniker,William M Gelbart,Manolis Kellis,Michael F Lin,Joseph W Carlson,Madeline A Crosby,Beverley B Matthews,Charles Yu,Soo Park,Kenneth H Wan,Andrew J Schroeder,L Sian Gramates,Susan E St Pierre,Margaret Roark,Kenneth L Wiley,Rob J Kulathinal,Peili Zhang,Kyl V Myrick,Jerry V Antone,Susan E Celniker,William M Gelbart,Manolis Kellis,Michael F Lin,Joseph W Carlson,Madeline A Crosby,Beverley B Matthews,Charles Yu,Soo Park,Kenneth H Wan,Andrew J Schroeder,L Sian Gramates,Susan E St Pierre,Margaret Roark,Kenneth L Wiley,Rob J Kulathinal,Peili Zhang,Kyl V Myrick,Jerry V Antone,Susan E Celniker,William M Gelbart,Manolis Kellis,

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.

Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes. Publishing Authors By Initials

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

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

PUBLICATION TYPE: Journal Article

Journal: Genome research

VOLUME: 17

Page Numbers: 1823-36

Journal Abbreviation: Genome Res.

ISSN: 1088-9051

DAY: 7

MONTH: 11

YEAR: 2007

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

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LANGUAGE: eng

NlmUniqueID: 9518021

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AFFILIATION: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA;

Country: United States

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MEDLINETA: Genome Res

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