The Drosophila melanogaster transcriptome by paired-end RNA sequencing.

TitleThe Drosophila melanogaster transcriptome by paired-end RNA sequencing.
Publication TypeJournal Article
Year of Publication2011
AuthorsDaines, B, Wang, H, Wang, L, Li, Y, Han, Y, Emmert, D, Gelbart, W, Wang, X, Li, W, Gibbs, R, Chen, R
JournalGenome Res
Volume21
Issue2
Pagination315-24
Date Published2011 Feb
ISSN1549-5469
KeywordsAlternative Splicing, Animals, Drosophila melanogaster, Female, Gene Expression Profiling, Genes, Y-Linked, Male, Molecular Sequence Annotation, Molecular Sequence Data, Oligonucleotide Array Sequence Analysis, Sequence Analysis, RNA
Abstract

RNA-seq was used to generate an extensive map of the Drosophila melanogaster transcriptome by broad sampling of 10 developmental stages. In total, 142.2 million uniquely mapped 64-100-bp paired-end reads were generated on the Illumina GA II yielding 356× sequencing coverage. More than 95% of FlyBase genes and 90% of splicing junctions were observed. Modifications to 30% of FlyBase gene models were made by extension of untranslated regions, inclusion of novel exons, and identification of novel splicing events. A total of 319 novel transcripts were identified, representing a 2% increase over the current annotation. Alternate splicing was observed in 31% of D. melanogaster genes, a 38% increase over previous estimations, but significantly less than that observed in higher organisms. Much of this splicing is subtle such as tandem alternate splice sites.

DOI10.1101/gr.107854.110
Alternate JournalGenome Res.
PubMed ID21177959
PubMed Central IDPMC3032934
Grant ListT32 EYO7102-16 / / PHS HHS / United States
F32 EY019430 / EY / NEI NIH HHS / United States
5U54HG003273 / HG / NHGRI NIH HHS / United States
EY19430-01 / EY / NEI NIH HHS / United States
U54 HG003273 / HG / NHGRI NIH HHS / United States
R01 EY016853 / EY / NEI NIH HHS / United States
R01EY016853 / EY / NEI NIH HHS / United States
T32 EY007102 / EY / NEI NIH HHS / United States