title: The Drosophila melanogaster transcriptome by paired-end RNA sequencing.
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.
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.
authors.forename: Bryce
authors.initials: B
authors.lastname: Daines
authors.forename: Hui
authors.initials: H
authors.lastname: Wang
authors.forename: Liguo
authors.initials: L
authors.lastname: Wang
authors.forename: Yumei
authors.initials: Y
authors.lastname: Li
authors.forename: Yi
authors.initials: Y
authors.lastname: Han
authors.forename: David
authors.initials: D
authors.lastname: Emmert
authors.forename: William
authors.initials: W
authors.lastname: Gelbart
authors.forename: Xia
authors.initials: X
authors.lastname: Wang
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: Richard
authors.initials: R
authors.lastname: Gibbs
authors.forename: Rui
authors.initials: R
authors.lastname: Chen
mesh_terms: D017398:Alternative Splicing / Q000235:genetics; D000818:Animals; D004331:Drosophila melanogaster / Q000235:genetics* / Q000378:metabolism*; D005260:Female; D020869:Gene Expression Profiling; D050173:Genes, Y-Linked; D008297:Male; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D017423:Sequence Analysis, RNA