The Drosophila melanogaster transcriptome by paired-end RNA sequencing

Bryce Daines, Hui Wang, Liguo Wang, Yumei Li, Yi Han, David Emmert, William Gelbart, Xia Wang, Wei Li, Richard Gibbs, Rui Chen

Research output: Contribution to journalArticlepeer-review

99 Scopus citations


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 356x 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.

Original languageEnglish (US)
Pages (from-to)315-324
Number of pages10
JournalGenome Research
Issue number2
StatePublished - Feb 2011

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


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