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 journalArticle

99 Scopus citations

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 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
Volume21
Issue number2
DOIs
StatePublished - Feb 2011

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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    Daines, B., Wang, H., Wang, L., Li, Y., Han, Y., Emmert, D., Gelbart, W., Wang, X., Li, W., Gibbs, R., & Chen, R. (2011). The Drosophila melanogaster transcriptome by paired-end RNA sequencing. Genome Research, 21(2), 315-324. https://doi.org/10.1101/gr.107854.110