The Drosophila melanogaster transcriptome by paired-end RNA sequencing
- Bryce Daines1,2,6,
- Hui Wang2,6,
- Liguo Wang3,6,
- Yumei Li1,2,
- Yi Han2,
- David Emmert4,
- William Gelbart4,
- Xia Wang1,2,
- Wei Li3,5,
- Richard Gibbs1,2,7 and
- Rui Chen1,2,7
- 1 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA;
- 2 Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
- 3 Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA;
- 4 Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA;
- 5 Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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↵6 These authors contributed equally to this work.
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.
Footnotes
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↵7 Corresponding authors.
E-mail ruichen{at}bcm.edu.
E-mail rgibbs{at}bcm.edu.
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[Supplemental material is available for this article. The sequencing data from this study have been submitted to the NCBI Sequence Read Archive (http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi) under accession no. SRA012173 and to the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) under accession no. GSE24324.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.107854.110.
- Received March 15, 2010.
- Accepted September 30, 2010.
- Copyright © 2011 by Cold Spring Harbor Laboratory Press
