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Genome Res. 2011 Feb;21(2):315-24. doi: 10.1101/gr.107854.110. Epub 2010 Dec 22.

The Drosophila melanogaster transcriptome by paired-end RNA sequencing.

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Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.


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.

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