The developmental transcriptome of Drosophila melanogaster

Brenton R. Graveley (), Angela N. Brooks, Joseph W. Carlson, Michael O. Duff, Jane M. Landolin, Li Yang, Carlo G. Artieri, Marijke J. van Baren, Nathan Boley, Benjamin W. Booth, James B. Brown, Lucy Cherbas, Carrie A. Davis, Alex Dobin, Renhua Li, Wei Lin, John H. Malone, Nicolas R. Mattiuzzo, David Miller, David Sturgill, Brian B. Tuch, Chris Zaleski, Dayu Zhang, Marco Blanchette, Sandrine Dudoit, Brian Eads, Richard E. Green, Ann Hammonds, Lichun Jiang, Phil Kapranov, Laura Langton, Norbert Perrimon, Jeremy E. Sandler, Kenneth H. Wan, Aarron Willingham, Yu Zhang, Yi Zou, Justen Andrews, Peter J. Bickel, Steven E. Brenner, Michael R. Brent, Peter Cherbas, Thomas R. Gingeras, Roger A. Hoskins, Thomas C. Kaufman, Brian Oliver and Susan E. Celniker ()
Additional contact information
Brenton R. Graveley: University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030-6403, USA
Angela N. Brooks: University of California
Joseph W. Carlson: Lawrence Berkeley National Laboratory
Michael O. Duff: University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030-6403, USA
Jane M. Landolin: Lawrence Berkeley National Laboratory
Li Yang: University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030-6403, USA
Carlo G. Artieri: Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health
Marijke J. van Baren: Washington University
Nathan Boley: University of California
Benjamin W. Booth: Lawrence Berkeley National Laboratory
James B. Brown: University of California
Lucy Cherbas: Center for Genomics and Bioinformatics, Indiana University, 1001 E. 3rd Street, Bloomington, Indiana 47405-7005, USA
Carrie A. Davis: Cold Spring Harbor Laboratory
Alex Dobin: Cold Spring Harbor Laboratory
Renhua Li: Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health
Wei Lin: Cold Spring Harbor Laboratory
John H. Malone: Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health
Nicolas R. Mattiuzzo: Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health
David Miller: Indiana University, 1001 E. 3rd Street, Bloomington, Indiana 47405-7005, USA
David Sturgill: Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health
Brian B. Tuch: Research and Development, Life Technologies, Foster City, California 94404, USA
Chris Zaleski: Cold Spring Harbor Laboratory
Dayu Zhang: Center for Genomics and Bioinformatics, Indiana University, 1001 E. 3rd Street, Bloomington, Indiana 47405-7005, USA
Marco Blanchette: Stowers Institute for Medical Research, 1000 East 50th street
Sandrine Dudoit: School of Public Health, University of California
Brian Eads: Indiana University, 1001 E. 3rd Street, Bloomington, Indiana 47405-7005, USA
Richard E. Green: Department of Biomolecular Engineering. University of California
Ann Hammonds: Lawrence Berkeley National Laboratory
Lichun Jiang: Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health
Phil Kapranov: Cold Spring Harbor Laboratory
Laura Langton: Washington University
Norbert Perrimon: Harvard Medical School
Jeremy E. Sandler: Lawrence Berkeley National Laboratory
Kenneth H. Wan: Lawrence Berkeley National Laboratory
Aarron Willingham: University of California
Yu Zhang: Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health
Yi Zou: Center for Genomics and Bioinformatics, Indiana University, 1001 E. 3rd Street, Bloomington, Indiana 47405-7005, USA
Justen Andrews: Indiana University, 1001 E. 3rd Street, Bloomington, Indiana 47405-7005, USA
Peter J. Bickel: University of California
Steven E. Brenner: University of California
Michael R. Brent: Washington University
Peter Cherbas: Center for Genomics and Bioinformatics, Indiana University, 1001 E. 3rd Street, Bloomington, Indiana 47405-7005, USA
Thomas R. Gingeras: Cold Spring Harbor Laboratory
Roger A. Hoskins: Lawrence Berkeley National Laboratory
Thomas C. Kaufman: Indiana University, 1001 E. 3rd Street, Bloomington, Indiana 47405-7005, USA
Brian Oliver: Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health
Susan E. Celniker: Lawrence Berkeley National Laboratory

Nature, 2011, vol. 471, issue 7339, 473-479

Abstract: Abstract Drosophila melanogaster is one of the most well studied genetic model organisms; nonetheless, its genome still contains unannotated coding and non-coding genes, transcripts, exons and RNA editing sites. Full discovery and annotation are pre-requisites for understanding how the regulation of transcription, splicing and RNA editing directs the development of this complex organism. Here we used RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages. We identified 111,195 new elements, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events, and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches. These data substantially expand the number of known transcribed elements in the Drosophila genome and provide a high-resolution view of transcriptome dynamics throughout development.

Date: 2011
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DOI: 10.1038/nature09715

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