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The developmental transcriptome of Drosophila melanogaster

Author

Listed:
  • 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
    Genome Analysis Unit, Amgen)

  • 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
    Kansas University Medical Center, 3901 Rainbow Boulevard, Kansas City, Kansas 66160, USA)

  • 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
    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
    Indiana University, 1001 E. 3rd Street, Bloomington, Indiana 47405-7005, USA)

  • Thomas R. Gingeras

    (Cold Spring Harbor Laboratory
    Affymetrix)

  • 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)

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.

Suggested Citation

  • 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 , 2011. "The developmental transcriptome of Drosophila melanogaster," Nature, Nature, vol. 471(7339), pages 473-479, March.
    • Handle: RePEc:nat:nature:v:471:y:2011:i:7339:d:10.1038_nature09715
    DOI: 10.1038/nature09715
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    Citations

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    Cited by:

    1. Safo, Sandra E. & Ahn, Jeongyoun, 2016. "General sparse multi-class linear discriminant analysis," Computational Statistics & Data Analysis, Elsevier, vol. 99(C), pages 81-90.
    2. Rizwanul Haque & Sonu Peedikayil Kurien & Hagar Setty & Yehuda Salzberg & Gil Stelzer & Einav Litvak & Hila Gingold & Oded Rechavi & Meital Oren-Suissa, 2024. "Sex-specific developmental gene expression atlas unveils dimorphic gene networks in C. elegans," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    3. Zhiping Zhang & Bongmin Bae & Winston H. Cuddleston & Pedro Miura, 2023. "Coordination of alternative splicing and alternative polyadenylation revealed by targeted long read sequencing," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

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