Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags

  1. Simon J. Hubbard1,
  2. Darren V. Grafham2,
  3. Kevin J. Beattie3,
  4. Ian M. Overton1,
  5. Stuart R. McLaren2,
  6. Michael D.R. Croning2,
  7. Paul E. Boardman1,
  8. James K. Bonfield2,
  9. Joan Burnside4,
  10. Robert M. Davies2,
  11. Elizabeth R. Farrell3,
  12. Matthew D. Francis2,
  13. Sam Griffiths-Jones2,
  14. Sean J. Humphray2,
  15. Christopher Hyland1,
  16. Carol E. Scott2,
  17. Haizhou Tang1,
  18. Ruth G. Taylor2,
  19. Cheryll Tickle3,
  20. William R.A. Brown5,
  21. Ewan Birney6,
  22. Jane Rogers2, and
  23. Stuart A. Wilson7,8
  1. 1 Faculty of Life Sciences, The University of Manchester, Manchester, M60 1QD, United Kingdom
  2. 2 The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom
  3. 3 Division of Cell and Developmental Biology, University of Dundee, Dundee, DD1 5EH, United Kingdom
  4. 4 Delaware Biotechnology Institute, Newark, Delaware 19711, USA
  5. 5 Institute of Genetics, Nottingham University, Queen's Medical Centre, Nottingham, NG7 2UH, United Kingdom
  6. 6 EMBL European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
  7. 7 Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, United Kingdom

Abstract

We present an analysis of the chicken (Gallus gallus) transcriptome based on the full insert sequences for 19,626 cDNAs, combined with 485,337 EST sequences. The cDNA data set has been functionally annotated and describes a minimum of 11,929 chicken coding genes, including the sequence for 2260 full-length cDNAs together with a collection of noncoding (nc) cDNAs that have been stringently filtered to remove untranslated regions of coding mRNAs. The combined collection of cDNAs and ESTs describe 62,546 clustered transcripts and provide transcriptional evidence for a total of 18,989 chicken genes, including 88% of the annotated Ensembl gene set. Analysis of the ncRNAs reveals a set that is highly conserved in chickens and mammals, including sequences for 14 pri-miRNAs encoding 23 different miRNAs. The data sets described here provide a transcriptome toolkit linked to physical clones for bioinformaticians and experimental biologists who wish to use chicken systems as a low-cost, accessible alternative to mammals for the analysis of vertebrate development, immunology, and cell biology.

Footnotes

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.3011405. Article published online before print in December 2004.

  • ↵8 Corresponding author. E-mail stuart.wilson{at}sheffield.ac.uk; fax 44-114-272-8697.

    • Accepted October 4, 2004.
    • Received July 15, 2004.
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  1. Published in Advance December 8, 2004, doi: 10.1101/gr.3011405 Genome Res. 15: 174-183 Cold Spring Harbor Laboratory Press

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