Open-reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans (original) (raw)

Nature Genetics volume 27, pages 332–336 (2001)Cite this article

Abstract

The genome sequences of Caenorhabditis elegans, Drosophila melanogaster and Arabidopsis thaliana have been predicted to contain 19,000, 13,600 and 25,500 genes, respectively1,2,3. Before this information can be fully used for evolutionary and functional studies, several issues need to be addressed. First, the gene number estimates obtained in silico and not yet supported by any experimental data need to be verified. For example, it seems biologically paradoxical that C. elegans would have 50% more genes than Drosophilia. Second, intron/exon predictions need to be tested experimentally. Third, complete sets of open reading frames (ORFs), or “ORFeomes,”4 need to be cloned into various expression vectors. To address these issues simultaneously, we have designed and applied to C. elegans the following strategy. Predicted ORFs are amplified by PCR from a highly representative cDNA library4 using ORF-specific primers, cloned by Gateway recombination cloning4,5,6 and then sequenced to generate ORF sequence tags (OSTs) as a way to verify identity and splicing. In a sample (n=1,222) of the nearly 10,000 genes predicted ab initio (that is, for which no expressed sequence tag (EST) is available so far), at least 70% were verified by OSTs. We also observed that 27% of these experimentally confirmed genes have a structure different from that predicted by GeneFinder. We now have experimental evidence that supports the existence of at least 17,300 genes in C. elegans. Hence we suggest that gene counts based primarily on ESTs may underestimate the number of genes in human and in other organisms.

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Acknowledgements

We thank S. Boulton, L. Matthews, J. Polanowska, M. Tewari and A.J.M. Walhout for comments on the manuscript and discussions; and L. Hillier and P. Green for the primer design program (OSP). This work was supported by grants from CREST, Japan Science and Technology Corporation and Grant-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Science, Sports and Culture of Japan (to Y.K.), and by grants 1 RO1 HG01715-01 from the National Human Genome Research Institute, 1 R21 CA81658 A 01 from the National Cancer Institute and 128 from the Merck Genome Research Institute (to M.V.).

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Author notes

  1. Jérôme Reboul and Philippe Vaglio: These authors contributed equally to this work.

Authors and Affiliations

  1. Dana-Farber Cancer Institute and Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
    Jérôme Reboul, Philippe Vaglio, Nia Tzellas, Nicolas Thierry-Mieg, Philippe E. Lamesch, David E. Hill & Marc Vidal
  2. Laboratoire LSR-IMAG, St-Martin D'Heres, France
    Nicolas Thierry-Mieg
  3. Research Genetics, Huntsville, Alabama, USA
    Troy Moore & Cindy Jackson
  4. Genome Biology Laboratory, National Institute of Genetics, Mishima, Japan
    Tadasu Shin-i & Yuji Kohara
  5. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    Danielle Thierry-Mieg & Jean Thierry-Mieg
  6. Genome Therapeutics Corp., Waltham, Massachusetts, USA
    Hongmei Lee, Joseph Hitti & Lynn Doucette-Stamm
  7. Life Technologies Inc., Rockville, Maryland, USA
    James L. Hartley, Gary F. Temple & Michael A. Brasch
  8. Département de Biologie, Facultés Universitaires Notre-Dame de la Paix, Namur, Belgium
    Jean Vandenhaute & Philippe E. Lamesch

Authors

  1. Jérôme Reboul
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  2. Philippe Vaglio
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  3. Nia Tzellas
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  4. Nicolas Thierry-Mieg
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  5. Troy Moore
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  6. Cindy Jackson
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  7. Tadasu Shin-i
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  8. Yuji Kohara
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  9. Danielle Thierry-Mieg
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  10. Jean Thierry-Mieg
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  11. Hongmei Lee
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  12. Joseph Hitti
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  13. Lynn Doucette-Stamm
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  14. James L. Hartley
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  15. Gary F. Temple
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  16. Michael A. Brasch
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  17. Jean Vandenhaute
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  18. Philippe E. Lamesch
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  19. David E. Hill
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  20. Marc Vidal
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Corresponding author

Correspondence toMarc Vidal.

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Reboul, J., Vaglio, P., Tzellas, N. et al. Open-reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans.Nat Genet 27, 332–336 (2001). https://doi.org/10.1038/85913

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