International Summer School

   From Genome to Life:

    Structural, Functional and Evolutionary approaches

 

ROEST-CROLLIUS Hugues

Genoscope, CNRS UMR8030, 2, Rue Gaston Cremieux, Evry 91000, France

title: Assembly and annotation of the Tetraodon nigroviridis DNA sequence, a tool for vertebrate genome analysis

H. Roest Crollius1, O. Jaillon1, M. Levy1, L. Bouneau1, S. Nicaud1, A. Bernot1, C. Fischer1, P. Wincker1, E. Pelletier1, V. Anthouard1, C. Ozouf-Costaz3, N. Stange-Thomann2, S. Dodge2, M. Zody2, R. Santos2, C. Nusbaum2, B. Birren2, W. Saurin1, C. Scarpelli1, E. S. Lander2 & J. Weissenbach 

  1. Genoscope, CNRS UMR8030, Evry, France.
  2. Whitehead Institute/MIT Center for Genome Research, Cambridge, U.S.A.
  3. Muséum National d’Histoire Naturelle, Paris, France

To assist in the identification of human genes, and to provide a tool for vertebrate genome analysis, we have undertaken to sequence the genome of the freshwater pufferfish Tetraodon nigrovridis. Its evolutionary distance from mammals, its compact format, and its paucity in repeat sequences makes this genome an ideal entry point to vertebrate genes, and to their identification in the human genome by similarity searches.

Shotgun DNA sequence reads representing 8 Tetraodon genome equivalents have now been produced by Genoscope and the Whitehead Institute/MIT Center for Genome Research. This sequence is being assembled and layered on top of a physical map of the genome. The physical map was produced by a combination of complementary approaches that include high throughput fluorescent library hybridizations, clone fingerprinting and FISH. Results on the integration and validation of the assembly with the progressing physical map will be presented.

To exploit the Tetraodon sequence, we have previously developed Exofish, a highly specific comparison tool to identify coding sequences in human. Comparisons between the Tetraodon and the human genome using Exofish enable us to provide a new estimate of the number of human genes. Conversely, Exofish is also the basis of our annotation protocol for the Tetraodon genome. We have identified approximately 31,000 gene models in the genome, and current comparative analyses with the genomes of other fishes and mammals will be presented.

ADDITIONAL DATA



HTTP LINK & References: 

                 
 http://www.genoscope.cns.fr/externe/tetraodon/


                  
Roest Crollius H, Jaillon O, Bernot A, Dasilva C, Bouneau L, Fischer C,
Fizames C, Wincker P, Brottier P, Quetier F, Saurin W, Weissenbach J.
Estimate of human gene number provided by genome-wide analysis using
Tetraodon nigroviridis DNA sequence. Nat Genet. 2000 Jun;25(2):235-8.
                  
Roest Crollius H, Jaillon O, Dasilva C, Ozouf-Costaz C, Fizames C, Fischer
C, Bouneau L, Billault A, Quetier F, Saurin W, Bernot A, Weissenbach J.
Characterization and repeat analysis of the compact genome of the
freshwater pufferfish Tetraodon nigroviridis. Genome Res. 2000
Jul;10(7):939-49.