International Mammalian Genome Society

The 15th International Mouse Genome Conference (2001)

Table of Contents * Complex Genetics * Developmental Genetics * Gene Annotation * Gene Discovery * Genome Sequencing * Functional Genomics * Mutagenesis * Presentations * Verne Chapman Memorial Lecture

USING THE PUFFERFISH DNA SEQUENCE TO ANALYZE MAMMALIAN GENOMES

Jean Weissenbach
Genoscope and CNRS UMR-8030
2 rue Gaston Cremieux
CP 5706
Evry Cedex 91057 France

Co-Authors: Olivier Jaillon, Michael Levy, Hugues Roest Crollius, Alain Bernot, Laurence Bouneau, Cécile Fischer, 1) Catherine Ozouf-Costaz, William Saurin
Institutions: Genoscope and CNRS UMR-8030, 1) Museum d'Histoire Naturelle

Despite the availability of most of the human genome sequence, the accurate identification of genes on the DNA sequence is not yet definitive and has to be continuously improved and updated. This relies on the combined use of a variety of tools including similarity searches and exon/gene prediction programs.

Similarity searches rely on a set of sequence data that has been increasing very substantially and rapidly during the past months. These include human cDNAs, mouse genomic DNA and cDNAs and puffer fish genomic sequences. With these resources, the definition of a vertebrate set of genes is progressively taking shape.

To contribute to the generation of these new datasets, we have undertaken a whole genome sequencing of the fresh water pufferfish Tetraodon nigroviridis. This programme relies on the establishment of a physical map based on several approaches including BAC fingerprinting, in situ hybridization, STS mapping etc. Shotgun DNA sequence reads representing nearly 3 X coverage of the genome of Tetraodon nigroviridis were produced.

In addition to their assembly, currently in progress, these sequence data were used for direct similarity searches with sequences from other genomes.Results of these large scale sequence comparisons will be presented.