Plant & Animal Genomes XI Conference

January 11-15, 2003
Town & Country Convention Center
San Diego, CA

Poster: Genome Sequencing & ESTs
            

EVOLUTIONARY PATTERNS IN 50,000 SALMONID EXPRESSED SEQUENCE TAGS

¹ Centre for Biomedical Research, University of Victoria, P.O. Box 3020 Stn CSC, Victoria, B.C., V8W 3N5, Canada

² Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, B.C., V5A 1S6, Canada

Salmonids are thought to have undergone a full-genome duplication 25 to 100 million years ago. Evidence for this event includes more than doubling of chromosomal material in salmonids as compared to closely related taxa, studies of families of paralogous genes, and the appearance of quadrivalents in meiosis. GRASP (the Genomic Research on Atlantic Salmon Project) has sequenced over 50,000 salmonid EST's (mostly from the 3' UTR, and representing about 19,000 distinct transcripts). We can refine the date of the genome duplication, by analyzing pairwise similarity scores for all pairs of consensus sequences: we expect a large number of paralogs that have diverged by approximately the same distance (in the 3' UTR, to avoid variations related to selection pressure). Preliminary experiments using BLAST and standard end-gaps-free global pairwise alignment indicate that paralogs arising from the genome duplication are less than 80% similar in the 3' UTR, suggesting that the genome duplication is more than 50 million years old. Other patterns are also evident: alleles show up as groups of highly similar transcripts, while gene families are less similar, but still detectably related. We continue to develop more refined similarity measures, with the objective of building models to detect genome duplications as well as other patterns in large EST sets.