W466 The Atlantic Salmon Genome: Past, Present and Future

Date: Sunday, January 15, 2012
Time: 2:20 PM
Room: Golden West
William S. Davidson , Simon Fraser University - Dept. of Molecular Biology & Biochemistry, Burnaby, BC, BC, Canada
Executive Scientific Committee Icsasg , International Cooperation to Sequence the Atlantic Salmon Genome
The genome of the Atlantic salmon (Salmo salar) has been selected to be the reference sequence for all salmonids based on its importance for the aquaculture industry and because so many genomic resources have been developed for this species. The International Cooperation to Sequence the Atlantic Salmon Genome (ICSASG), which represents researchers, funding agencies and industry from Canada, Chile and Norway, was established to undertake this task. The goals of the ICSASG are to produce a genome sequence that (1) identifies and physically maps all of the genes in the Atlantic salmon genome and (2) can act as a reference sequence for the genomes of other salmonids (e.g., rainbow trout and Pacific salmon) and more distantly related fish (e.g., pike). The salmon genome is large (~3 Mb) and complicated by a whole genome duplication event (~60 MYA) as well as the presence of many repetitive families that are ~1,500 bp in length. The quality of the Atlantic salmon genome sequence will be critical if it is to support detailed analyses such as comparisons of duplicated regions within the genome and the identification of genes associated with complex behavioural and production traits. It was decided that sequencing the Atlantic salmon genome should proceed in two phases: the first would use the "old fashioned" Sanger approach while the second would make use of "next generation" technology to complete the project. The salmon whose genome was chosen to be sequenced is a double haploid female, which should aid in the assembly of the genome, particularly the homeologous regions. Phase 1 of the project produced a 4  fold coverage using paired end reads from a combination of short insert (3-5 kb) plasmid clones, fosmids (~30 kb) and BACs (~120 kb). Phase 2 of the project is underway. The contigs from an initial assembly have been submitted to GenBank. A robust linkage map comprising 5,600 SNPs is being used to order the contigs and their related scaffolds. The availability of a salmonid reference sequence should be a tremendous benefit for sequencing other salmonids and identifying candidate genes for QTL associated with production traits.