Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

Towards A Physical Map Of The Atlantic Salmon Genome

Siemon HS Ng¹ , Leslie Mitchell¹ , Carlo Artieri¹ , Jacquie Schein² , Heesun Shin² , Ben F Koop³ , William S Davidson¹

¹  Department of Molecular Biology and Biochemistry Simon Fraser University Burnaby, BC, Canada, V5A

²  Genome Science Centre, BC Cancer Agency Suite 100, 570 West 7th Ave. Vancouver, BC, Canada, V5Z 4S6

³  Centre for Biomedical Research, Department of Biology, University of Victoria Victoria, BC, Canada, V8P 5C2

We have generated physical map of the Atlantic salmon (Salmo salar) genome based on HindIII, fingerprints of an EcoRI partial digest BAC library from DNA isolated from a Norwegian aquaculture strain Atlantic salmon male. Approximately 11.5 haploid genome equivalents (185,938 clones) have been successfully HindIII fingerprinted, averaging 41.6 bands per BAC, and arranged into contigs via FPC to create the first physical map of a salmonid genome. The contigs were first assembled using high stringency values and then end to end joined at a lower stringency, resulting in 4,354 contigs and 37, 285 singletons. About 9.9% of the BACs in the library, including many of the singletons, gave fewer than 5 bands when digested with HindIII. BglI digestion of these “HindIII refractive BACs” allowed us to identify three classes: (1) BACs encoding histone genes; (2) BACs containing rRNA repeating units; and (3) those that do not have BglI recognition sites. This was further confirmed by DNA sequence analysis of selected BACs from the first two classes and suggested that the third class contain highly repetitive DNA. Characterization of this third class has shown a subset of BACs correspond to AluI/SmaI/DraI/PstI repeats. This BAC library will be especially useful for integrating the physical and genetic maps and the karyotype of Atlantic salmon, functional and comparative genomics and map-based cloning of QTL.