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Salmon Consortium Seeks Sequencing Center

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – A consortium representing Canada, Chile, and Norway have requested proposals for a center to finish sequencing a salmon genome that will serve as a model fish for researchers around the world.

The International Cooperation to Sequence the Atlantic Salmon Genome (ICSASG) wants to fund a center that will conduct the second phase of a next-generation sequencing effort to create a useful and publicly available map of the Atlantic salmon genome.

The goal of the two-phase project is to identify and physically map all the genes in the Atlantic salmon, which will serve as a reference sequence for other salmonids, including commercially important fish such as Pacific salmon, grayling, and whitefish, as well as for related fish such as rainbow trout, pike, smelt, and others.

The first phase of the project, which kicked off in late 2009 and should be completed in 2011, gave Beckman Coulter Genomics a $6 million contract to use Sanger sequencing to create a ~4 fold coverage draft of the fish's genome.

This second phase will turn primarily to next-generation sequencing tools that will generate a high-definition, well annotated genome that will then be integrated with the physical map, a linkage map, the karyotype data, and an extensive database.

The ICSASG partners include Genome British Columbia, the Chilean Economic Development Agency, InnovaChile, the Norwegian Research Council, and the Norwegian Fishery and Aquaculture Industry and Research Fund.

The final result of this project will not be considered a finished sequence like the human and mouse genome projects created, but the Atlantic salmon sequence will need to support detailed analysis, particularly comparative genomics studies of other fish species.

ICSASG wants all of this data to be made publicly available through a genome browser, which will be used in managing populations of wild fish stocks, for food security and traceability purposes, for conservation, and for the study and development of commercially important traits.

According to the ICSASG request for proposals, this genome will "form the foundation for re-sequencing projects involving naturally occurring Atlantic salmon from both sides of the Atlantic. The genome also will be compared to those of other fishes that are currently available including the zebrafish and stickleback, and others that are to come.

The sequence also will be used to provide resources and tools, such as enhanced SNP and expression arrays, that will be useful to the aquaculture industry, conservation biologists, and for monitoring the aquatic environment.

Centers seeking to apply for the RFP should have a record of sequencing complex vertebrate genomes, expertise with next-generation technologies, and the current capacity to handle the project, ICSASG said.

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