Centres that wish to apply for the proposal must have a record of sequencing complex vertebrate genomes. (Photo: genomebc.ca/FIS)
Consortium on salmon genome requests new centre
Monday, November 22, 2010, 23:50 (GMT + 9)
The International Cooperation to Sequence the Atlantic Salmon Genome (ICSASG) has called for proposals for a centre to complete the sequencing of a salmon genome. The consortium - involving Canada, Chile and Norway - wants to finance a foundation to run the second phase of a next-generation sequencing venture to develop a publicly available map of the genome.
This two-phase project aims to identify and physically map all the Atlantic salmon genes. The findings would be a reference sequence for other salmonids, such as commercially important fish like Pacific salmon, grayling and whitefish, plus for related species such as rainbow trout, pike and smelt.
Launched last year, the first phase of the project is expected to be finalised next year. This phase provided Beckman Coulter Genomics with a USD 6 million contract to use Sanger sequencing to create a ~4 fold coverage draft of the Atlantic salmon genome, GenomeWeb News reports.
In contrast, the second phase will mainly use next-generation sequencing technologies to produce a high-definition and well annotated genome that will be integrated with the physical map, a linkage map, the karyotype data and a detailed database.
Although the final findings will not be considered a finished sequence, they will have to support detailed analysis and especially comparative genomics studies of other species.
The data will be made available to the public via a genome browser to be employed in the fish stock management, food security and traceability purposes, protection and for research and development on commercially important traits.
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,” ICSASG said.
As well, the sequence will be used to offer resources and tools, including enhanced SNP and expression arrays, useful to the aquaculture sector, conservation biologists and monitoring marine habitat.
ICSASG informed that centres that wish to apply for the proposal must have a record of sequencing complex vertebrate genomes, next-generation technologies and a capacity to tackle the project.
Partners of the consortium include Genome British Columbia, the Chilean Economic Development Agency, InnovaChile, the Norwegian Research Council and the Norwegian Fishery and Aquaculture Industry and Research Fund.
- Atlantic salmon genome project to take off
By Natalia Real