This article was originally published Dec. 7.
The International Cooperation to Sequence the Atlantic Salmon Genome said this week that it has awarded Beckman Coulter Genomics — formerly Agencourt Bioscience and Cogenics — a $6 million contract to complete the first phase of a project to sequence the salmon genome.
The contract is the first of multiple phases to produce a complete genome that can act as a reference genome for all salmonid species. Phase one is set to be completed and made public by early 2011.
The announcement did not specify what technology Beckman Coulter Genomics would use to sequence the salmon genome. But, in June, the ICSASG said it wanted the first phase to be completed with Sanger technology or an equivalent, and that later phases of the project could use other sequencing technologies (see In Sequence 6/23/2009).
In the original RFP, issued in June, the ICSASG said that it wanted to use Sanger technology because there is no current reference genome for the salmon or a related species, so "sequencing and assembly will be extremely challenging." The group also wanted to ensure that it could produce a good scaffold and decided that Sanger's 750-base-pair-plus reads would be the best way to do that.
Last year, ICSASG members tested the 454 GS FLX platform for the project but concluded "that in its present form (average read length of 250 bp) the GS FLX technology is limited to gene mining and establishing a set of ordered sequence contigs with many gaps," according to the RFP.
In the meantime, however, a Norwegian research consortium has successfully sequenced and assembled the cod genome using the 454 technology (see In Sequence 11/3/2009).
The ICSASG is made up of researchers, industry, and funding agencies from Canada, Chile, and Norway. Its goal is to produce a genome sequence of the Atlantic salmon that identifies and maps all of its genes and that can act as a reference genome for other salmonids. A sequenced genome could lead to better management of fish stocks and the identification of commercially valuable traits, as well as a better understanding of pathogens and disease resistance, the consortium said.
"The genomic data that we will acquire will be crucial to the development of new methods and products that will assist the world's wild fisheries and aquaculture industries," Genome BC's chief scientific officer Pierre Meulien said in a statement.