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Salmon Consortium Seeks Next-Gen Sequencing for Second Phase of Project


This article was originally published Nov. 19.

The International Cooperation to Sequence the Atlantic Salmon Genome has issued a request for proposals for the second phase of the multi-phase project to sequence the Atlantic salmon genome, to finish sequencing, assemble, and annotate the salmon genome.

Phase one was awarded to Beckman Coulter Genomics last December to use Sanger sequencing to produce a genome to four-fold coverage, using paired-end, fosmid, and BACs. The award was for $6 million and is scheduled to be completed in January 2011 (IS 12/15/2009), and publicly released in July 2011.

For the second phase, the consortium is looking for primarily next-gen sequencing technologies to complete the sequencing. The RFP, available here, is "targeting large-scale sequencing centers or a consortium of academic and/or commercial centers that are believed to have the expertise and capacity to participate in a project of this scale."

Proposals must be submitted by Jan. 14, 2011, and the ICSASG expects to make a decision by March 2011 with the sequencing for the second phase to be completed by Oct. 1, 2011, and the annotated genome publicly available by 2012.

The ICSASG chose to use Sanger sequencing for the first phase because it wanted to create a reference genome, and consortia members said that the newer sequencing technologies were still not up to par with Sanger, particularly for sequencing a genome as complex as the salmon, which is a pseudo-tetraploid around the size of the human genome with many duplicated regions.

According to the RFP, the draft genome will have a minimum contig N50 size of 50 kilobases and be assembled into scaffolds greater than 1 megabase.

While the genome will be not be considered complete, the goal is for it to act as a reference sequence for the genomes of other salmonids including the Pacific salmon and rainbow, as well as more distantly related fish like smelt and pike.

Additionally, the genome will be used in population management of fish stocks, food security, and conservation of at-risk populations. It will also be used to support aquaculture, by identifying genes relevant for commercially important traits.

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

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