ARS | Publication request: Salmonid Genomic Sequencing Initiative: the Case for Sequencing the Genomics of Atlantic Salmon (Salmo Salar) and Rainbow Trout (Oncorynchus Mykiss)

Submitted to: Government Publication/Report
Publication Type: Government Publication
Publication Acceptance Date: March 1, 2006
Publication Date: June 1, 2006
Citation: Davidson, W., Chevalet, C., Rexroad III, C.E., Omholt, S. 2006. Salmonid genomic sequencing initiative: the case for sequencing the genomics of atlantic salmon (salmo salar) and rainbow trout (oncorynchus mykiss). Government Publication/Report. p. 1-22.

Technical Abstract: Salmonids are members of the Salmonidae family and include the whitefishes and ciscos (subfamily Coregoninae), graylings (subfamily Thymallinae) and trout, salmon and charr (subfamily Salmoninae). These fish have been further classified into nine genera and roughly sixty-eight species. The salmonids comprise several species of substantial importance for aquaculture, wild stock fisheries, and recreational sport fisheries. Besides their great economic and societal importance, the salmonids are also of considerable scientific importance in such fields as evolutionary biology, ecology, physiology, genetics, immunology, toxicology, nutritional and environmental science. There is no other species group that receives such a comprehensive combined commercial and scientific human attention. There is thus a large and diverse scientific community working and publishing in the field of salmonid biology and genomics. During the last 10 years more than 26,000 scientific papers have been published on salmonids, and more is known about the biology, life history, population dynamics, biogeography and evolution of salmonids than any other fish family. The increasing interest in making use of genomics tools for salmonid research and development is reflected by the considerable accumulation of genomic resources for Atlantic salmon and rainbow trout in the last 5 years. The work has been carried out by groups in several countries, and the groups have interacted with one another to various extents in rather informal ways. However, in 2005 the complexities involved in ensuring that existing and upcoming resources were made accessible to the community as a whole and that the invested money was used as efficiently as possible through concerted actions and sound priorities, forced the construction of a more formal international collaborative body to coordinate and quality assure these processes. At a workshop held on October 25-26, 2005 at the Norwegian University for Life Sciences at Aas, Norway, the participants formed the Consortium for Genomic Research on All Salmonids Program (cGRASP), with the intention that this would be the international collaborative structure for establishing and maintaining salmonid genomic resources. The meeting resolved very clearly the need for at least one high-quality whole genome salmonid sequence for making optimal use of genomics tools within salmonid research and development, that most of the needed pre-sequencing phase resources will be in place before the end of 2007, that the task is technically feasible, and that the community is strongly committed to build and maintain the necessary organizational apparatus for handling the pre-sequencing phase, the draft sequence phase, and the post draft sequence phase in a professional way. More specifically, after considering the various options, the participants reached the conclusion that the Atlantic salmon genome should be targeted as the reference sequence (6-8 fold coverage), and that a low-survey coverage of the rainbow trout genome should be done as a proof of principle of how the reference sequence can be exploited in other salmonid species.