Sequencing the genome of the Atlantic salmon (Salmo salar)

The family Salmonidae comprises 11 genera and includes salmon, trout, charr, freshwater whitefishes, ciscos and graylings [1]. Many salmonid species are of considerable economic, social and environmental importance. Salmonids contribute to local and global economies through aquaculture, wild stock fisheries and recreational sport fisheries. In addition, they are a traditional food source for aboriginal peoples in Canada and have a central role in their culture. Salmon and trout are sentinel species for monitoring the aquatic environment and therefore they are used extensively for ecotoxicology studies. As a result of human activities related to the rearing of salmon and trout and the need to make management decisions concerning stock assessment and harvesting plans, there is a large salmonid research community working on the biology, life histories, population dynamics, biogeography, phylogenetic relationships, physiology and nutrition of salmonids.Some fundamental scientific questions can be explored using salmonid genomes. The common ancestor of salmon and trout experienced a whole genome duplication, and modern species may be considered pseudo-tetraploid as they are in the process of reverting to a stable diploid state [2]. This makes them ideal organisms for examining the consequences of genome and gene duplications, processes that are considered to have had pivotal roles in generating gene diversity and the functional specialization found in modern vertebrates [3]. How a genome reorganizes itself to cope with duplicated chromosomes and the importance of gene duplications for evolution and adaptation are long-standing issues in biology that remain unresolved [3,4].As illustrated in Table S1 in Additional file 1, no other group of fish species receives such comprehensive combined commercial and scientific attention as the salmonids [5], but as yet there is no genome sequence available for any salmonid. The genome of the Atlantic salmon (Salmo salar) was selected