SalmoBase

The Atlantic salmon (Salmo salar) is arguably one of the most iconic and well-studied salmonid species, with great societal, economic, and ecological importance. Its mammalian sized genome has undergone extensive restructuring since a whole genome duplication event ~80 million years ago, which creates opportunities to explore the evolutionary process of rediploidization. Today, a genome assembly is publically available (Lien et al. 2016) , wherein 9447 scaffolds (N50 = 3.18Mb) are ordered into 29 chromosome files. On the SalmoBase pages you will find a GBrowse interface for exploring the chromosome sequence. Using public RNAseq data we have performed an annotation and identified 37,000 high confidence protein coding genes, wherein almost half show splice variants. BLAST functionality is included as are links to expression levels, gene and SNP information.

Salgene atlantic salmon brown_trout

Phylogenetic tree of [major] or [culturally and economically important] lineages of salmonids. Timing of evolution of anadromous behaviour is indicated, although anadromy in white fish is not likely to involve extensive stays in marine environments.

The Sequencing Project

The International Cooperation to Sequence the Atlantic Salmon Genome (ICSASG) have sequenced the Atlantic salmon genome in a collaboration between researchers in Canada, Chile and Norway. Funds have been provided from the Research Council of Norway , the Norwegian Fishery and Aquaculture Industry Research Fund , Genome British Columbia , the Chilean Economic Development Agency and the InnovaChile Committee . Commercial partners are Marine Harvest , AquaGen, Cermaq and Salmobreed .

ELIXIR.NO Project

This website is developed and hosted as a part of the national infrastructure project ELIXIR.NO, by researchers at Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences. It presents both the latest S. salar assembly and includes various metadata such as gene content.

Salmon_circos

Homeologous regions in the Atlantic salmon genome subdivided into 98 collinear blocks along the 29 salmon chromosomes. Source: Nature 2016 doi:10.1038/nature17164

Citing SalmoBase

SalmoBase: an integrated molecular data resource for Salmonid species. Jeevan Karloss Antony Samy, Teshome Dagne Mulugeta, Torfinn Nome, Simen Rød Sandve, Fabian Grammes, Matthew Peter Kent, Sigbjørn Lien and Dag Inge Våge. BMC Genomics 2017 18:482

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