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BMC Genomics. 2017 Jun 26;18(1):482. doi: 10.1186/s12864-017-3877-1.

SalmoBase: an integrated molecular data resource for Salmonid species.

Author information

1
Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences (IHA), Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), 1432, Ås, Akershus, Norway. jeevan.karloss@nmbu.no.
2
Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences (IHA), Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), 1432, Ås, Akershus, Norway.

Abstract

BACKGROUND:

Salmonids are ray-finned fishes which constitute 11 genera and at least 70 species including Atlantic salmon, whitefishes, graylings, rainbow trout, and char. The common ancestor of all Salmonidae experienced a whole genome duplication (WGD) ~80 million years ago, resulting in an autotetraploid genome. Genomic rediplodization is still going on in salmonid species, providing an unique system for studying evolutionary consequences of whole genome duplication. In recent years, high quality genome sequences of Atlantic salmon and Rainbow trout has been established, due to their scientific and commercial values. In this paper we introduce SalmoBase ( http://www.salmobase.org/ ), a tool for making molecular resources for salmonids public available in a framework of visualizations and analytic tools.

RESULTS:

SalmoBase has been developed as a part of the ELIXIR.NO project. Currently, SalmoBase contains molecular resources for Atlantic salmon and Rainbow trout. Data can be accessed through BLAST, Genome Browser (GBrowse), Genetic Variation Browser (GVBrowse) and Gene Expression Browser (GEBrowse).

CONCLUSIONS:

To the best of our knowledge, SalmoBase is the first database which integrates salmonids data and allow users to study salmonids in an integrated framework. The database and its tools (e.g., comparative genomics tools, synteny browsers) will be expanded as additional public resources describing other Salmonidae genomes become available.

KEYWORDS:

Atlantic salmon; Genome browser; Salmobase; Salmonids

PMID:
28651544
PMCID:
PMC5485693
DOI:
10.1186/s12864-017-3877-1
[Indexed for MEDLINE]
Free PMC Article

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