SalmoBase: an integrated molecular data resource for Salmonid species

BMC Genomics

Database

Teshome Dagne Mulugeta¹  Simen Rød Sandve¹  Sigbjørn Lien¹  Matthew Peter Kent¹  Dag Inge Våge¹  Jeevan Karloss Antony Samy¹  Torfinn Nome¹  Fabian Grammes¹ 

[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;

关键词: Salmobase;    Atlantic salmon;    Salmonids;    Genome browser;   

DOI  :  10.1186/s12864-017-3877-1

 received in 2017-03-03, accepted in 2017-06-20,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundSalmonids 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.ResultsSalmoBase 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).ConclusionsTo 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.

【 授权许可】

CC BY   
© The Author(s). 2017