SalmoBase: an integrated molecular data resource for Salmonid species.
SalmoBase: an integrated molecular data resource for Salmonid species.
复制标题
DOI：
10.1186/s12864-017-3877-1
复制
发表时间：
2017-06-26
期刊：
影响因子：
4.4
通讯作者：
Våge DI
中科院分区：
文献类型：
--
作者：
Samy JKA;Mulugeta TD;Nome T;Sandve SR;Grammes F;Kent MP;Lien S;Våge DI
鲑科是鳍鱼，包括11属和至少70种，包括大西洋鲑鱼，白鱼，graylings，虹鳟鱼和char。所有鲑科的共同祖先在约8000万年前经历了全基因组复制（WGD），导致同源四倍体基因组。鲑科鱼类的基因组重二倍体化仍在继续，为研究全基因组重复的进化后果提供了一个独特的系统。近年来，由于其科学和商业价值，已经建立了大西洋鲑鱼和虹鳟鱼的高质量基因组序列。在本文中，我们介绍了SalmoBase（http：//www.salmobase.org/），一个工具，使分子资源的鲑鱼公共可视化和分析工具的框架。SalmoBase是作为ELIXIR.NO项目的一部分开发的。目前，SalmoBase包含大西洋鲑鱼和虹鳟鱼的分子资源。数据可通过BLAST、基因组浏览器（GBrowse）、遗传变异浏览器（GVBrowse）和基因表达浏览器（GEBrowse）访问。据我们所知，SalmoBase是第一个整合了鲑鱼数据的数据库，允许用户在一个综合框架中研究鲑鱼。数据库及其工具（例如，比较基因组学工具、同线性浏览器）将随着描述其他鲑科基因组的更多公共资源的可用而扩展。
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. 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). 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.