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鲑鱼数据库：鲑科鱼类的综合分子数据资源。

SalmoBase: an integrated molecular data resource for Salmonid species.

作者信息

Samy Jeevan Karloss Antony, Mulugeta Teshome Dagne, Nome Torfinn, Sandve Simen Rød, Grammes Fabian, Kent Matthew Peter, Lien Sigbjørn, Våge Dag Inge

机构信息

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.

出版信息

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

DOI:10.1186/s12864-017-3877-1
PMID:28651544
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5485693/
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.

摘要

背景

鲑科鱼类是辐鳍鱼，包括11个属，至少70个物种，如大西洋鲑、白鲑、茴鱼、虹鳟和红点鲑。所有鲑科鱼类的共同祖先在约8000万年前经历了一次全基因组复制（WGD），产生了一个同源四倍体基因组。鲑科物种的基因组仍在进行二倍体化，为研究全基因组复制的进化后果提供了一个独特的系统。近年来，由于大西洋鲑和虹鳟的科学和商业价值，它们的高质量基因组序列已被建立。在本文中，我们介绍了SalmoBase（http://www.salmobase.org/），这是一个在可视化和分析工具框架下使鲑科鱼类分子资源公开可用的工具。

结果

SalmoBase是作为ELIXIR.NO项目的一部分开发的。目前，SalmoBase包含大西洋鲑和虹鳟的分子资源。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。

结论

据我们所知，SalmoBase是第一个整合鲑科鱼类数据并允许用户在综合框架下研究鲑科鱼类的数据库。随着描述其他鲑科基因组的更多公共资源的出现，该数据库及其工具（如比较基因组学工具、同线性浏览器）将得到扩展。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9656/5485693/8fc46af7cbca/12864_2017_3877_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9656/5485693/343602dc5844/12864_2017_3877_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9656/5485693/1bf9a8673b41/12864_2017_3877_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9656/5485693/16d7d16909f6/12864_2017_3877_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9656/5485693/8fc46af7cbca/12864_2017_3877_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9656/5485693/343602dc5844/12864_2017_3877_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9656/5485693/1bf9a8673b41/12864_2017_3877_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9656/5485693/16d7d16909f6/12864_2017_3877_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9656/5485693/8fc46af7cbca/12864_2017_3877_Fig4_HTML.jpg

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