SalmoBase: an integrated molecular data resource for Salmonid species
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...
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| Format: | Article |
| Language: | English |
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BMC
2017-06-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-017-3877-1 |
| _version_ | 1818772910004764672 |
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| author | Jeevan Karloss Antony Samy Teshome Dagne Mulugeta Torfinn Nome Simen Rød Sandve Fabian Grammes Matthew Peter Kent Sigbjørn Lien Dag Inge Våge |
| author_facet | Jeevan Karloss Antony Samy Teshome Dagne Mulugeta Torfinn Nome Simen Rød Sandve Fabian Grammes Matthew Peter Kent Sigbjørn Lien Dag Inge Våge |
| author_sort | Jeevan Karloss Antony Samy |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-18T10:16:51Z |
| format | Article |
| id | doaj.art-3ad46f17c571497b86b53b23529fff80 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-18T10:16:51Z |
| publishDate | 2017-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-3ad46f17c571497b86b53b23529fff802022-12-21T21:11:16ZengBMCBMC Genomics1471-21642017-06-011811510.1186/s12864-017-3877-1SalmoBase: an integrated molecular data resource for Salmonid speciesJeevan Karloss Antony Samy0Teshome Dagne Mulugeta1Torfinn Nome2Simen Rød Sandve3Fabian Grammes4Matthew Peter Kent5Sigbjørn Lien6Dag Inge Våge7Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences (IHA), Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU)Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences (IHA), Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU)Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences (IHA), Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU)Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences (IHA), Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU)Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences (IHA), Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU)Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences (IHA), Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU)Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences (IHA), Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU)Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences (IHA), Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU)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.http://link.springer.com/article/10.1186/s12864-017-3877-1SalmobaseAtlantic salmonSalmonidsGenome browser |
| spellingShingle | Jeevan Karloss Antony Samy Teshome Dagne Mulugeta Torfinn Nome Simen Rød Sandve Fabian Grammes Matthew Peter Kent Sigbjørn Lien Dag Inge Våge SalmoBase: an integrated molecular data resource for Salmonid species BMC Genomics Salmobase Atlantic salmon Salmonids Genome browser |
| title | SalmoBase: an integrated molecular data resource for Salmonid species |
| title_full | SalmoBase: an integrated molecular data resource for Salmonid species |
| title_fullStr | SalmoBase: an integrated molecular data resource for Salmonid species |
| title_full_unstemmed | SalmoBase: an integrated molecular data resource for Salmonid species |
| title_short | SalmoBase: an integrated molecular data resource for Salmonid species |
| title_sort | salmobase an integrated molecular data resource for salmonid species |
| topic | Salmobase Atlantic salmon Salmonids Genome browser |
| url | http://link.springer.com/article/10.1186/s12864-017-3877-1 |
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