SalmoBase: an integrated molecular data resource for Salmonid species
- 1.7k Downloads
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.
KeywordsSalmobase Atlantic salmon Salmonids Genome browser
European Molecular Biology Laboratory
Functional Analysis of All Salmonid Genomes
Fragments per Kilobase of Exon per Million Fragments Mapped
Gene Expression Browser
Genetic Variation Browser
International Cooperation to Sequence the Atlantic Salmon
single nucleotide polymorphisms
Whole Genome Duplicatio
Salmonids (e.g. Atlantic salmon (Salmo salar), Rainbow trout (Oncorhynchus mykiss), Brown trout (Salmo trutta)) has considerable socio- and economic importance. From a biological perspective the anadromous migration pattern of salmon is of great interest, and allow investigations of unique physiological traits such as smoltification and flesh pigmentation. The evolutionary history of salmonids is particularly interesting. A whole genome duplication (WDG) event took place in a common ancestor to all salmonids ~80 million years ago , which makes it possible to study post duplication phenomena in a recent time frame, in contrast to other polyploid origin vertebrates whose WGDs date back further in time. These phenomena include the effects of WGDs on gene diversity and functional specialization, as well as consequences on evolution and adaptation .
A high quality, annotated Atlantic salmon and Rainbow trout genome sequences are now available thanks to the efforts from the International Cooperation to Sequence the Atlantic Salmon (ICSASG) and associated partners  and The international collaboration to sequence Rainbow trout genome, and we expect that genome sequences and genomic data for other salmonid species will be available in the near future. SalmoBase (www.salmobase.org) was developed to make these substantial amounts of data accessible through visualizations and analytic tools in a common framework. We expect that genome sequences and genomic data for other salmonid species will be available in the near future and plan to integrate this information with SalmoBase.
As a first step, the genome and genome annotations for Atlantic salmon and Rainbow trout are made available through SalmoBase. For Atlantic salmon, tissue specific gene expression data and single nucleotide polymorphisms (SNP) data are also available. Similar resources for other salmonid species will be added to SalmoBase when they become available.
Construction and content
Atlantic salmon genome reference (fasta file), annotation (gff3 file) and gene expression data (Sequence Read Archive accession: PRJNA260929) were produced as the part of ICSASG. The RefSeq annotation for Atlantic salmon was added later when it became available. New Rainbow trout genome reference (fasta file) and annotations (gff3) were produced by The international collaboration to sequence the Rainbow trout genome.
Utility and discussion
Genome browser (GBrowse)
Data tracks can be downloaded in a variety of formats including GFF3, Genbank, and EMBL (European Molecular Biology Laboratory), while gene, protein and transcript sequences can be downloaded in FASTA, Genbank, and EMBL formats etc. Users can upload their own data (custom track option) in a variety of file formats and can customize track displays to visualize their data. Users can easily save and share search results as links, or export the results as PNG, SVG and other file formats for publication purposes. Navigation in the database is eased by clickable questionmarks.
Genetic variation browser (GVBrowse)
It is possible to quickly obtain flanking sequence for each variation by following the link from the “SNP ID”. By clicking the genomic view image in the SNP ID link, additional information can also be obtained such as location of the genetic variation in genome sequence, nearby gene annotations and other genomic features. Flanking sequences for multiple genetic variations can be downloaded by selecting the wanted genetic variations and clicking the download button at the bottom of the result table.
Gene expression browser (GEBrowse)
Future plans and intergration of other resources
SalmoBase was developed in close collaboration with ICSASG research groups. Through this collaboration more resources from other projects on salmonids will become available in the near future. As more data becomes available for Atlantic salmon, Rainbow trout and other salmonid species, new tools and resources will be added to SalmoBase. The SalmoBase team is also working closely with Functional Analysis of All Salmonid Genomes (FAASG)  and the results from FAASG will be accessible through Salmobase in the future.
Database access and feedback
Data are available for download under the ‘Download’ option in SalmoBase. User support is available through the ‘Contact’ form in SalmoBase. Suggestions for improvements and other comments are welcomed through the ‘Contact’ form. We will consider to include data from users who wish to deposit data into SalmoBase.
To the best of our knowledge SalmoBase is the only online database to access, visualize and download genomics data of salmonids. Due to rapid improvements in high-throughput sequencing technologies we expect a deluge for salmonids’ genomics data. SalmoBase is designed to accommodate the challenges. And, SalmoBase will play a vital role in studying salmonids.
Availability and requirements
SalmoBase can be accessed at www.salmobase.org.
We thank International Cooperation to Sequence the Atlantic Salmon Genome (ICSASG) for generating data presented in SalmoBase. Norwegian metacenter for computational science (under project nn4653k).
This project has received financial support from the Research Council of Norway, project no. 208481 (ELIXIR.NO). The funding source had no role in study design, data collection and interpretation and in writing the manuscript.
Availability of data and materials
This work does not contain additional data.
SL, DIV and JKAS conceived the idea of developing SalmoBase. JKAS developed salmobase with the help of TDM and suggestions from TN, SRS, MPK, FG, SL and DIV. JKAS wrote the draft and included comments from co-authors. All authors read and approved the final manuscript.
Ethics approval and consent to participate
The authors declare that they have no competing interests.
Consent for publication
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
- 2.Davidson WS, Koop BF, Jones SJ, Iturra P, Vidal R, Maass A, et al. Sequencing the genome of the Atlantic salmon (Salmo salar). Genome Biol. 2010;11(9):403.Google Scholar
- 3.Lien S, Koop BF, Sandve SR, Miller JR, Kent MP, Nome T, et al. The Atlantic salmon genome provides insights into rediploidization. Nature. 2016;533:200–5.Google Scholar
- 6.Macqueen DJ, Primmer CR, Houston RD, Nowak BF, Bernatchez L, Bergseth S, Davidson WS, Gallardo-Escarate C, Goldammer T, Guiguen Y, et al. Functional Analysis of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture. bioRxiv. 2016.Google Scholar
Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.