The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly

PLoS One. 2018 Sep 13;13(9):e0204076. doi: 10.1371/journal.pone.0204076. eCollection 2018.


Arctic charr have a circumpolar distribution, persevere under extreme environmental conditions, and reach ages unknown to most other salmonids. The Salvelinus genus is primarily composed of species with genomes that are structured more like the ancestral salmonid genome than most Oncorhynchus and Salmo species of sister genera. It is thought that this aspect of the genome may be important for local adaptation (due to increased recombination) and anadromy (the migration of fish from saltwater to freshwater). In this study, we describe the generation of a new genetic map, the sequencing and assembly of the Arctic charr genome (GenBank accession: GCF_002910315.2) using the newly created genetic map and a previous genetic map, and present several analyses of the Arctic charr genes and genome assembly. The newly generated genetic map consists of 8,574 unique genetic markers and is similar to previous genetic maps with the exception of three major structural differences. The N50, identified BUSCOs, repetitive DNA content, and total size of the Arctic charr assembled genome are all comparable to other assembled salmonid genomes. An analysis to identify orthologous genes revealed that a large number of orthologs could be identified between salmonids and many appear to have highly conserved gene expression profiles between species. Comparing orthologous gene expression profiles may give us a better insight into which genes are more likely to influence species specific phenotypes.

Publication types

  • Research Support, Non-U.S. Gov't
  • Retracted Publication

MeSH terms

  • Adaptation, Physiological / genetics
  • Animals
  • Arctic Regions
  • Chromosome Mapping
  • Cold Temperature
  • Female
  • Genetic Linkage
  • Genetic Markers
  • Genetic Speciation*
  • Genome*
  • Male
  • Oncorhynchus mykiss / classification
  • Oncorhynchus mykiss / genetics
  • Phenotype
  • Phylogeny*
  • Salmo salar / classification
  • Salmo salar / genetics
  • Transcriptome*
  • Trout / classification
  • Trout / genetics*


  • Genetic Markers

Grant support

This project was funded by an Natural Sciences and Engineering Research Council of Canada (NSERC) strategic grant “Integration of Genomic Resources into an Arctic Charr Broodstock Program” to BK and WSD, and funding from the Atlatn. BK received funding from the NSERC grant entitled "Salmonid Genome Duplication Drives Specialization and Adaptation.” KAC was supported by funds from Fisheries and Oceans Canada and the Canadian Regulatory System for Biotechnology. CN was supported by the Atlantic Innovation Fund/Atlantic Canada Opportunities Agency for the project “Aquaculture development and profitable commercialization of Arctic charr in Canada. Icy Waters Ltd. provided support in the form of salaries for authors RM and ME and provided Arctic charr samples, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. Involvement with Icy Waters Ltd. was based on the “Integration of Genomic Resources into an Arctic Charr Broodstock Program” grant to improve broodstock. The specific roles of RM and ME authors are articulated in the ‘author contributions’ section.