The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly
Authors: Kris A Christensen
Robert H Devlin
David R Minkley
Moira M Ferguson
Eric B Rondeau
Michael Edwards
Jong S Leong
Agnieszka Stadnik
Ben F Koop
William S Davidson
Cameron M Nugent
Robin Muzzerall
Roy G Danzmann
Journal: PLoS ONE (2018)
Discipline: Multidisciplinary
Keywords: Arctic charr; genetic map; genome assembly; orthologous genes; local adaptation
Affiliations: Fisheries and Oceans Canada, Centre for Aquaculture and Environmental Research, West Vancouver, British Columbia, Canada., University of Victoria, Department of Biology, Victoria, British Columbia, Canada., Simon Fraser University, Molecular Biology and Biochemistry, Burnaby, British Columbia, Canada., University of Guelph, Department of Integrative Biology, Guelph, Ontario, Canada., Icy Waters Ltd, Whitehorse, Yukon, Canada.

Abstract:  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. 

Retracted: Yes

PubPeer comments:
 2021 retraction. https: journals.plos.org plosone article?id=10.1371 journal.pone.0247083 After this article [1] was published, further analysis revealed that the sample used for the reported genome analysis was more likely from the closely related species, Dolly Varden (Salvelinus malma), or may have been from a hybrid between the two species. We stand by the genome and transcriptome assembly as scientifically valid and representative of the sample analyzed. However, the identity of that individual is now in question and consequently the articleu2019s title, results, and conclusions attributing the sequences to Arctic charr are not upheld. In light of this issue, we retract the article. We have also requested that NCBI change the species name on the genome sequence deposition to indicate that the data were derived from unclassified species in the Salvelinus genus, or Salvelinus sp. The authors apologize for the issues with this article. AS and RM either could not be reached or did not respond to correspondence about this retraction. The other authors all agreed with the retraction decision. Reference 1. Christensen KA, Rondeau EB, Minkley DR, Leong JS, Nugent CM, Danzmann RG, et al. (2018) The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly. PLoS ONE 13(9): e0204076. https: doi.org 10.1371 journal.pone.0204076 ,