The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome
Public Library of Science
Sockeye salmon (Oncorhynchus nerka) is a commercially and culturally important species to the people that live along the northern Pacific Ocean coast. There are two main sockeye salmon ecotypes—the ocean-going (anadromous) ecotype and the fresh-water ecotype known as kokanee. The goal of this study was to better understand the population structure of sockeye salmon and identify possible genomic differences among populations and between the two ecotypes. In pursuit of this goal, we generated the first reference sockeye salmon genome assembly and an RNA-seq transcriptome data set to better annotate features of the assembly. Resequenced whole-genomes of 140 sockeye salmon and kokanee were analyzed to understand population structure and identify genomic differences between ecotypes. Three distinct geographic and genetic groups were identified from analyses of the resequencing data. Nucleotide variants in an immunoglobulin heavy chain variable gene cluster on chromosome 26 were found to differentiate the northwestern group from the southern and upper Columbia River groups. Several candidate genes were found to be associated with the kokanee ecotype. Many of these genes were related to ammonia tolerance or vision. Finally, the sex chromosomes of this species were better characterized, and an alternative sex-determination mechanism was identified in a subset of upper Columbia River kokanee.
Correction: The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome. Published: December 30, 2021 https://doi.org/10.1371/journal.pone.0262189 This article  cites a PLOS ONE article that was retracted on February 9, 2021 [2, 3] because the sample used for genome analysis was found to have been misidentified. The genomic assembly reported in  is still available at GenBank, but it has been relabelled as an unclassified species in the Salvelinus genus, or Salvelinus sp. (GenBank accession: GCF_002910315.2).