The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome

Abstract

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.

The pink salmon genome: uncovering the genomic consequences of a strict two-year life-cycle

“…It is expected that near the sdY gene, recombination is reduced and mutations would accumulate between the X and Y-chromosomes as a result of reduced recombination. Females tend to have long runs of homozygous genotypes where recombination is reduced and males tend to have long stretches of heterozygous genotypes when reads from the X and Y-chromosome align at the same location (77). Since the males with the CGGA sdY haplotype have long runs of homozygous genotypes at the LG20_El14.2 region, as most of the females do, we suggest that the CGGA sdY is at another location in the genome in these individuals.…”

“…HaplotypeCaller (GATK) was then used to generate .gvcf files (parameters: --genotyping_mode DISCOVERY, --emitRefConfidence GVCF) for each sample. The GenotypeGVCF command from GATK was then used to genotype the individuals in 10 Mbp intervals (see (77) for python script used to split into 10 Mbp intervals). The CatVariants command was used to merge the intervals afterwards.…”

“…Additional filtering was done for some analyses, which are sensitive to linkage disequilibrium. Variants were filtered if heterozygous allele counts were not evenly represented -also known as allele balance (minor allele count < 20% of the major allele count, see (77) for python script). Variants in linkage disequilibrium were thinned using BCFtools (79) (parameters: +prune, -w 20kb, -l 0.4, and -n 2).…”

“…Variation in immune related genes is a common phenomenon between salmonid populations (e.g., (77,120,121)). Between odd and even-year pink salmon, five eigenGWAS peaks were identified near or in genes with immune related functions.…”

EigenGWAS: An online visualizing and interactive application for detecting genomic signatures of natural selection

“…Recently, EigenGWAS has been successfully applied in human genetics (Galinsky et al, 2016;Shen et al, 2016), ecology (Armstrong et al, 2018;Bosse et al, 2017;Chai et al, 2020;Christensen et al, 2020;Kim et al, 2017), breeding programmes (Li et al, 2019;Liu et al, 2017;Ma et al, 2016;Zhao et al, 2018) and other populationbased genomic studies involving various resequencing projects (Table S1). In addition, the EigenGWAS algorithm and analysis procedures have also been adopted for use in statistical packages, such as GEnetic Analysis Repository (gear), pcadapt and sommer (Chen et al, 2016;Covarrubias-Pazaran, 2016;Luu et al, 2017).…”