Abstract
Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to the western Pacific Ocean. Pink salmon are also the most abundant of these species and account for a large proportion of the commercial value of the salmon fishery worldwide. A two-year life history of pink salmon generates temporally isolated populations that spawn either in even-years or odd-years. To uncover the influence of this genetic isolation, reference genome assemblies were generated for each year-class and whole genome re-sequencing data was collected from salmon of both year-classes. The salmon were sampled from six Canadian rivers and one Japanese river. At multiple centromeres we identified peaks of Fst between year-classes that were millions of base-pairs long. The largest Fst peak was also associated with a million base-pair chromosomal polymorphism found in the odd-year genome near a centromere. These Fst peaks may be the result of a centromere drive or a combination of reduced recombination and genetic drift, and they could influence speciation. Other regions of the genome influenced by odd-year and even-year temporal isolation and tentatively under selection were mostly associated with genes related to immune function, organ development/maintenance, and behaviour.
Highlights
Pink salmon are an economically important species under heavy exploitation and have been the subject of intense mitigation efforts to maintain current levels of exploitation
We present genome assemblies for both odd-year and even-year lineages, develop a transcriptome to help in the annotation of these assemblies, and analyze polymorphisms found between groups
In British Columbia, the even-year lineage appeared to be more homogeneous than the odd-year lineage based on the admixture analysis and several population metrics such as nucleotide diversity
Summary
Pink salmon are an economically important species under heavy exploitation and have been the subject of intense mitigation efforts to maintain current levels of exploitation. Commercial catches of pink salmon comprise roughly half of all Pacific salmon catches by weight and a much greater percentage by count as they are the smallest of the commercially important Pacific salmon [1, 2]. Since the late 1980s, more than a billion pink salmon are released annually from hatcheries [1] to maintain the abundance of this fishery.
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