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

• Published in: PLOS ONE
• Main Authors: Christensen, Kris A., Rondeau, Eric B., Sakhrani, Dionne, Biagi, Carlo A., Johnson, Hollie, Joshi, Jay, Flores, Anne-Marie, Leelakumari, Sreeja, Moore, Richard, Pandoh, Pawan K., Withler, Ruth E., Beacham, Terry D., Leggatt, Rosalind A., Tarpey, Carolyn M., Seeb, Lisa W., Seeb, James E., Jones, Steven J. M., Devlin, Robert H., Koop, Ben F.
• Other Authors: Ruggeri, Paolo, canadian regulatory system for biotechnology, fisheries and oceans canada, genome canada, genome british columbia, génome québec
• Format: Article in Journal/Newspaper
• Language: English
• Published: Public Library of Science (PLoS) 2021
• Subjects: Oncorhynchus gorbuscha; Pink salmon
• Online Access: http://dx.doi.org/10.1371/journal.pone.0255752; https://dx.plos.org/10.1371/journal.pone.0255752

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.