The genome assembly of the westslope cutthroat trout, Oncorhynchus lewisi, reveals interspecific chromosomal rearrangements with the rainbow trout, Oncorhynchus mykiss

Authors: FLORES, ANNE-MARIE - University Of Victoria; CHRISTENSEN, KRIS - University Of Victoria; GODIN, THERESA - Freshwater Fisheries Of British Columbia; Palti, Yniv; CAMPBELL, MATTHEW - Idaho Department Of Fish & Game; Waldbieser, Geoffrey; Simpson, Sheron; Scheffler, Brian; SMITH, SETH - Washington Department Of Fish & Wildlife; WHITELEY, ANDREW - University Of Montana; KOVACH, RYAN - Montana Fish And Game; LUIKART, GORDON - University Of Montana; BOYER, MATTHEW - Montana Fish And Game; KARDOS, MARTY - University Of Montana; RELYEA, SCOTT - Montana Fish And Game; WELLS, CRAIG - University Of Idaho; KOOP, BEN - University Of Victoria

Submitted to: G3: Genes, genomics, genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/3/2025
Publication Date: 3/19/2025
Citation: Flores, A., Christensen, K., Godin, T., Palti, Y., Campbell, M., Waldbieser, G.C., Simpson, S.A., Scheffler, B.E., Smith, S., Whiteley, A., Kovach, R., Luikart, G., Boyer, M., Kardos, M., Relyea, S., Wells, C., Koop, B. 2025. The genome assembly of the westslope cutthroat trout, Oncorhynchus lewisi, reveals interspecific chromosomal rearrangements with the rainbow trout, Oncorhynchus mykiss. G3: Genes, genomics, genetics. jkaf064. https://doi.org/10.1093/g3journal/jkaf064.
DOI: https://doi.org/10.1093/g3journal/jkaf064

Interpretive Summary: A high-quality reference physical genome map is important for facilitating meaningful genetic analyses and enhancing research on the biology of a species and the evolution of related species. In this study, we produced a chromosomal-level genome assembly from one of the major species in the cutthroat trout species complex, the westslope cutthroat trout. Cutthroat trout are popular among anglers throughout their native range along the West Coast and interior of North America. As cutthroat trout colonized the interior of North America, they diverged into several genetically distinct groups. Hybrids between cutthroat trout and rainbow trout occur naturally in cohabitation and can also be produced from a manual cross in the hatchery. Such hybrids and their genetics attract great scientific interest due to their negative impact on the ecology of the cutthroat trout species complex, but also due to their potential positive role in the transfer of genetic disease resistance to aquaculture strains of rainbow trout. We used the new genome assemblies in this study to identify large differences in chromosomal structures between rainbow trout and the westslope cutthroat trout. The genome assemblies and chromosome structure variation data that we generated provide valuable resources and insights on the genetic variation within cutthroat trout and in hybrids of rainbow and cutthroat trout.

Technical Abstract: Cutthroat trout (Oncorhynchus clarkii) are popular among anglers throughout their native range along the West Coast and interior of North America. As cutthroat trout colonized the interior of North America, they diverged into several genetically distinct groups. Many of these groups are now threatened by habitat destruction, hybridization with rainbow trout (Oncorhynchus mykiss), and competition from introduced species. These groups were previously classified as subspecies, but recent research suggests they represent distinct species. In this study, we produced a chromosomal-level genome assembly from one of the major species in the cutthroat trout species complex, the westslope cutthroat trout (O. lewisi—formerly O. clarki lewisi), as well as haplotype resolved assemblies from a westslope cutthroat-rainbow trout F1 hybrid. Additionally, we used the new genome assemblies to identify major chromosomal rearrangements between the two Oncorhynchus species including fusions, fissions, and inversions. These genome assemblies and chromosome data provide valuable insights on the genetic variation within cutthroat trout and in hybrids of rainbow and cutthroat trout.