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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #421576
Research Project: Integrated Research Approaches for Improving Production Efficiency in Rainbow Trout

Location: Cool and Cold Water Aquaculture Research

Title: The De-novo genome assembly of the Westslope cutthroat trout (Oncorhynchus clarkii lewisi) reveals chromosomal rearrangements with the rainbow trout genome

Author
item FLORES, ANNE-MARIE - UNIVERSITY OF VICTORIA
item CHRISTENSEN, KRIS - UNIVERSITY OF VICTORIA
item GODIN, THERESA - FRESHWATER FISHERIES OF BRITISH COLUMBIA
item PALTI, YNIV
item CAMPBELL, MATTHEW - IDAHO DEPARTMENT OF FISH & GAME
item WALDBIESER, GEOFFREY - Geoff
item SIMPSON, SHERON
item SCHEFFLER, BRIAN
item SMITH, SETH - WASHINGTON DEPARTMENT OF FISH & WILDLIFE
item WHITELEY, ANDREW - UNIVERSITY OF MONTANA
item KOVACH, RYAN - MONTANA FISH AND GAME
item LUIKART, GORDON - UNIVERSITY OF MONTANA
item BOYER, MATTHEW - MONTANA FISH AND GAME
item KARDOS, MARTY - UNIVERSITY OF MONTANA
item RELYEA, SCOTT - MONTANA FISH AND GAME
item WELLS, CRAIG - UNIVERSITY OF IDAHO
item KOOP, BEN - UNIVERSITY OF VICTORIA

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 11/17/2024
Publication Date: 11/17/2024
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. 2024. The De-novo genome assembly of the Westslope cutthroat trout (Oncorhynchus clarkii lewisi) reveals chromosomal rearrangements with the rainbow trout genome. bioRxiv. 11.15.623813. https://doi.org/10.1101/2024.11.15.623813.
DOI: https://doi.org/10.1101/2024.11.15.623813

Interpretive Summary:

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.