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

Cutthroat trout (Oncorhynchus clarkii) are popular among anglers throughout their native range along the West Coast and interior of North America. As they colonized the interior of North America, cutthroat trout diverged into several genetically distinct groups. Many of these groups are now threatened by habitat destruction, hybridization with rainbow trout (O. mykiss), and competition from introduced species. These groups were previously classified as subspecies, but recent research suggests they may represent distinct species. In this study, we produced a chromosomal-level genome assembly and a genetic map for one of the species in the cutthroat trout species complex, the westslope cutthroat trout (O. lewisi--formerly O. clarki lewisi). We also constructed haplotype-resolved assemblies from a westslope cutthroat-rainbow trout F1 hybrid. We used the new genome assemblies to identify major interspecific chromosomal rearrangements between the two sister species, including fusions, fissions, and inversions. These genome assemblies and chromosome data provide valuable insights regarding genetic variation within cutthroat trout and in hybrids between rainbow and cutthroat trout. Article SummaryWestslope cutthroat trout inhabit bodies of water in several states and provinces near the Rocky Mountains and are well-known among anglers. In this study, we produced the first publicly available genome assemblies and a high-density genetic map for this species. These are research tools that allow detailed genetic analyses, including identifying differences among the genomes of related species. These comparisons allow researchers to understand the evolution of these species better and may provide insight into why successful interbreeding is possible among cutthroat and rainbow trout.