A genome assembly for Lahontan Cutthroat Trout, Oncorhynchus clarkii henshawi

Cutthroat trout (Oncorhynchus clarkii) are diverse Pacific salmonids widely distributed throughout western North America. Distinct lineages of cutthroat trout have been defined based on morphology, geography, and genetic differences. Several of these, including Lahontan cutthroat trout (Oncorhynchus clarkii henshawi), are classified as threatened or in danger of extinction. Despite their precarious conservation status, few genomic resources have been developed for these lineages. In an effort to promote the development and application of genomic approaches for research and conservation of this group, we present the first high-quality reference genome for Lahontan cutthroat trout. We use this genome assembly to describe genomic synteny and structural rearrangements with their sister species, rainbow trout (O. mykiss), as well as with the diverged westslope cutthroat trout (O. clarkii lewisi) lineage.