De-Novo Genome Assembly for the Westslope Cutthroat Trout (Oncorhynchus clarkii lewisi)

To generate genome resources for Cutthroat Trout (Oncorhynchus clarkii) we used the trio-binning approach for generating De-novo genome assemblies. Hybrid F1progeny were produced from a manual cross between a female Westslope Cutthroat Trout (Oncorhynchus clarkii lewisi) and a male Rainbow Trout (Oncorhynchus mykiss) at the Hayspur Hatchery, Idaho. At the age of approximately 1 year, blood samples were obtained from a single F1 hybrid male offspring to generate ~30x genome coverage PacBio HiFi whole genome shotgun sequence data, HiC libraries and Illumina HiC sequence data, and 30x-60x genome coverage Illumina whole genome shotgun sequence data. In addition, fin tissue samples were obtained from the Cutthroat Trout mother and the Rainbow Trout father of the F1 hybrid. Genomic DNA was extracted from the fin clips and was used to generate 30x-60x genome coverage with Illumina whole genome shotgun sequence data from each parent to facilitate separation of the PacBio sequence data from the F1 hybrid in the bioinformatic pipeline for generating two separate De-novo genome assemblies for each of the two parental species.