Currently, we are working towards generating a rainbow trout pan-genome reference that will better represent the genetic diversity in this species using de-novo chromosome level assemblies. Previously we have submitted the current reference genome from the Arlee line (USDA_OmykA_1.1 GCA_013265735.3) and an improved assembly for the Swanson line (Omyk_2.0 GCA_025558465.1). The Swanson YY male line was originated from a semi-domesticated resident fish from the Kenai Peninsula in Alaska with a haploid number of 29 chromosomes. The Arlee doubled haploid YY male line has a different genetic background from the Swanson line. It was originated from a well-known domesticated hatchery strain that was originally collected from the northern California coast. It has a haploid number of 32 chromosomes. The three Swanson chromosomes that are being divided to two acrocentric chromosomes are Omy04, 14 and 25. The Whale Rock line we used for this de-novo genome assembly is also a YY male. Similar to the Arlee line, it has 2N=64 chromosomes and it was originated from the Central California Coast. The one known major difference is that it was originated from a wild fish from a landlocked steelhead population. The de-novo chromosome level assembly of the rainbow trout WRM line genome has helped correcting minor errors in the previous genome assembly and will aid in better characterization of structural genome variants in rainbow trout and other salmonids and in the pan-gene annotation of multiple rainbow trout and salmonids genomes.