In an effort to improve the rainbow trout reference genome sequence, we have re-sequenced the doubled haploid Swanson line using PacBio long reads. The current version of the Swanson line rainbow trout genome assembly contains 420,055 spanned gaps and 7,839 un-spanned gaps (GCA_002163495.1) (Pearse et al., 2019). Hence, there is still a need to improve the contiguity and completeness of this reference assembly, which is now possible with long-read DNA sequencing technologies. Currently, we are also working towards generating a rainbow trout pan-genome reference that will better represent the genetic diversity in this species. Towards that end we have recently generated a much-improved assembly for the genome of the rainbow trout Arlee doubled haploid line using long-read sequence data from the PacBio RS II system (GCA_013265735.3) (Gao et al., 2021). This new Swanson line genome assembly will be pivotal to our ability to improve the accuracy of the genome annotation and to characterize structural genome variance among lines that represent important part of the genetic diversity in rainbow trout.