This USDA NIFA-funded project aims to provide a high-quality assembly and well-annotated reference genome of the rainbow trout. The USDA/ARS/NCCCWA lab released significantly improved de-novo genome assemblies for the Arlee clonal line (USDA_OmykA_1.1) and Swanson clonal line (USDA_Omyk_2.0), which can improve the identification of genetic markers and genes related to disease resistance and other physiological traits. Efforts are still ongoing to add a third de-novo assembly from the Whale Rock line toward developing a pan-genome reference for rainbow trout.
A new assembly of the rainbow trout transcriptome (Swanson clonal line) using long reads sequencing has been published, identifying new alternative splicing associated with essential traits, including fish growth, muscle accretion, disease resistance, stress response, and fish migration. The new transcriptome was used for annotation of the USDA_Omyk_2.0 genome assembly.
ATAC-Seq data from four tissues and Chip-Seq data from six tissues were generated to annotate chromatin accessibility of the genome. In addition, Methyl Mini-seq was used for genome-wide profiling of DNA methylation in male and female rainbow trout. The improved assembly and annotation of various genome references will allow comparative functional genomics analyses and identification of genes controlling aquaculture production and animal welfare traits.