Improve genomic resources and gene annotation of the rainbow trout genome.

The overall aim of this project is to improve reference pan-genome resources for rainbow trout by generating a bioinformatic pipeline for genome annotation of multiple de-novo genome assemblies. To that end, we have enriched the transcriptome resources available for genome annotation by sequencing RNA from immune response enriched samples using long reads IsoSeq (PacBio) and short reads (Illumina) sequencing datasets. Specifically for this SRA submission, we included data from sequencing of 5 pools of samples from 5-10 fish per pool. Four of the samples were from spleen tissue and one was from white blood cells that were filtered from head kidney tissue samples. The spleen samples were from the USDA-ARS resistant or susceptible rainbow trout lines that were challenged by two strains of Flavobacterium psychrophilum (Fp), the causative agent of bacterial cold water disease in salmonids. One of the Fp strains was a wildtype (Accession CSF 259-93) and the second was a less pathogenic mutated strain of the wildtype (FpC8). The head kidney sample was obtained from rainbow trout from the susceptible line that were challenged with the Fp wildtype strain.