Location: Cool and Cold Water Aquaculture Research
Project Number: 8082-10600-002-008-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Sep 1, 2026
End Date: Aug 31, 2027
Objective:
To annotate the protein coding genes in the de-novo genome assemblies that were recently generated for rainbow trout and cutthroat trout. The annotation of the genomes will be used for pan-gene analysis and for in-silico functional comparative genomics between genetic lineages within species and between species. The new genome annotations will be viewable on a public Genome Browser.
Approach:
The cooperator will use their previously developed computational pipeline for functional annotation of reference genomes in salmonid species. The annotation of coding genes will be used for pan-gene evolutionary analysis between lineages within the same species (intra-specific) and between the two Oncorhynchus species (inter-specific). The framework for the analysis will be based on the de-novo genome assembly and transcriptome resources that were recently developed by USDA-ARS and other research collaborators. The de-novo genome annotations will be viewable through a public Genome Browser that will be hosted by the cooperator.