Location: Cool and Cold Water Aquaculture Research
Project Number: 8082-31000-013-013-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: May 1, 2023
End Date: Apr 30, 2024
To contribute to the pan-genome reference of Atlantic salmon, rainbow trout and cutthroat trout by developing a bioinformatic pipeline for functional genome annotation and use it for annotation of protein coding genes in the de-novo genome assemblies that were recently generated for those salmonid species. In addition, the 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 cooperator will use computational genomics methods to develop a pipeline for comparative functional annotation of reference genomes in salmonid species. The annotation of coding genes will then be used for pan-gene evolutionary analysis between lineages within the same species (intra-specific) and between the three salmonid 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.