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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Research Project #443853

Research Project: Functional and Comparative Annotation of Salmonid Genomes

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

Objective:
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.

Approach:
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.