Profiling the T Cell Receptor Alpha/Delta Locus in Salmonids

Area of Science:

• Immunology
• Genomics
• Aquaculture

Background:

• Jawed vertebrates possess two main T cell types: alpha/beta (α/β) and gamma/delta (γ/δ) T cells, distinguished by their T cell receptor (TCR).
• Salmonids, including Atlantic salmon and rainbow trout, are vital aquaculture species and important models for fish immunology and vaccine research.
• Accurate analysis of adaptive immune responses requires comprehensive T cell receptor (TCR) locus annotation, especially for high-throughput sequencing data.

Purpose of the Study:

• To re-annotate the T cell receptor alpha/delta (TRA/TRD) locus in Atlantic salmon and two rainbow trout strains.
• To establish a unified nomenclature for salmonid TRA/TRD genes to facilitate comparative analysis.
• To analyze the expressed T cell receptor alpha (TRA) repertoire in these species.

Main Methods:

• Utilized high-quality genome assemblies of Atlantic salmon and two rainbow trout strains (Swanson and Arlee).
• Performed phylogenetic analysis of functional TRA/TRD V genes.
• Identified and characterized TRAJ genes.
• Analyzed expressed TRA repertoire data from mucosal and systemic tissues.

Main Results:

• Defined 25 shared subgroups of functional TRA/TRD V genes between Atlantic salmon and rainbow trout, some with unique characteristics.
• Identified 128 TRAJ genes in Atlantic salmon, with most having counterparts in rainbow trout.
• Demonstrated that most TRAV gene subgroups are expressed at both mucosal and systemic levels.
• Confirmed the feasibility and benefits of a common salmonid TRA/TRD nomenclature.

Conclusions:

• A standardized salmonid TRA/TRD nomenclature is feasible and advantageous for accurate analysis of high-throughput sequencing data.
• This annotation facilitates a deeper understanding of adaptive immunity in salmonids.
• The findings support improved vaccine development and fish health management in aquaculture.