Profiling the T Cell Receptor Alpha/Delta Locus in Salmonids
In jawed vertebrates, two major T cell populations have been characterized. They are defined as α/β or γ/δ T cells, based on the expressed T cell receptor. Salmonids (family Salmonidae) include two key teleost species for aquaculture, rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo sa...
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ftpubmed:oai:pubmedcentral.nih.gov:8559430 2023-05-15T15:31:46+02:00 Profiling the T Cell Receptor Alpha/Delta Locus in Salmonids Edholm, Eva-Stina Fenton, Christopher Graham Mondot, Stanislas Paulssen, Ruth H. Lefranc, Marie-Paule Boudinot, Pierre Magadan, Susana 2021-10-18 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8559430/ http://www.ncbi.nlm.nih.gov/pubmed/34733285 https://doi.org/10.3389/fimmu.2021.753960 en eng Frontiers Media S.A. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8559430/ http://www.ncbi.nlm.nih.gov/pubmed/34733285 http://dx.doi.org/10.3389/fimmu.2021.753960 Copyright © 2021 Edholm, Fenton, Mondot, Paulssen, Lefranc, Boudinot and Magadan https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. CC-BY Front Immunol Immunology Text 2021 ftpubmed https://doi.org/10.3389/fimmu.2021.753960 2021-11-07T01:51:07Z In jawed vertebrates, two major T cell populations have been characterized. They are defined as α/β or γ/δ T cells, based on the expressed T cell receptor. Salmonids (family Salmonidae) include two key teleost species for aquaculture, rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) which constitute important models for fish immunology and important targets for vaccine development. The growing interest to decipher the dynamics of adaptive immune responses against pathogens or vaccines has resulted in recent efforts to sequence the immunoglobulin (IG) or antibodies and T cell receptor (TR) repertoire in these species. In this context, establishing a comprehensive and coherent locus annotation is the fundamental basis for the analysis of high-throughput repertoire sequencing data. We therefore decided to revisit the description and annotation of TRA/TRD locus in Atlantic salmon and two strains of rainbow trout (Swanson and Arlee) using the now available high-quality genome assemblies. Phylogenetic analysis of functional TRA/TRD V genes from these three genomes led to the definition of 25 subgroups shared by both species, some with particular feature. A total of 128 TRAJ genes were identified in Salmo, the majority with a close counterpart in Oncorhynchus. Analysis of expressed TRA repertoire indicates that most TRAV gene subgroups are expressed at mucosal and systemic level. The present work on TRA/TRD locus annotation along with the analysis of TRA repertoire sequencing data show the feasibility and advantages of a common salmonid TRA/TRD nomenclature that allows an accurate annotation and analysis of high-throughput sequencing results, across salmonid T cell subsets. Text Atlantic salmon Salmo salar PubMed Central (PMC) Frontiers in Immunology 12 |
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Immunology |
spellingShingle |
Immunology Edholm, Eva-Stina Fenton, Christopher Graham Mondot, Stanislas Paulssen, Ruth H. Lefranc, Marie-Paule Boudinot, Pierre Magadan, Susana Profiling the T Cell Receptor Alpha/Delta Locus in Salmonids |
topic_facet |
Immunology |
description |
In jawed vertebrates, two major T cell populations have been characterized. They are defined as α/β or γ/δ T cells, based on the expressed T cell receptor. Salmonids (family Salmonidae) include two key teleost species for aquaculture, rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) which constitute important models for fish immunology and important targets for vaccine development. The growing interest to decipher the dynamics of adaptive immune responses against pathogens or vaccines has resulted in recent efforts to sequence the immunoglobulin (IG) or antibodies and T cell receptor (TR) repertoire in these species. In this context, establishing a comprehensive and coherent locus annotation is the fundamental basis for the analysis of high-throughput repertoire sequencing data. We therefore decided to revisit the description and annotation of TRA/TRD locus in Atlantic salmon and two strains of rainbow trout (Swanson and Arlee) using the now available high-quality genome assemblies. Phylogenetic analysis of functional TRA/TRD V genes from these three genomes led to the definition of 25 subgroups shared by both species, some with particular feature. A total of 128 TRAJ genes were identified in Salmo, the majority with a close counterpart in Oncorhynchus. Analysis of expressed TRA repertoire indicates that most TRAV gene subgroups are expressed at mucosal and systemic level. The present work on TRA/TRD locus annotation along with the analysis of TRA repertoire sequencing data show the feasibility and advantages of a common salmonid TRA/TRD nomenclature that allows an accurate annotation and analysis of high-throughput sequencing results, across salmonid T cell subsets. |
format |
Text |
author |
Edholm, Eva-Stina Fenton, Christopher Graham Mondot, Stanislas Paulssen, Ruth H. Lefranc, Marie-Paule Boudinot, Pierre Magadan, Susana |
author_facet |
Edholm, Eva-Stina Fenton, Christopher Graham Mondot, Stanislas Paulssen, Ruth H. Lefranc, Marie-Paule Boudinot, Pierre Magadan, Susana |
author_sort |
Edholm, Eva-Stina |
title |
Profiling the T Cell Receptor Alpha/Delta Locus in Salmonids |
title_short |
Profiling the T Cell Receptor Alpha/Delta Locus in Salmonids |
title_full |
Profiling the T Cell Receptor Alpha/Delta Locus in Salmonids |
title_fullStr |
Profiling the T Cell Receptor Alpha/Delta Locus in Salmonids |
title_full_unstemmed |
Profiling the T Cell Receptor Alpha/Delta Locus in Salmonids |
title_sort |
profiling the t cell receptor alpha/delta locus in salmonids |
publisher |
Frontiers Media S.A. |
publishDate |
2021 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8559430/ http://www.ncbi.nlm.nih.gov/pubmed/34733285 https://doi.org/10.3389/fimmu.2021.753960 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
Front Immunol |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8559430/ http://www.ncbi.nlm.nih.gov/pubmed/34733285 http://dx.doi.org/10.3389/fimmu.2021.753960 |
op_rights |
Copyright © 2021 Edholm, Fenton, Mondot, Paulssen, Lefranc, Boudinot and Magadan https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fimmu.2021.753960 |
container_title |
Frontiers in Immunology |
container_volume |
12 |
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1766362286729986048 |