Profiling the T Cell Receptor Alpha/Delta Locus in Salmonids
International audience 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 At...
Published in: | Frontiers in Immunology |
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Main Authors: | , , , , , , |
Other Authors: | , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
HAL CCSD
2021
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Subjects: | |
Online Access: | https://hal.science/hal-03434949 https://hal.science/hal-03434949/document https://hal.science/hal-03434949/file/2021_Edholm_fimmu.pdf https://doi.org/10.3389/fimmu.2021.753960 |
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ftunivnantes:oai:HAL:hal-03434949v1 |
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openpolar |
institution |
Open Polar |
collection |
Université de Nantes: HAL-UNIV-NANTES |
op_collection_id |
ftunivnantes |
language |
English |
topic |
adaptive immunity gene rearrangement repertoire salmonid fish T cell receptor TRA/TRD locus VDJ annotation [SDV.IMM]Life Sciences [q-bio]/Immunology |
spellingShingle |
adaptive immunity gene rearrangement repertoire salmonid fish T cell receptor TRA/TRD locus VDJ annotation [SDV.IMM]Life Sciences [q-bio]/Immunology Edholm, Eva Stina Isabella Fenton, Christopher Graham Mondot, Stanislas Paulssen, Ruth Hracky Lefranc, Marie Paule Boudinot, Pierre Magadan, Susana Profiling the T Cell Receptor Alpha/Delta Locus in Salmonids |
topic_facet |
adaptive immunity gene rearrangement repertoire salmonid fish T cell receptor TRA/TRD locus VDJ annotation [SDV.IMM]Life Sciences [q-bio]/Immunology |
description |
International audience 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. |
author2 |
University of Tromsø (UiT) MICrobiologie de l'ALImentation au Service de la Santé (MICALIS) AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) Génétique Animale et Biologie Intégrative (GABI) Laboratoire d'ImmunoGénétique Moléculaire (LIGM) Virologie et Immunologie Moléculaires (VIM (UR 0892)) Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) Universidade de Vigo Instituto de Investigación Sanitaria Galicia Sur Vigo, Spain Tromsø Research Foundation Starting Grant Aquaculture program of The Research Council of Norway (Grant No. 295036) INRAE UVIGO Xunta de Galicia (GRC-ED431C 2020/02) ANR-16-CE20-0002,Fish-RNAvax,Vaccins ARN éco-compatibles pour l'induction de réponses immunitaires protectrices chez le poisson d'élevage(2016) European Project: 311993,EC:FP7:KBBE,FP7-KBBE-2012-6-singlestage,TARGETFISH(2012) |
format |
Article in Journal/Newspaper |
author |
Edholm, Eva Stina Isabella Fenton, Christopher Graham Mondot, Stanislas Paulssen, Ruth Hracky Lefranc, Marie Paule Boudinot, Pierre Magadan, Susana |
author_facet |
Edholm, Eva Stina Isabella Fenton, Christopher Graham Mondot, Stanislas Paulssen, Ruth Hracky Lefranc, Marie Paule Boudinot, Pierre Magadan, Susana |
author_sort |
Edholm, Eva Stina Isabella |
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 |
HAL CCSD |
publishDate |
2021 |
url |
https://hal.science/hal-03434949 https://hal.science/hal-03434949/document https://hal.science/hal-03434949/file/2021_Edholm_fimmu.pdf https://doi.org/10.3389/fimmu.2021.753960 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
ISSN: 1664-3224 EISSN: 1664-3224 Frontiers in Immunology https://hal.science/hal-03434949 Frontiers in Immunology, 2021, 12, ⟨10.3389/fimmu.2021.753960⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.3389/fimmu.2021.753960 info:eu-repo/semantics/altIdentifier/pmid/34733285 info:eu-repo/grantAgreement/EC/FP7/311993/EU/Targeted disease prophylaxis in European fish farming/TARGETFISH hal-03434949 https://hal.science/hal-03434949 https://hal.science/hal-03434949/document https://hal.science/hal-03434949/file/2021_Edholm_fimmu.pdf doi:10.3389/fimmu.2021.753960 PUBMED: 34733285 WOS: 000715733700001 |
op_rights |
http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.3389/fimmu.2021.753960 |
container_title |
Frontiers in Immunology |
container_volume |
12 |
_version_ |
1766362414319665152 |
spelling |
ftunivnantes:oai:HAL:hal-03434949v1 2023-05-15T15:31:55+02:00 Profiling the T Cell Receptor Alpha/Delta Locus in Salmonids Edholm, Eva Stina Isabella Fenton, Christopher Graham Mondot, Stanislas Paulssen, Ruth Hracky Lefranc, Marie Paule Boudinot, Pierre Magadan, Susana University of Tromsø (UiT) MICrobiologie de l'ALImentation au Service de la Santé (MICALIS) AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) Génétique Animale et Biologie Intégrative (GABI) Laboratoire d'ImmunoGénétique Moléculaire (LIGM) Virologie et Immunologie Moléculaires (VIM (UR 0892)) Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) Universidade de Vigo Instituto de Investigación Sanitaria Galicia Sur Vigo, Spain Tromsø Research Foundation Starting Grant Aquaculture program of The Research Council of Norway (Grant No. 295036) INRAE UVIGO Xunta de Galicia (GRC-ED431C 2020/02) ANR-16-CE20-0002,Fish-RNAvax,Vaccins ARN éco-compatibles pour l'induction de réponses immunitaires protectrices chez le poisson d'élevage(2016) European Project: 311993,EC:FP7:KBBE,FP7-KBBE-2012-6-singlestage,TARGETFISH(2012) 2021-10-18 https://hal.science/hal-03434949 https://hal.science/hal-03434949/document https://hal.science/hal-03434949/file/2021_Edholm_fimmu.pdf https://doi.org/10.3389/fimmu.2021.753960 en eng HAL CCSD Frontiers info:eu-repo/semantics/altIdentifier/doi/10.3389/fimmu.2021.753960 info:eu-repo/semantics/altIdentifier/pmid/34733285 info:eu-repo/grantAgreement/EC/FP7/311993/EU/Targeted disease prophylaxis in European fish farming/TARGETFISH hal-03434949 https://hal.science/hal-03434949 https://hal.science/hal-03434949/document https://hal.science/hal-03434949/file/2021_Edholm_fimmu.pdf doi:10.3389/fimmu.2021.753960 PUBMED: 34733285 WOS: 000715733700001 http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess ISSN: 1664-3224 EISSN: 1664-3224 Frontiers in Immunology https://hal.science/hal-03434949 Frontiers in Immunology, 2021, 12, ⟨10.3389/fimmu.2021.753960⟩ adaptive immunity gene rearrangement repertoire salmonid fish T cell receptor TRA/TRD locus VDJ annotation [SDV.IMM]Life Sciences [q-bio]/Immunology info:eu-repo/semantics/article Journal articles 2021 ftunivnantes https://doi.org/10.3389/fimmu.2021.753960 2023-02-22T02:41:21Z International audience 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. Article in Journal/Newspaper Atlantic salmon Salmo salar Université de Nantes: HAL-UNIV-NANTES Frontiers in Immunology 12 |