Standardized IMGT® Nomenclature of Salmonidae IGH Genes, the Paradigm of Atlantic Salmon and Rainbow Trout: From Genomics to Repertoires
International audience In teleost fish as in mammals, humoral adaptive immunity is based on B lymphocytes expressing highly diverse immunoglobulins (IG). During B cell differentiation, IG loci are subjected to genomic rearrangements of V, D, and J genes, producing a unique antigen receptor expressed...
Published in: | Frontiers in Immunology |
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Main Authors: | , , , , , , , , , , , , |
Other Authors: | , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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HAL CCSD
2019
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Subjects: | |
Online Access: | https://hal.inrae.fr/hal-02867815 https://hal.inrae.fr/hal-02867815/document https://hal.inrae.fr/hal-02867815/file/Magadan%20et%20al.2019_Frontiers%20in%20Immunol.pdf https://doi.org/10.3389/fimmu.2019.02541 |
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topic |
immunoglobulin antibody repertoire salmonid fish VDJ annotation comparative immunology [SDV]Life Sciences [q-bio] [SDV.IMM]Life Sciences [q-bio]/Immunology [SDV.IMM.IA]Life Sciences [q-bio]/Immunology/Adaptive immunology |
spellingShingle |
immunoglobulin antibody repertoire salmonid fish VDJ annotation comparative immunology [SDV]Life Sciences [q-bio] [SDV.IMM]Life Sciences [q-bio]/Immunology [SDV.IMM.IA]Life Sciences [q-bio]/Immunology/Adaptive immunology Magadan, Susana Krasnov, Aleksei Hadi-Saljoqi, Saida Afanasyev, Sergey Mondot, Stanislas Lallias, Delphine Castro, Rosario Salinas, Irene Sunyer, Oriol Hansen, John Koop, Ben Lefranc, Marie-Paule Boudinot, Pierre Standardized IMGT® Nomenclature of Salmonidae IGH Genes, the Paradigm of Atlantic Salmon and Rainbow Trout: From Genomics to Repertoires |
topic_facet |
immunoglobulin antibody repertoire salmonid fish VDJ annotation comparative immunology [SDV]Life Sciences [q-bio] [SDV.IMM]Life Sciences [q-bio]/Immunology [SDV.IMM.IA]Life Sciences [q-bio]/Immunology/Adaptive immunology |
description |
International audience In teleost fish as in mammals, humoral adaptive immunity is based on B lymphocytes expressing highly diverse immunoglobulins (IG). During B cell differentiation, IG loci are subjected to genomic rearrangements of V, D, and J genes, producing a unique antigen receptor expressed on the surface of each lymphocyte. During the course of an immune response to infections or immunizations, B cell clones specific of epitopes from the immunogen are expanded and activated, leading to production of specific antibodies. Among teleost fish, salmonids comprise key species for aquaculture. Rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) are especially important from a commercial point of view and have emerged as critical models for fish immunology. The growing interest to capture accurate and comprehensive antibody responses against common pathogens and vaccines has resulted in recent efforts to sequence the IG repertoire in these species. In this context, a unified and standardized nomenclature of salmonid IG heavy chain (IGH) genes is urgently required, to improve accuracy of annotation of adaptive immune receptor repertoire dataset generated by high-throughput sequencing (AIRRseq) and facilitate comparisons between studies and species. Interestingly, the assembly of salmonids IGH genomic sequences is challenging due to the presence of two large size duplicated IGH loci and high numbers of IG genes and pseudogenes. We used data available for Atlantic salmon to establish an IMGT standardized nomenclature of IGH genes in this species and then applied the IMGT rules to the rainbow trout IGH loci to set up a nomenclature, which takes into account the specificities of Salmonid loci. This unique, consistent nomenclature for Salmonid IGH genes was then used to construct IMGT sequence reference directories allowing accurate annotation of AIRRseq data. The complex issues raised by the genetic diversity of salmon and trout strains are discussed in the context of IG repertoire annotation. |
author2 |
Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)) Institut National de la Recherche Agronomique (INRA) Norwegian Institute of Food,Fisheries and Aquaculture Research (NOFIMA) Immunité et cancer (U932) Université Paris Descartes - Paris 5 (UPD5)-Institut Curie Paris -Institut National de la Santé et de la Recherche Médicale (INSERM) Génétique Animale et Biologie Intégrative (GABI) Institut National de la Recherche Agronomique (INRA)-AgroParisTech Department of Animal Health, Faculty of Veterinary Sciences Universidad Complutense de Madrid = Complutense University of Madrid Madrid (UCM) The University of New Mexico Albuquerque New Mexico Consortium (NMC) Department of Pathobiology Philadelphia University of Pennsylvania Institut de génétique humaine (IGH) Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS) ANR-16-CE20-0002,Fish-RNAvax,Vaccins ARN éco-compatibles pour l'induction de réponses immunitaires protectrices chez le poisson d'élevage(2016) |
format |
Article in Journal/Newspaper |
author |
Magadan, Susana Krasnov, Aleksei Hadi-Saljoqi, Saida Afanasyev, Sergey Mondot, Stanislas Lallias, Delphine Castro, Rosario Salinas, Irene Sunyer, Oriol Hansen, John Koop, Ben Lefranc, Marie-Paule Boudinot, Pierre |
author_facet |
Magadan, Susana Krasnov, Aleksei Hadi-Saljoqi, Saida Afanasyev, Sergey Mondot, Stanislas Lallias, Delphine Castro, Rosario Salinas, Irene Sunyer, Oriol Hansen, John Koop, Ben Lefranc, Marie-Paule Boudinot, Pierre |
author_sort |
Magadan, Susana |
title |
Standardized IMGT® Nomenclature of Salmonidae IGH Genes, the Paradigm of Atlantic Salmon and Rainbow Trout: From Genomics to Repertoires |
title_short |
Standardized IMGT® Nomenclature of Salmonidae IGH Genes, the Paradigm of Atlantic Salmon and Rainbow Trout: From Genomics to Repertoires |
title_full |
Standardized IMGT® Nomenclature of Salmonidae IGH Genes, the Paradigm of Atlantic Salmon and Rainbow Trout: From Genomics to Repertoires |
title_fullStr |
Standardized IMGT® Nomenclature of Salmonidae IGH Genes, the Paradigm of Atlantic Salmon and Rainbow Trout: From Genomics to Repertoires |
title_full_unstemmed |
Standardized IMGT® Nomenclature of Salmonidae IGH Genes, the Paradigm of Atlantic Salmon and Rainbow Trout: From Genomics to Repertoires |
title_sort |
standardized imgt® nomenclature of salmonidae igh genes, the paradigm of atlantic salmon and rainbow trout: from genomics to repertoires |
publisher |
HAL CCSD |
publishDate |
2019 |
url |
https://hal.inrae.fr/hal-02867815 https://hal.inrae.fr/hal-02867815/document https://hal.inrae.fr/hal-02867815/file/Magadan%20et%20al.2019_Frontiers%20in%20Immunol.pdf https://doi.org/10.3389/fimmu.2019.02541 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
ISSN: 1664-3224 EISSN: 1664-3224 Frontiers in Immunology https://hal.inrae.fr/hal-02867815 Frontiers in Immunology, 2019, 10, ⟨10.3389/fimmu.2019.02541⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.3389/fimmu.2019.02541 hal-02867815 https://hal.inrae.fr/hal-02867815 https://hal.inrae.fr/hal-02867815/document https://hal.inrae.fr/hal-02867815/file/Magadan%20et%20al.2019_Frontiers%20in%20Immunol.pdf doi:10.3389/fimmu.2019.02541 |
op_rights |
http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.3389/fimmu.2019.02541 |
container_title |
Frontiers in Immunology |
container_volume |
10 |
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1810432425475440640 |
spelling |
ftanrparis:oai:HAL:hal-02867815v1 2024-09-15T17:56:13+00:00 Standardized IMGT® Nomenclature of Salmonidae IGH Genes, the Paradigm of Atlantic Salmon and Rainbow Trout: From Genomics to Repertoires Magadan, Susana Krasnov, Aleksei Hadi-Saljoqi, Saida Afanasyev, Sergey Mondot, Stanislas Lallias, Delphine Castro, Rosario Salinas, Irene Sunyer, Oriol Hansen, John Koop, Ben Lefranc, Marie-Paule Boudinot, Pierre Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)) Institut National de la Recherche Agronomique (INRA) Norwegian Institute of Food,Fisheries and Aquaculture Research (NOFIMA) Immunité et cancer (U932) Université Paris Descartes - Paris 5 (UPD5)-Institut Curie Paris -Institut National de la Santé et de la Recherche Médicale (INSERM) Génétique Animale et Biologie Intégrative (GABI) Institut National de la Recherche Agronomique (INRA)-AgroParisTech Department of Animal Health, Faculty of Veterinary Sciences Universidad Complutense de Madrid = Complutense University of Madrid Madrid (UCM) The University of New Mexico Albuquerque New Mexico Consortium (NMC) Department of Pathobiology Philadelphia University of Pennsylvania Institut de génétique humaine (IGH) Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS) ANR-16-CE20-0002,Fish-RNAvax,Vaccins ARN éco-compatibles pour l'induction de réponses immunitaires protectrices chez le poisson d'élevage(2016) 2019-11-12 https://hal.inrae.fr/hal-02867815 https://hal.inrae.fr/hal-02867815/document https://hal.inrae.fr/hal-02867815/file/Magadan%20et%20al.2019_Frontiers%20in%20Immunol.pdf https://doi.org/10.3389/fimmu.2019.02541 en eng HAL CCSD Frontiers info:eu-repo/semantics/altIdentifier/doi/10.3389/fimmu.2019.02541 hal-02867815 https://hal.inrae.fr/hal-02867815 https://hal.inrae.fr/hal-02867815/document https://hal.inrae.fr/hal-02867815/file/Magadan%20et%20al.2019_Frontiers%20in%20Immunol.pdf doi:10.3389/fimmu.2019.02541 http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess ISSN: 1664-3224 EISSN: 1664-3224 Frontiers in Immunology https://hal.inrae.fr/hal-02867815 Frontiers in Immunology, 2019, 10, ⟨10.3389/fimmu.2019.02541⟩ immunoglobulin antibody repertoire salmonid fish VDJ annotation comparative immunology [SDV]Life Sciences [q-bio] [SDV.IMM]Life Sciences [q-bio]/Immunology [SDV.IMM.IA]Life Sciences [q-bio]/Immunology/Adaptive immunology info:eu-repo/semantics/article Journal articles 2019 ftanrparis https://doi.org/10.3389/fimmu.2019.02541 2024-07-31T23:35:34Z International audience In teleost fish as in mammals, humoral adaptive immunity is based on B lymphocytes expressing highly diverse immunoglobulins (IG). During B cell differentiation, IG loci are subjected to genomic rearrangements of V, D, and J genes, producing a unique antigen receptor expressed on the surface of each lymphocyte. During the course of an immune response to infections or immunizations, B cell clones specific of epitopes from the immunogen are expanded and activated, leading to production of specific antibodies. Among teleost fish, salmonids comprise key species for aquaculture. Rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) are especially important from a commercial point of view and have emerged as critical models for fish immunology. The growing interest to capture accurate and comprehensive antibody responses against common pathogens and vaccines has resulted in recent efforts to sequence the IG repertoire in these species. In this context, a unified and standardized nomenclature of salmonid IG heavy chain (IGH) genes is urgently required, to improve accuracy of annotation of adaptive immune receptor repertoire dataset generated by high-throughput sequencing (AIRRseq) and facilitate comparisons between studies and species. Interestingly, the assembly of salmonids IGH genomic sequences is challenging due to the presence of two large size duplicated IGH loci and high numbers of IG genes and pseudogenes. We used data available for Atlantic salmon to establish an IMGT standardized nomenclature of IGH genes in this species and then applied the IMGT rules to the rainbow trout IGH loci to set up a nomenclature, which takes into account the specificities of Salmonid loci. This unique, consistent nomenclature for Salmonid IGH genes was then used to construct IMGT sequence reference directories allowing accurate annotation of AIRRseq data. The complex issues raised by the genetic diversity of salmon and trout strains are discussed in the context of IG repertoire annotation. Article in Journal/Newspaper Atlantic salmon Salmo salar Portail HAL-ANR (Agence Nationale de la Recherche) Frontiers in Immunology 10 |