Standardized IMGT® Nomenclature of Salmonidae IGH Genes, the Paradigm of Atlantic Salmon and Rainbow Trout: From Genomics to Repertoires
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...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-11-01
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| Series: | Frontiers in Immunology |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fimmu.2019.02541/full |
| _version_ | 1819014808858525696 |
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| author | Susana Magadan Susana Magadan Aleksei Krasnov Saida Hadi-Saljoqi Sergey Afanasyev Stanislas Mondot Delphine Lallias Rosario Castro Irene Salinas Oriol Sunyer John Hansen Ben F. Koop Marie-Paule Lefranc Pierre Boudinot |
| author_facet | Susana Magadan Susana Magadan Aleksei Krasnov Saida Hadi-Saljoqi Sergey Afanasyev Stanislas Mondot Delphine Lallias Rosario Castro Irene Salinas Oriol Sunyer John Hansen Ben F. Koop Marie-Paule Lefranc Pierre Boudinot |
| author_sort | Susana Magadan |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-21T02:21:44Z |
| format | Article |
| id | doaj.art-6d0ab8ee5edf4b4b96373c27329bfcc8 |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-12-21T02:21:44Z |
| publishDate | 2019-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj.art-6d0ab8ee5edf4b4b96373c27329bfcc82022-12-21T19:19:07ZengFrontiers Media S.A.Frontiers in Immunology1664-32242019-11-011010.3389/fimmu.2019.02541494896Standardized IMGT® Nomenclature of Salmonidae IGH Genes, the Paradigm of Atlantic Salmon and Rainbow Trout: From Genomics to RepertoiresSusana Magadan0Susana Magadan1Aleksei Krasnov2Saida Hadi-Saljoqi3Sergey Afanasyev4Stanislas Mondot5Delphine Lallias6Rosario Castro7Irene Salinas8Oriol Sunyer9John Hansen10Ben F. Koop11Marie-Paule Lefranc12Pierre Boudinot13Immunology Laboratory, Biomedical Research Center, University of Vigo, Vigo, SpainDepartment of Biology, Center of Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, United StatesNofima AS, Norwegian Institute of Food, Fisheries and Aquaculture Research, Tromsø, NorwayIMGT®, The International ImMunoGeneTics Information System® (IMGT), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), CNRS, University of Montpellier, Montpellier, FranceSechenov Institute of Evolutionary Physiology and Biochemistry, Saint Petersburg, RussiaMICALIS, Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, FranceGénétique Animale et Biologie Intégrative (GABI), INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, FranceVirologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Jouy-en-Josas, FranceDepartment of Biology, Center of Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, United StatesPathobiology Department, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States0Western Fisheries Research Center, U.S. Geological Survey, Seattle, WA, United States1Department of Biology, University of Victoria, Victoria, BC, CanadaIMGT®, The International ImMunoGeneTics Information System® (IMGT), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), CNRS, University of Montpellier, Montpellier, FranceVirologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Jouy-en-Josas, FranceIn 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.https://www.frontiersin.org/article/10.3389/fimmu.2019.02541/fullimmunoglobulinantibody repertoiresalmonid fishVDJ annotationcomparative immunology |
| spellingShingle | Susana Magadan Susana Magadan Aleksei Krasnov Saida Hadi-Saljoqi Sergey Afanasyev Stanislas Mondot Delphine Lallias Rosario Castro Irene Salinas Oriol Sunyer John Hansen Ben F. Koop Marie-Paule Lefranc Pierre Boudinot Standardized IMGT® Nomenclature of Salmonidae IGH Genes, the Paradigm of Atlantic Salmon and Rainbow Trout: From Genomics to Repertoires Frontiers in Immunology immunoglobulin antibody repertoire salmonid fish VDJ annotation comparative immunology |
| title | 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_short | Standardized IMGT® Nomenclature of Salmonidae IGH Genes, the Paradigm of Atlantic Salmon and Rainbow Trout: From Genomics to Repertoires |
| title_sort | standardized imgt r nomenclature of salmonidae igh genes the paradigm of atlantic salmon and rainbow trout from genomics to repertoires |
| topic | immunoglobulin antibody repertoire salmonid fish VDJ annotation comparative immunology |
| url | https://www.frontiersin.org/article/10.3389/fimmu.2019.02541/full |
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