Standardized IMGT® Nomenclature of Salmonidae IGH Genes, the Paradigm of Atlantic Salmon and Rainbow Trout: From Genomics to Repertoires

• Published in: Frontiers in Immunology
• Main Authors: Magadan, Susana, Krasnov, Aleksei, Hadi-Saljoqi, Saida, Afanasyev, Sergey, Mondot, Stanislas, S., Lallias, Delphine, Castro, Rosario, Salinas, Irene, Sunyer, Oriol, Hansen, John, Koop, Ben, Lefranc, Marie-Paule, Boudinot, Pierre
• Other Authors: 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, 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
• Language: English
• Published: HAL CCSD 2019
• Subjects: 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; Atlantic salmon; Salmo salar
• 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

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.