Genomic analysis of a second rainbow trout line (Arlee) leads to an extended description of the IGH VDJ gene repertoire

• Published in: Developmental & Comparative Immunology
• Main Authors: Magadan, Susana, Mondot, Stanislas, Palti, Yniv, Gao, Guangtu, Lefranc, Marie Paule, Boudinot, Pierre
• Other Authors: Universidade de Vigo, 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), National Center for Cool and Cold Water Aquaculture, ARS-USDA, USDA-ARS : Agricultural Research Service, Institut de génétique humaine (IGH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), 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), U.S. Department of Agriculture, USDA: 8082-31000-012 Institut National de la Recherche Agronomique, INRA Universidade de Vigo, This work was supported by the Institut National de la Recherche Agronomique , by the ANR-16-CE20-0002-01 (FishRNAVax). Xunta de Galicia “Grupo Referencia Competitiva 2020” (ED431C 2020/02). SM also acknowledges the contract from Retención de Talento Investigador- Universidade de Vigo. We are grateful to Ben Koop for discussions and for sharing information about salmonid genomics. The assembly of the Arlee line rainbow trout genome was supported by funds from the USDA Agricultural Research Service in house project number 8082-31000-012 . Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer., 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 2021
• Subjects: IMGT; Immune repertoires; Immunoglobulin; Rainbow trout; Salmonids; [SDV.IMM]Life Sciences [q-bio]/Immunology; Atlantic salmon
• Online Access: https://hal.science/hal-03230900; https://hal.science/hal-03230900/document; https://hal.science/hal-03230900/file/S0145305X21000069.pdf; https://doi.org/10.1016/j.dci.2021.103998

International audience High-throughput sequencing technologies brought a renewed interest for immune repertoires. Fish Ab and B cell repertoires are no exception, and their comprehensive analysis can both provide new insights into poorly understood immune mechanisms, and identify markers of protection after vaccination. However, the lack of genomic description and standardized nomenclature of IG genes hampers accurate annotation of Ig mRNA deep sequencing data. Complete genome sequences of Atlantic salmon and rainbow trout (Swanson line) recently allowed us to establish a comprehensive and coherent annotation of Salmonid IGH genes following IMGT standards. Here we analyzed the IGHV, D, and J genes from the newly released genome of a second rainbow trout line (Arlee). We confirmed the validity of salmonid IGHV subgroups, and extended the description of the rainbow trout IGH gene repertoire with novel sequences, while keeping nomenclature continuity. This work provides an important resource for annotation of high-throughput Ab repertoire sequencing data.