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Research Project: Integrated Research Approaches for Improving Production Efficiency in Rainbow Trout

Location: Cool and Cold Water Aquaculture Research

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

item MAGADAN, SUSANA - University Of Vigo
item MONDOT, STANISLAS - Institut National De La Recherche Agronomique (INRA)
item Palti, Yniv
item Gao, Guangtu
item LEFRANC, MARIE PAULE - University Of Montpellier
item BOUDINOT, PIERRE - Institut National De La Recherche Agronomique (INRA)

Submitted to: Developmental and Comparative Immunology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/7/2021
Publication Date: 5/1/2021
Citation: Magadan, S., Mondot, S., Palti, Y., Gao, G., Lefranc, M., Boudinot, P. 2021. Genomic analysis of a second rainbow trout line (Arlee) leads to an extended description of the IGH VDJ gene repertoire. Developmental and Comparative Immunology. 118: 103998.

Interpretive Summary: Immunoglobulins (IG) – also known as antibodies - are the antigen specific receptors expressed by B cells in the blood of all vertebrates and are a key component in the adaptive, or learned, specific immune response. Complete sequences and maps of the genome are crucial for cataloging and characterization of the complex repertoire of IG genes in all animals, and specifically in fish. This in turn allows for better design of studies and better understanding of the host-pathogen interactions and the development of more effective vaccines and other drugs and therapeutics for pathogenic diseases. In the current study reported in this article the new whole-genome sequence of a distinct rainbow trout genetic line known as the 'Arlee line' was used to improve the genome mapping and to generate an improved catalog of the IG genes repertoire in rainbow trout.

Technical Abstract: 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.