Genomic analysis of a second rainbow trout line (Arlee) leads to an extended description of the IGH VDJ gene repertoire. (May 2021)

• Record Type: Journal Article
• Authors: Magadan, Susana; Mondot, Stanislas; Palti, Yniv; Gao, Guangtu; Lefranc, Marie Paule; Boudinot, Pierre
• Is Part Of: Developmental and comparative immunology. Volume 118(2021)
• Publication Date: 2021-05
• Subjects: IMGT -- Immunoglobulin -- Immune repertoires -- Salmonids -- Rainbow trout; Immunology -- Periodicals; Developmental immunology -- Periodicals; 616.079
• DOI: 10.1016/j.dci.2021.103998
• Languages: English
• ISSNs: 0145-305X

Abstract

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. Highlights: We provide a complete annotation of the IGH VDH genes of the rainbow trout line « Arlee ». IGH annotation of lines Swanson and Arlee provides a quasi full description of the functional IGH VDJ genes repertoires. The standardized nomenclature of salmonid IGH VDJ genes is a resource for Ab repertoire analysis.