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

Susana Magadan (1) , Stanislas Mondot (2) , Yniv Palti (3) , Guangtu Gao (3) , Marie Paule Lefranc (4) , Pierre Boudinot (5)

1 Universidade de Vigo
2 MICALIS - MICrobiologie de l'ALImentation au Service de la Santé
3 National Center for Cool and Cold Water Aquaculture, ARS-USDA
4 IGH - Institut de génétique humaine
5 VIM (UR 0892) - Virologie et Immunologie Moléculaires

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.

Mots clés: IMGT; Immune repertoires; Immunoglobulin; Rainbow trout; Salmonids

Domaines: Immunologie

Susana Magadan, Stanislas Mondot, Yniv Palti, Guangtu Gao, Marie Paule Lefranc, et al.. Genomic analysis of a second rainbow trout line (Arlee) leads to an extended description of the IGH VDJ gene repertoire. Developmental and Comparative Immunology, 2021, 118, pp.103998. ⟨10.1016/j.dci.2021.103998⟩. ⟨hal-03230900⟩