Résumé
The advances in high throughput sequencing (HTS), and the availability of improved versions of genome assemblies, open new avenues to characterize the adaptive immune responses in vertebrates through the adaptive immune receptor repertoire sequencing (AIRRseq). However, establishing a comprehensive and coherent immunoglobulin (IG) and T cell receptor (TR) loci description and nomenclature is a fundamental prerequisite for accurate annotation of repertoire sequencing datasets. In some species, such as those belonging to Salmonids, it is especially challenging due to the presence of really complex loci. Based on recent high-quality assemblies of rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) genomes, we performed a thorough annotation of IG genes (immunoglobulin, IGH loci) and TR genes (T cell receptor, TRA/D and TRB loci) genes. We established a consistent and standardized IMGT-based nomenclature of IGH, TRA/D and TRB loci which allows accurate annotation and analysis of high-throughput sequencing B and T cell repertoire data, across salmonid species. We paid a particular attention to define a nomenclature that is possible to update and adapt to new assemblies of other strains or species within Salmonids. We believe that such nomenclature will facilitate evolutionary studies of IG/TR and comparison of AIRRseq data across salmonid species and strains, avoiding multiple and conflicting nomenclature issues. Furthermore, we hope these results encourage similar procedures in other vertebrate groups for a better understanding of adaptive immune response.