Characterization of T-cell receptor loci and expressed repertoire reveals a capacity for robust T-cell response in Atlantic cod (Gadus morhua)

The Atlantic cod presents a peculiar case in fish immunology, due to the loss of MHCII and CD4 genes. Despite the absent antibody response to T cell-dependent antigens, it is a prolific species. Characterization of T-cell receptor loci and the expressed repertoire is necessary to further our understanding of how the Atlantic cod can mount an effective immune response and to characterize its immune system on the molecular level. A comprehensive annotation of the Atlantic cod genome (gadmor3.0) revealed all four chains of T-cell receptors, residing on chromosomes 5 and 8. Moderate germline diversity was observed with signs of recent expansion in the triplicate TRB locus. Sequencing of the expressed repertoire showed a surprisingly high repertoire diversity for TRA, TRB and TRD chains. Only small fractions of the repertoires were public with further untapped diversity available through differential gene usage especially for TRA and TRD chains. Our study revealed that despite its modest genomic T-cell receptor sequence diversity, the Atlantic cod maintains a diverse, mostly private expressed repertoire. This work provides a baseline for comparative studies and investigations of TR repertoire changes during vaccination and infection experiments.