Atlantic cod scRNAseq Immune system

Atlantic Cod (Gadus morhua) has lost the entire set of major histocompatibility complex class II genes and the cd4 gene has become pseudogenised due to deletions and stop codons. Little is known about the potential implications and the immune adaptations triggered by the absence of CD4-positive T lymphocytes in cod. We have recently identified CD8-positive T cells, B cells, and plasma cells, but further characterization of lymphocyte subsets has yet to be elucidated. Here we use the significant power of single-cell RNA sequencing to examine the lymphocyte heterogeneity present more closely in Atlantic cod spleen. We describe seven TCR-positive T cell subsets and eight BCR-positive B cell subsets and propose their trajectories of differentiation. Notably, we identify a significant subpopulation of cod spleen T cells that are CD8-negative. The majority of CD8-negative T lymphocytes highly express the monocyte chemotactic protein 1, and another subset of CD8-negative T lymphocytes express the scavenger receptor cd163. Uncovering the multiple lymphocyte cell sub-clusters reveals the different immune states present within the B and T cell populations, building a foundation for further exploratory work.