Annotation and comparative analysis of T cell receptor germline genes reveal lineage-specific patterns in pinnipeds

Adaptive immunity in jawed vertebrates relies on V(D)J recombination, yet the expansion-contraction dynamics of germline genes remain underexplored, especially in secondary aquatic mammals. We present the first systematic annotation of TRA/TRB germline genes in semi-aquatic carnivores-pinnipeds (Eumetopias jubatus, Zalophus californianus, Mirounga angustirostris, Neomonachus schauinslandi) and the sea otter (Enhydra lutris)-and compare them with terrestrial carnivores (represented by bears), artiodactyls, primates, rodents, reptiles, and ray-finned fishes. Pinnipeds harbor fewer TRBV genes and DJC clusters than terrestrial carnivores, whereas artiodactyls show pronounced TRBV expansions; phylogeny/synteny reveal recurrent TRBV5 proliferation in carnivorans. Structural modeling indicates highly conserved mammalian TRAC/TRBC, consistent with TCR-CD3 stabilization. Transcriptome-based repertoires show that, despite reduced germline copy number, pinnipeds maintain diversity comparable to water buffalo; expanded TRBV families dominate usage and contracted families are under-utilized. These findings support TRA conservation, TRB contraction, and pinnipeds maintain repertoire diversity despite reduced germline copy number.