Data Sheet 1_Annotation and comparative analysis of T cell receptor germline genes reveal lineage-specific patterns in pinnipeds.docx

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.