Genomic structure of the whole D–J–C clusters and the upstream region coding V segments of the TRB locus in pig

In the vertebrate immune system, T cells play a central role in host defense against microbial or viral infection. Previous studies suggested that at least two sets of TRBD–J–C clusters are harbored in the porcine genome. In this study, we determined 212,193 bp of a continuous porcine genomic sequence covering the entire TRBC region. EPHB6, TRPV6, TRY, and ten TRBV genes were conserved in the vicinity of the TRBD–J–C clusters. Interestingly, three TRBD–J–C clusters were identified in this sequence; each TRBD–J–C cluster consisted of one TRBD and seven TRBJ segments, with one TRBC region composed of four exons. The distribution of repetitive sequences and phylogenetic analysis indicated that the TRBD–J–C cluster, located at the center of the three clusters identified, had a structure combined with the others. Most of the TRBJ segments were available in public databases, suggesting that all three TRBD–J–C clusters are functional in pigs.