Annotation and classification of the bovine T cell receptor delta genes

Background: gamma delta T cells differ from alpha beta T cells with regard to the types of antigen with which their T cell receptors interact; gamma delta T cell antigens are not necessarily peptides nor are they presented on MHC. Cattle are considered a "gamma delta T cell high" species indicating they have an increased proportion of gamma delta T cells in circulation relative to that in "gamma delta T cell low" species such as humans and mice. Prior to the onset of the studies described here, there was limited information regarding the genes that code for the T cell receptor delta chains of this gamma delta T cell high species. Results: By annotating the bovine (Bos taurus) genome Btau_3.1 assembly the presence of 56 distinct T cell receptor delta (TRD) variable (V) genes were found, 52 of which belong to the TRDV1 subgroup and were comingled with the T cell receptor alpha variable (TRAV) genes. In addition, two genes belonging to the TRDV2 subgroup and single TRDV3 and TRDV4 genes were found. We confirmed the presence of five diversity (D) genes, three junctional (J) genes and a single constant (C) gene and describe the organization of the TRD locus. The TRDV4 gene is found downstream of the C gene and in an inverted orientation of transcription, consistent with its orthologs in humans and mice. cDNA evidence was assessed to validate expression of the variable genes and showed that one to five D genes could be incorporated into a single transcript. Finally, we grouped the bovine and ovine TRDV1 genes into sets based on their relatedness. Conclusions: The bovine genome contains a large and diverse repertoire of TRD genes when compared to the genomes of "gamma delta T cell low" species. This suggests that in cattle gamma delta T cells play a more important role in immune function since they would be predicted to bind a greater variety of antigens.