Herzig et al. BMC Genomics 2010, 11:100 http://www.biomedcentral.com/1471-2164/11/100 R E S E A R C H A R T I C L E Open Access Annotation and classification of the bovine T cell receptor delta genes Carolyn TA Herzig1,4*, Marie-Paule Lefranc2, Cynthia L Baldwin1,3 Abstract Background: gδ T cells differ from ab T cells with regard to the types of antigen with which their T cell receptors interact; gδ T cell antigens are not necessarily peptides nor are they presented on MHC. Cattle are considered a “gδ T cell high” species indicating they have an increased proportion of gδ T cells in circulation relative to that in “gδ 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 gδ 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 co- mingled 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 “gδ T cell low” species. This suggests that in cattle gδ T cells play a more important role in immune function since they would be predicted to bind a greater variety of antigens. Background T lymphocytes can be subdivided into at least two types based on the expression of either the ab or gδ T cell receptor. Although both perceive antigen, they differ in the types of antigens with which they react. ab T cell receptors react with antigenic protein peptides in the context of self major histocompatibility complex (MHC) proteins while gδ T cell receptors may react with pro- teins but this does not involve MHC presentation. They also react with autologous molecules on cells [1-6] as well as nonproteinaceous molecules [7]. The gene reper- toires that code for the gδ T cell receptor chains and the T cell receptor gamma (TRG) and delta (TRD) gene locus organizations have been extensively described for humans and mice but to a lesser extent for the artiodac- tyls which includes ruminants and swine. These latter * Correspondence: cth2115@columbia.edu 1Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA 01003, USA are “gδ T cell high” species because of their high levels of gδ T cells in circulation ("gδ T cell low” species exhi- bit much lower levels of gδ T cells in circulation). It is clear that while both ab and gδ T cells have large and diverse T cell receptor gene repertoires [8-14], “gδ T cell high” species have a TRD gene repertoire that is much more extensive than that in the “gδ T cell low” species [15-21]. The bovine (Bos taurus) locus organization and TRD gene repertoire are the subject of this work. T cell receptor delta and beta chains are encoded by the rearrangement of variable (V), joining (J) and diver- sity (D) genes making them more complex than the T cell receptor gamma and alpha chains which lack D gene products. In all mammals evaluated the genes encoding the T cell receptor beta and gamma chains are found at the T cell receptor beta (TRB) and TRG loci, respectively. The genes that encode the T cell receptor delta and alpha chains are found at a single chromoso- mal location with the TRD genes embedded within the © 2010 Herzig et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.