Herzig et al. BMC Genomics 2010, 11:100 http://www.biomedcentral.com/1471-2164/11/100 has been reported [17] but the ability of TRDV or TRAV genes (as defined based on sequence character- istics) to rearrange with either TRDD or TRAJ must be determined experimentally and will be evaluated in future studies. Evaluation of the genes contained within the TRA/TRD locus was reported [22] following the initial submission of this work with overall findings similar to those discussed here. The question remains as to whether or not the find- ings reported here represent the complete TRD gene repertoire because of the gaps in the Btau_3.1 assembly. The presence of additional TRDV1 genes is almost cer- tain because of extensive gaps in this region although it is unlikely that additional TRDD or TRDJ genes are pre- sent in the genome since that region is fully scaffolded and has been carefully evaluated for the presence of additional genes. That region also contains TRDV4 and its analysis is likely definitive. In addition, previous cDNA evidence supports the existence of only two TRDV2 genes [17] and is consistent with our findings. The existence of two TRDV3 genes has been reported [20] but is not supported by our findings which may be due to gaps in the genome assembly. Even with gaps, locus organization can be assisted by comparison to other species. Indeed, all mammals studied have genes that are closely related to human TRDV1 with some being distributed among the TRAV genes. The bovine TRDV4 gene is located downstream of the single TRDC gene in inverse orientation, as found for the human TRDV3 and mouse TRDV5 genes. It is notable that there is significant sequence conservation among the orthologous bovine TRDV4, human TRDV3, mouse TRDV5 and ovine TRDV4 genes as well as their entire RS. This suggests that they derive from a common ancestral gene that appeared before the separation of these species. By comparison, there are no human or mouse genes that are equivalent to bovine TRDV2 or TRDV3. The enormous expansion of the TRDV1 reper- toire that has been observed for cattle, sheep and pig [15,21] is striking when compared with the single TRDV1 gene found in human (and its two orthologs in mouse) and thus does not assist us in predicting the extent of the possible missing information. TRDV1 gene subgroup expansion is also striking when compared with other TRDV gene subgroups which, even in artiodactyls, are found to contain only one or two members. While the number of TRGV genes found in each species does not vary considerably [31,35,36], expansion of the TRDV1 genes in bovine, sheep and pig is consistent with them being “gδ T cell high” species, implying that this increase in antigen receptor diversity permits them to be stimulated by and to respond to more types of antigens. The presence of fewer TRDV genes in “gδ T cell low” species, such as humans and Page 15 of 19 mice, suggests that these species evolved so that gδ T cells play a less important role in their immune func- tion. Sequence conservation among bovine TRDV1 RS (including the 23-bp spacer sequences), supports the concept that the large TRDV1 subgroup arose from multiple duplication events. Many bovine TRDV1 genes share high percent identities, indicating that in some cases this subgroup is not as diverse as the number of individual genes might suggest. For example, some TRDV1 sequences differed by as few as four (TRDV1m and TRDV1s), three (TRDV1v and TRDV1as) or even one (TRDV1aa and TRDV1bn) nucleotide in their cod- ing regions even though all were determined to be dis- tinct genes based on analysis of the flanking genomic sequences. However, it cannot be ruled out that some of these gene models represent the same gene but do not appear as such due to sequencing and/or assembly anomalies. The question of why numerous and highly similar TRDV1 genes have been maintained in the bovine genome is compelling and studies to evaluate their functions will be pursued. Based on phylogenetic sequence analysis and gene fea- tures, we subdivided the bovine TRDV1 genes into ele- ven sets. Each set corresponds to intraspecies gene duplications of ancestral genes that were present before the separation between bovine and ovine species. We also assigned bovine cDNA sequences to germline genes identified in this work (see Table 5). Of 55 previously identified TRDV1 cDNA sequences evaluated, 20 could not be assigned to a germline gene, possibly because of gaps in that region of the genome assembly. Of the 52 TRDV1 genes identified in this study, cDNA evidence existed for only 16. It is possible that, because a majority of the previously identified TRDV1 cDNA sequences were derived from peripheral blood mononuclear cells [16-20], the remaining TRDV1 genes that lack cDNA verification might be expressed in other tissues that have not been evaluated. It is also possible that other factors, such as age or immunological experience, might impact the expression of particular genes and thus pre- vented verification of those genes. Future studies will focus on specifically amplifying individual TRDV1 tran- scripts in order to verify that they are functional and to determine whether they are expressed in an age and/or tissue dependent manner. The potential importance of the role of the T cell receptor delta rearranged CDR3 is evident instudies evaluating the binding of the T10 and T22 antigens [26,37,38] by murine gδ T cells since antigen recognition by the CDR3 was found to be autonomous, that is, not dependent on the TRDV gene associated with it [39]. It could be reasoned that, because the genomes of humans and mice lack the extensive TRDV repertoirethat has been observed in artiodactyls, thiswould be compensated