Herzig et al. BMC Genomics 2010, 11:100 http://www.biomedcentral.com/1471-2164/11/100 Page 9 of 19 Figure 4 Phylogenetic tree of bovine TRDV genes. The Neighbor-Joining method [47] was used to classify TRDV genes using non-redundant bovine (bo) genomic TRDV sequences identified here and the previously classified ovine (ov), murine (mo) and human (hu) TRDV sequences (described in Methods). Bovine TRAV (GenBank accession number BC148926) was included in the analysis and was used to root the tree. The optimal tree with the sum of branch length = 5.37540770 is shown. Complete deletion to eliminate gaps was performed and the final dataset included a total of 207 positions. Eleven phylogenetic sets are indicated along with the percentage interior branch test value based on 1000 replicates for each set. sequences used in the comparisons (because few TRDD and TRDJ genes exist in the genomes of those species) there appeared to be conserved heptamer and nonamer sequences among the RS for all species evaluated. Although heptamers were found to vary, as expected, they all contained the 5’ CAC (or 3’ GTG for 5’D-RS and J’RS) consensus sequence which has been found to be critical for recombination [25]. Nonamers generally contained the previously reported consensus sequence ACAAAAACC [34] (or GGTTTTTGT for 5’D-RS and J’RS) although this was found to be less conserved. This is consistent with findings that the nonamer sequence requirements are less rigid than those for the heptamer sequence in order to obtain efficient recombination [25].