Figure 6

TRDJ gene sequence alignments and phylogenetic tree. Alignments of TRDJ gene (A) nucleotide and (B) deduced amino acid sequences, using bovine (bo) genomic TRDJ sequences identified here and previously classified ovine (ov), swine (sw), human (hu) and murine (mo) TRDJ sequences (described in Methods) are shown with identities indicated by a dot (.) and gaps indicated by a dash (-). The Neighbor-Joining method [47] was used to infer evolutionary history of the above mentioned sequences. The optimal tree (C) with the sum of branch length = 2.43145392 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches [48]. The Maximum Composite Likelihood method [49] was used to compute evolutionary distances. Complete deletion to eliminate gaps was performed and the final dataset included a total of 42 positions.