All TRAV_TRDV phylogenetic tree

Neighbour-joining phylogenetic tree of all murine, human and bovine (from the UMD3.1 assembly) TRAV/TRDV genes. Analysis of the nucleotide sequence of the V-REGION (IMGT nomenclature) following pairwise deletion to remove gaps in the alignment. The final dataset included 400 positions. The sequence of bTRBV3a was used to root the tree. Based on a 1000 boot strap replicates the phylogenetically inferred orthologous TRAV/TRDV subgroups were supported by percentage bootstrap values (PB) of >90% in all cases except for bTRAV38 (PB= 83%), bTRAV5 (PB= 59%), bTRAV13 (PB= 85%) and bTRAV8 (PB= 68%). Sequence identity between bovine and human genes in orthologous groups ranged from 63.1-84.9%, sufficient to assign them as inter-species orthologues. Generally the phylogenetically defined bovine TRAV/TRDV subgroups adhered to the convention of members sharing >75% nucleotide identity. However, within both the bTRDV1 and bTRAV8 subgroups identity between some members was <75% (down to 68.0 and 69.7% respectively) and conversely the identity between some bTRAV5/13 and some bTRAVX/18 members was >75%. Due to difficulties in alignment the following genes were excluded from the analysis i) bovine genes for which only incomplete or partial genomic sequences were available, ii) bTRAV11a – due to the presence of a large insert and iii) mTRAV15-3, mTRAV15D-3, hTRAV8.5. h = human, b = bovine and m = murine.