Background: The TRA/TRD locus contains the genes for V(D)J somatic rearrangement of TRA and TRD chains expressed by αβ and γδ T cells respectively. Previous studies have demonstrated that the bovine TRA/TRD locus contains an exceptionally large number of TRAV/TRDV genes. In this study we combine genomic and transcript analysis to provide insights into the evolutionary development of the bovine TRA/TRD locus and the remarkable TRAV/TRDV gene repertoire. Results: Annotation of the UMD3.1 assembly identified 371 TRAV/TRDV genes (distributed in 42 subgroups), 3 TRDJ, 6 TRDD, 62 TRAJ and single TRAC and TRDC genes, most of which were located within a 3.5 Mb region of chromosome 10. Most of the TRAV/TRDV subgroups have multiple members and several have undergone dramatic expansion, most notably TRDV1 (60 genes). Wide variation in the proportion of pseudogenes within individual subgroups, suggest that differential ‘birth’ and ‘death’ rates have been used to form a functional bovine TRAV/TRDV repertoire which is phylogenetically distinct from that of humans and mice. The expansion of the bovine TRAV/TRDV gene repertoire has predominantly been achieved through a complex series of homology unit (regions of DNA containing multiple gene) replications. Frequent co-localisation within homology units of genes from subgroups with low and high pseudogene proportions suggest that replication of homology units driven by evolutionary selection for the former may have led to a ‘collateral’ expansion of the latter. Transcript analysis was used to define the TRAV/TRDV subgroups available for recombination of TRA and TRD chains and demonstrated preferential usage of different subgroups by the expressed TRA and TRD repertoires, indicating that TRA and TRD selection have had distinct impacts on the evolution of the TRAV/TRDV repertoire. Conclusion: Both TRA and TRD selection have contributed to the evolution of the bovine TRAV/TRDV repertoire. However, our data suggest that due to homology unit duplication TRD selection for TRDV1 subgroup expansion may have substantially contributed to the genomic expansion of several TRAV subgroups. Such data demonstrate how integration of genomic and transcript data can provide a more nuanced appreciation of the evolutionary dynamics that have led to the dramatically expanded bovine TRAV/TRDV repertoire.
All TRAV_TRDV genes aligned
Alignment of the nucleotide sequence of the V-REGION (IMGT nomenclature) of all human, murine and bovine TRAV/TRDV genes following pairwise deletion to remove gaps. The alignment was performed using MEGA5 software (http://megasoftware.net/). The final dataset included 400 positions. The sequence of bTRBV3a was used to root the tree.
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.
All TRAJ genes aligned
Alignment of the nucleotide sequence of the coding domain of all human, murine and bovine TRAJ genes following pairwise deletion to remove gaps in the alignment. The alignment was performed using MEGA5 software (http://megasoftware.net/). The final dataset had a total of 85 positions.
All TRAJ genes phylogenetic tree
Neighbour-joining phylogenetic tree of all murine, human and bovine (from the UMD3.1 assembly) TRAJ genes. Analysis of the nucleotide sequence of the coding domain of TRAJ genes following pairwise deletion to remove gaps in the alignment. The final dataset had a total of 85 positions. Based on a 1000 boot strap replicates the orthologous TRAJ genes from mouse, human and cattle (where all genes were functional) formed phylogenetic groups supported by percentage bootstrap values (PB) of >75% (with the exception of TRAJ6 (PB = 54%), 9 (53%) and 48 (67%)). PB values supporting the phylogenetic groups of TRAJ orthologues which included non-functional members were generally high but in several cases were <50%. h = human, b = bovine and m = murine. The formation of ‘triads’ composed of single genes from each species (except TRAJ10 which lacks a murine gene and TRAJ8 which contains 2 bovine genes) that have the same relative position in the genome (as denoted by their numerical designation) demonstrates conserved synteny. The level of nucleotide identity between orthologous bovine and human TRAJ genes ranges from 63.2% to 95.2%.
Functional TRAV_TRDV genes aligned
Alignment of the nucleotide sequence of the V-REGION (IMGT nomenclature) of human, murine and bovine TRAV/TRDV genes that are predicted by in silico sequence analysis to be functional, following pairwise deletion to remove gaps. The alignment was performed using MEGA5 software (http://megasoftware.net/). The final dataset included 340 positions. The sequence of bTRBV3a was used to root the tree.
Functional TRAV_TRDV genes phylogenetic tree
Phylogenetic analysis of the repertoires of functional TRAV/TRDV genes in mice, humans and cattle. A - Neighbour-joining phylogenetic tree of all functional 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 340 positions. The sequence of bTRBV3a was used to root the tree. Based on 1000 boot strap replicates support for Groups 1 (purple), 3 (green) and 4 (red) was high with PB >97%. Support for Group 2 (blue) was low (PB= 13%) but examination of the data using UPMGA and minimum evolution models generated the same phylogenic groups, suggesting it was reliable (data not shown). h = human, b = bovine and m = murine. Percentage of the functional (B) and total (C) TRAV/TRDV genes in humans, mice and cattle in the 4 phylogenetic Groups defined from neighbour-joining analysis.
