DOI: 10.5061/dryad.h8j92
title: Data from: Genomic analysis offers insights into the evolution of the bovine TRA/TRD locus

description: 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.
description: All TRAV_TRDV genes
 alignedAlignment 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 treeNeighbour-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 &gt;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 &gt;75%
 nucleotide identity. However, within both the bTRDV1 and bTRAV8 subgroups
 identity between some members was &lt;75% (down to 68.0 and 69.7%
 respectively) and conversely the identity between some bTRAV5/13 and some
 bTRAVX/18 members was &gt;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
 alignedAlignment 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 treeNeighbour-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 &gt;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 &lt;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 alignedAlignment 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 treePhylogenetic 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 &gt;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.