Data from: Genomic analysis offers insights into the evolution of the bovine TRA/TRD locus

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.