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Genomic analysis offers insights into the evolution of the bovine TRA/TRD locus.

Connelley TK, Degnan K, Longhi CW, Morrison WI - BMC Genomics (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian EH25 9RG, Scotland, UK. timothy.connelley@ed.ac.uk.

ABSTRACT

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.

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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.
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Fig2: 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.

Mentions: Neighbour-joining analysis resolved functional murine, human and bovine TRAV/TRDV genes into 4 monophylogenic groups (Figure 2). In mice and humans there is marked inter-species similarity in the distribution between these monophylogenic groups, with Groups 1, 2, 3 and 4 containing approximately 50%, 35%, 1% and 10% of the functional TRAV/TRDV genes respectively in both species (Figure 2B). In contrast, the distribution of functional genes in bovine is different with a relative contraction of Group 1 (34.4%) and expansion of Group 4 (30.7%); the latter due to the high number of TRDV1 genes. In contrast to mice and humans, in which the relative proportions of the 4 Groups within the total gene repertoires (Figure 2C) are similar to that observed in the functional repertoires, in bovine the representation of Group 1 is higher (42.3%) and that of Group 4 is lower (24.3%) in the total than in the functional repertoires. Thus, it is apparent that massive expansion of particular TRAV/TRDV subgroups (most prominently TRDV1) combined with the preferential retention of functionality in some of these subgroups act synergistically to cause a profound phylogenetic shift in the repertoire of functional TRAV/TRDV genes available for rearrangement of TRA/TRD chains.Figure 2


Genomic analysis offers insights into the evolution of the bovine TRA/TRD locus.

Connelley TK, Degnan K, Longhi CW, Morrison WI - BMC Genomics (2014)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4289303&req=5

Fig2: 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.
Mentions: Neighbour-joining analysis resolved functional murine, human and bovine TRAV/TRDV genes into 4 monophylogenic groups (Figure 2). In mice and humans there is marked inter-species similarity in the distribution between these monophylogenic groups, with Groups 1, 2, 3 and 4 containing approximately 50%, 35%, 1% and 10% of the functional TRAV/TRDV genes respectively in both species (Figure 2B). In contrast, the distribution of functional genes in bovine is different with a relative contraction of Group 1 (34.4%) and expansion of Group 4 (30.7%); the latter due to the high number of TRDV1 genes. In contrast to mice and humans, in which the relative proportions of the 4 Groups within the total gene repertoires (Figure 2C) are similar to that observed in the functional repertoires, in bovine the representation of Group 1 is higher (42.3%) and that of Group 4 is lower (24.3%) in the total than in the functional repertoires. Thus, it is apparent that massive expansion of particular TRAV/TRDV subgroups (most prominently TRDV1) combined with the preferential retention of functionality in some of these subgroups act synergistically to cause a profound phylogenetic shift in the repertoire of functional TRAV/TRDV genes available for rearrangement of TRA/TRD chains.Figure 2

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian EH25 9RG, Scotland, UK. timothy.connelley@ed.ac.uk.

ABSTRACT

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.

Show MeSH