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

Connelley TK, Degnan K, Longhi CW, Morrison WI

Date Published: December 9, 2014

DOI: http://dx.doi.org/10.5061/dryad.h8j92

 

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Title All TRAV_TRDV genes aligned
Downloaded 18 times
Description 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.
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Title All TRAV_TRDV phylogenetic tree
Downloaded 22 times
Description 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.
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Title All TRAJ genes aligned
Downloaded 5 times
Description 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.
Download All TRAJ genes aligned.mas (21.71 Kb)
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Title All TRAJ genes phylogenetic tree
Downloaded 20 times
Description 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%.
Download All TRAJ genes phylogenetic tree.pdf (14.35 Kb)
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Title Functional TRAV_TRDV genes aligned
Downloaded 2 times
Description 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.
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Title Functional TRAV_TRDV genes phylogenetic tree
Downloaded 9 times
Description 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.
Download Functional TRAV_TRDV genes phylogenetic tree.pdf (1.254 Mb)
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When using this data, please cite the original publication:

Connelley TK, Degnan K, Longhi CW, Morrison WI (2014) Genomic analysis offers insights into the evolution of the bovine TRA/TRD locus. BMC Genomics 15: 994. http://dx.doi.org/10.1186/1471-2164-15-994

Additionally, please cite the Dryad data package:

Connelley TK, Degnan K, Longhi CW, Morrison WI (2014) Data from: Genomic analysis offers insights into the evolution of the bovine TRA/TRD locus. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.h8j92
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