Article Figures & Data
Figures
- FIGURE 1.
Graphic illustration of the comparisons between hybrid error-corrected TCR loci presented in this study against the TCR loci of chicken genome assembly (Galgal 4) and the corresponding BAC clone numbers.
(A) TCRα/TCRδ locus. (B) TCRβ locus. (C) TCRγ locus.
- FIGURE 2.
Genome map of the chicken TCRα/TCRδ locus.
TRAV (red), TRDV (yellow), TRAJ (light green), TRDJ (dark green), and TRDD (brown) gene segments are shown numbered by their corresponding location in order across the locus. TRAC (light blue) and TRDC (dark blue) are also indicated. TRAV segments are designated with a subgroup number followed by a period and a designated number according to their genomic location. Transcriptional orientation is indicated by the direction of the arrow on each gene segment. Arrows are not in proportion to the actual gene sizes. Interchangeably used V gene segments are indicated with a φ. Broken lines indicate the sequence gaps in the study, which is supplemented by the currently available Gallus gallus genome assembly (Galgal 4) accordingly. Syntenic and some unrelated genes are presented as gray boxes.
- FIGURE 3.
Phylogenetic tree of 54 chicken Vα and 61 Vα gene sequences from 2 cartilaginous fish, 6 bony fish, 2 amphibian, 15 mammalian, and 1 avian species.
The eight major phylogenetic clusters are bracketed. Chicken Vα sequences are indicated with the gene number assigned previously. The three-digit number following the Vα animal names are the last three digits of the GenBank accession number referenced in Supplemental Table III.
- FIGURE 4.
Phylogenetic tree of 31 chicken Vδ and 35 Vδ gene sequences from 2 cartilaginous fish, 6 bony fish, 2 amphibian, 15 mammalian, and 1 avian species.
The eight major phylogenetic clusters are bracketed. Chicken Vδ sequences are indicated with the gene number assigned previously. The three-digit number following the Vδ animal names are the last three digits of the GenBank accession number referenced in Supplemental Table III.
- FIGURE 5.
Annotated map of the chicken TCRβ locus showing the location of the Vβ (red), Dβ (orange), Jβ (green), and Cβ (blue).
Conserved syntenic genes are indicated in gray box.
- FIGURE 6.
Genomic organization of the chicken TCRβ Vβ gene segments.
The decamer (purple), Vβ coding region (light blue), and RSS (gray) are indicated. Genomic splice donors (GT) and acceptors (AG) are indicated, and intron sizes are indicated. Vβ2.4 is found approximately 5.2 kb downstream of the Cβ on the complementary strand in reverse orientation.
- FIGURE 7.
Phylogenetic tree of eight chicken Vβ and 54 Vβ gene sequences from 2 cartilaginous fish, 2 bony fish, 2 amphibian, 15 mammalian, and 1 avian species.
The eight major phylogenetic clusters are bracketed. Chicken Vβ sequences are indicated with the gene number assigned previously. The three-digit number following the Vβ animal names are the last three digits of the GenBank number referenced in Supplemental Table III.
- FIGURE 8.
Annotated map of the chicken TRG locus showing the location of the Vγ (red), Jγ (green), and Cγ (blue).
Conserved syntenic genes are indicated in the gray box.
- FIGURE 9.
Phylogenetic tree of 37 chicken Vγ and 52 Vγ gene sequences from 2 cartilaginous fish, 3 bony fish, 1 amphibian, 12 mammalian, and 1 avian species.
The seven major phylogenetic clusters are bracketed. Chicken TCRGV sequences are indicated with the gene number assigned previously. The three-digit number following the TCRBV animal names are the last three digits of the GenBank number referenced in Supplemental Table III.
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