Abstract
The access to whole genome sequences has provided the opportunity to study the evolution and organization of immunologically related genes on a large scale. The genes encoding the T cell receptor (TCR) α and δ chains are part of a complex locus that has shown remarkable conserved organization across different amniote lineages. In this study we have examined and annotated the TCRα/δ locus in chicken (Gallus gallus) and compared it to that of zebra finch (Taeniopygia guttata) and other avian species using the current available genome data. We also analyzed the expressed chicken TCRα/δ transcript repertoire and compared it with that previously described for zebra finch. The analyses conducted in this study show that the TCRα/δ locus in birds has undergone major rearrangements and expansion of the germ line repertoire in chicken, compared to zebra finch. A major expansion of the chicken variable gene repertoire appears to be driven by selection for genes from a limited number of subgroups.
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Acknowledgments
This article was made possible in part by support from a National Institutes of Health grant no. IP20RR18754 from the Institutional Development Award program and National Science Foundation award IOS-0641382.
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Supplementary Fig. 2
Alignment of predicted amino acid sequence of avian Vα/δ gene segments. Representative gene segments from the chicken and zebra finch were aligned by group to available sequences from turkey, duck, parrot, and grouse. a Vα1, b Vα2, c Vδ1, and d zebra finch Vδ2 and Vδ4. Conserved cysteine residues involved in intrachain disulfide bonds are highlighted in gray. Alignments were performed as in Fig. 2. Chromosome location: chicken: chr27: a 834130, 791237, 578060, 561959, 524524, 392324, 372896; b 827857, 559594, 445728, 731817, 454878, 469158; c 354411, 339894, 213690, 199617, 184349. Finch: chr27: a 3074837, 3074164, 3068198, 3063816; b 3078066, 3071571, 3065419; c 3054507, 3051702, 3047500; d 3049227, 3033533. GenBank accession numbers: turkey: a ADDD01150225, ADDD01152688; b XM003214154, ADDD01149483, ADDD01151410, ADDD01148254; c ADDD01147795, ADDD01052097. Duck: c AY446069, AY446070, AF323922. Grouse: GW705681. Parrot: a AGAI01024880, AGAI01025999; b AGAI01023412; c AGAI01044297a, AGAI01044297b, AGAI01011509, AGAI01045807, AGAI01030128 (PDF 110 kb)
Supplementary Table 1
GenBank accession numbers of sequences used in Fig. 2 (PDF 49 kb)