Characterization of the chicken T cell receptor γ repertoire by high-throughput sequencing

Background: As one of gamma delta-high species, chicken is an excellent model for the study of gamma delta T cells in non-mammalian animals. However, a comprehensive characterization of the TCR gamma delta repertoire is still missing in chicken. The objective of this study was to characterize the expressed TCR gamma repertoire in chicken thymus using high-throughput sequencing. Methods: In this study, we first obtained the detailed genomic organization of the TCR gamma locus of chicken based on the latest assembly of the red jungle fowl genome sequences (GRCg6a) and then characterized the TCR gamma repertoire in the thymus of four chickens by using 5' Rapid Amplification of cDNA Ends (5' RACE) along with high-throughput sequencing (HTS). Results: The chicken TCR gamma locus contains a single C gamma gene, three functional J gamma segments and 44 V gamma segments that could be classified into six subgroups, each containing six, nineteen, nine, four, three and three members. Dot-plot analysis of the chicken TCR gamma locus against itself showed that almost all the entire zone containing V gamma segments had arisen through tandem duplication events, and the main homology unit, containing 9 or 10 V gamma gene segments, has tandemly duplicated for four times. For the analysis of chicken TCR gamma repertoire, more than 100,000 unique V gamma-region nucleotide sequences were obtained from the thymus of each chicken. After alignment to the germline V gamma and J gamma segments identified above, we found that the four chickens had similar repertoire profile of TCR gamma. In brief, four V gamma segments (including V gamma 3.7, V gamma 2.13, V gamma 1.6 and V gamma 1.3) and six V gamma-J gamma pairs (including V gamma 3.7-J gamma 3, V gamma 2.13-J gamma 1, V gamma 2.13-J gamma 3, V gamma 1.6-J gamma 3, V gamma 3.7-J gamma 1 and V gamma 1.6-J gamma 1) were preferentially utilized by all four individuals, and vast majority of the unique CDR3 gamma sequences encoded 4 to 22 amino acids with mean 12.90 amino acids, which exhibits a wider length distribution and/or a longer mean length than CDR3 gamma of human, mice and other animal species. Conclusions: In this study, we present the first in-depth characterization of the TCR gamma repertoire in chicken thymus. We believe that these data will facilitate the studies of adaptive immunology in birds.

Automated summary

This study provides the first comprehensive characterization of the TCR gamma repertoire in chicken thymus, revealing similar features among the four chickens analyzed. Specific V gamma segments and V gamma-J gamma pairs were preferentially utilized by all individuals, and the CDR3 gamma sequences encoded a wider length distribution with a longer mean length compared to human, mice, and other animal species.