As one of “γδ-high” species, chicken is an excellent model for the study of γδ T cells in non-mammalian animals. However, a comprehensive characterization of the TCRγδ repertoire is still missing in chicken. The objective of this study was to characterize the expressed TCRγ repertoire in chicken thymus using high-throughput sequencing. In this study, we first obtained the detailed genomic organization of the TCRγ locus of chicken based on the latest assembly of the red jungle fowl genome sequences (GRCg6a) and then characterized the TCRγ repertoire in the thymus of four chickens by using 5′ Rapid Amplification of cDNA Ends (5′ RACE) along with high-throughput sequencing (HTS). The chicken TCRγ locus contains a single Cγ gene, three functional Jγ segments and 44 Vγ segments that could be classified into six subgroups, each containing six, nineteen, nine, four, three and three members. Dot-plot analysis of the chicken TCRγ locus against itself showed that almost all the entire zone containing Vγ segments had arisen through tandem duplication events, and the main homology unit, containing 9 or 10 Vγ gene segments, has tandemly duplicated for four times. For the analysis of chicken TCRγ repertoire, more than 100,000 unique Vγ-region nucleotide sequences were obtained from the thymus of each chicken. After alignment to the germline Vγ and Jγ segments identified above, we found that the four chickens had similar repertoire profile of TCRγ. In brief, four Vγ segments (including Vγ3.7, Vγ2.13, Vγ1.6 and Vγ1.3) and six Vγ-Jγ pairs (including Vγ3.7-Jγ3, Vγ2.13-Jγ1, Vγ2.13-Jγ3, Vγ1.6-Jγ3, Vγ3.7-Jγ1 and Vγ1.6-Jγ1) were preferentially utilized by all four individuals, and vast majority of the unique CDR3γ 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 CDR3γ of human, mice and other animal species. In this study, we present the first in-depth characterization of the TCRγ repertoire in chicken thymus. We believe that these data will facilitate the studies of adaptive immunology in birds.

中文翻译：

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通过高通量测序表征鸡 T 细胞受体 γ 库

作为“γδ高”物种之一，鸡是研究非哺乳动物γδT细胞的绝佳模型。然而，在鸡中仍然缺少对 TCRγδ 谱的全面表征。本研究的目的是使用高通量测序表征鸡胸腺中表达的 TCRγ 库。在这项研究中，我们首先根据最新组装的红原鸡基因组序列 (GRCg6a) 获得了鸡 TCRγ 基因座的详细基因组组织，然后使用 5' 快速扩增技术表征了四只鸡胸腺中的 TCRγ 库cDNA 末端 (5' RACE) 以及高通量测序 (HTS)。鸡 TCRγ 基因座包含一个 Cγ 基因、三个功能性 Jγ 片段和 44 个 Vγ 片段，可分为六个亚组，每个亚组包含 6、19、九、四、三、三名成员。对鸡 TCRγ 基因座对其自身的点阵分析表明，几乎所有包含 Vγ 片段的区域都是通过串联复制事件产生的，并且主要同源单元，包含 9 或 10 个 Vγ 基因片段，已经串联复制了 4 次。为了分析鸡的 TCRγ 库，从每只鸡的胸腺中获得了超过 100,000 个独特的 Vγ 区核苷酸序列。在与上述确定的种系 Vγ 和 Jγ 片段对齐后，我们发现四只鸡具有相似的 TCRγ 谱。简而言之，四个Vγ片段（包括Vγ3.7、Vγ2.13、Vγ1.6和Vγ1.3）和六个Vγ-Jγ对（包括Vγ3.7-Jγ3、Vγ2.13-Jγ1、Vγ2.13-Jγ3、 Vγ1.6-Jγ3、Vγ3.7-Jγ1 和 Vγ1.6-Jγ1) 被所有四个个体优先利用，绝大多数独特的 CDR3γ 序列编码 4 到 22 个氨基酸，平均 12.90 个氨基酸，与人类、小鼠和其他动物物种的 CDR3γ 相比，其显示出更宽的长度分布和/或更长的平均长度。在这项研究中，我们首次对鸡胸腺中的 TCRγ 库进行了深入表征。我们相信这些数据将有助于鸟类适应性免疫学的研究。