Based on the latest assembly of the red jungle fowl (Gallus gallus) genome sequence, we characterized the detailed genomic organization of the T cell receptor beta (TCRβ) locus of chicken. The chicken TCRβ locus spans approximately 210 kb, and is organized in a typical translocon organization as previously reported. Within this locus, a total of 16 germline Vβ gene segments were classified into three subgroups, containing 11, four, and one members, respectively. Phylogenetic analysis revealed that the chicken Vβ3.1 segment was homologous with the duck Vβ1 subgroup, and further clustered with Vβ  segments from reptiles but not amphibians. We also identified nine protease serine 1 (PRSS1) and three protease serine 2 (PRSS2) genes, which were interspersed within the chicken TCRβ locus. Dot-plot analysis of the chicken TCRβ locus against itself revealed that the 5' part of the locus had arisen through a series of tandem duplication events. The homology units were composed of one Vβ1 segment followed by a PRSS1 gene, or one Vβ2 segment followed by a PRSS2 gene. This duplication pattern, in which the Vβ segments and trypsinogen genes form a duplication unit, was unique to TCRβ loci of chicken and duck, but not observed in TCRβ loci of other tetrapods studied thus far. By analyzing the cloned TCRβ cDNA sequences, we found that the usage pattern of Vβ segments was consistent with the results of previous studies. These studies showed that members of the Vβ1 subgroup are preferentially utilized in V-D-J recombination. Furthermore, we found that the Vβ3.1 segment participated into V-D-J recombination, but at a very low frequency. The length distribution of the chicken complementarity-determining region 3β (CDR3β) showed a tendency similar to that observed for the duck.

中文翻译：

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鸡TCRβ基因座的基因组组织起源于Vβ片段与胰蛋白酶原基因的重复复制。

基于红色丛林鸡（Gallus gallus）基因组序列的最新组装，我们表征了鸡T细胞受体β（TCRβ）基因座的详细基因组组织。鸡TCRβ基因座跨度约为210 kb，并且如先前报道的那样以典型的translocon组织进行组织。在该基因座中，总共16个种系Vβ基因片段被分为三个亚组，分别包含11个，4个和1个成员。系统发育分析表明，鸡的Vβ3.1区段与鸭的Vβ1亚群同源，并且进一步与来自爬行动物但不是两栖动物的Vβ区段聚集在一起。我们还确定了九个蛋白酶丝氨酸1（PRSS1）和三个蛋白酶丝氨酸2（PRSS2）基因，它们散布在鸡TCRβ基因座中。对鸡TCRβ基因座的点图分析表明，该基因座的5'部分是通过一系列串联复制事件产生的。同源单位由一个Vβ1片段后接PRSS1基因，或一个Vβ2片段后接PRSS2基因组成。Vβ片段和胰蛋白酶原基因形成一个复制单元的这种复制模式是鸡和鸭的TCRβ基因座所特有的，但迄今为止在其他四足动物的TCRβ基因座中未观察到。通过分析克隆的TCRβcDNA序列，我们发现Vβ片段的使用方式与先前的研究结果一致。这些研究表明，Vβ1亚组的成员在VDJ重组中被优先利用。此外，我们发现Vβ3.1片段以非常低的频率参与了VDJ重组。