Antonacci Rachele, Giannico Francesco, Moschetti Roberta, Pala Angela, Jambrenghi Anna Caputi, Massari Serafina
Department of Biosciences, Biotechnologies and Environment, University of Bari "Aldo Moro", 70125 Bari, Italy.
Department of Veterinary Medicine, University of Bari "Aldo Moro", 70010 Bari, Italy.
Animals (Basel). 2024 Sep 29;14(19):2817. doi: 10.3390/ani14192817.
In this paper, we report a comprehensive and consistent annotation of the locus encoding the β-chain of the equine T-cell receptor (TRB), as inferred from recent genome assembly using bioinformatics tools. The horse TRB locus spans approximately 1 Mb, making it the largest locus among the mammalian species studied to date, with a significantly higher number of genes related to extensive duplicative events. In the region, 136 TRBV (belonging to 29 subgroups), 2 TRBD, 13 TRBJ, and 2 TRBC genes, were identified. The general genomic organization resembles that of other mammals, with a V cluster of 135 TRBV genes located upstream of two in-tandem aligned TRBD-J-C clusters and an inverted TRBV gene at the 3' end of the last TRBC gene. However, the horse b-chain repertoire would be affected by a high number of non-functional TRBV genes. Thus, we queried a transcriptomic dataset derived from splenic tissue of a healthy adult horse, using each TRBJ gene as a probe to analyze clonotypes encompassing the V(D)J junction. This analysis provided insights into the usage of the TRBV, TRBD, and TRBJ genes and the variability of the non-germline-encoded CDR3. Our results clearly demonstrated that the horse β-chain constitutes a complex level of variability, broadly like that described in other mammalian species.
在本文中，我们报告了对马T细胞受体（TRB）β链编码基因座的全面且一致的注释，该注释是通过使用生物信息学工具从最近的基因组组装中推断出来的。马的TRB基因座跨度约为1 Mb，使其成为迄今为止研究的哺乳动物物种中最大的基因座，与广泛的重复事件相关的基因数量显著更多。在该区域，鉴定出了136个TRBV（属于29个亚组）、2个TRBD、13个TRBJ和2个TRBC基因。其总体基因组组织与其他哺乳动物相似，135个TRBV基因的V簇位于两个串联排列的TRBD-J-C簇的上游，且在最后一个TRBC基因的3'端有一个反向的TRBV基因。然而，马的β链库会受到大量无功能TRBV基因的影响。因此，我们使用每个TRBJ基因作为探针，查询了来自一匹健康成年马脾脏组织的转录组数据集，以分析包含V(D)J连接的克隆型。该分析为TRBV、TRBD和TRBJ基因的使用情况以及非种系编码的CDR3的变异性提供了见解。我们的结果清楚地表明，马的β链构成了一个复杂的变异水平，大致与其他哺乳动物物种中描述的情况相似。
