Zhou Hao, Jiko Chimari, Gerle Christoph, Lefranc Marie-Paule, Katoh Kazutaka, Standley Daron M
Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan.
Department of Systems Immunology, Immunology Frontier Research Center, Osaka University, Suita, Japan.
BMC Genomics. 2025 Sep 25;26(1):809. doi: 10.1186/s12864-025-12081-z.
T cell receptors (TR) are essential components of the adaptive immune system, typically classified into and types. In humans and mice, T cells predominate, with T cells comprising only a small percentage of the total T cell population. T cells are mainly distributed in peripheral tissues rather than lymphoid organs and have limited diversity. However, in ruminant species, the proportion of T cells is significantly higher. To better understand bovine T cells, comprehensive annotation of the bovine TRG locus is essential. Recent advancements in sequencing technologies have led to the availability of high-quality chromosome-level genomes, enabling more precise annotation of TR loci. In this study, by using the LAST alignment tool and comparative genomic analysis, we identified previously unannotated TRG genes in the bovine genome, including 1 novel TRGV gene, 11 novel TRGJ genes and 1 novel TRGC gene. We compared and integrated information from three different assemblies of the bovine genome to provide an updated annotation of the bovine TRG locus. Expression of one newly identified TRGJ gene was experimentally validated through next-generation sequencing. This study expands our knowledge of the bovine TRG locus and repertoire through improved TRG locus annotation and expression data, providing a more complete picture of bovine T cell diversity and function, which may help explain the unique immunobiology of cattle.
The online version contains supplementary material available at 10.1186/s12864-025-12081-z.
T细胞受体（TR）是适应性免疫系统的重要组成部分，通常分为αβ和γδ类型。在人类和小鼠中，αβ T细胞占主导，γδ T细胞仅占总T细胞群体的一小部分。γδ T细胞主要分布在外周组织而非淋巴器官，并且多样性有限。然而，在反刍动物物种中，γδ T细胞的比例显著更高。为了更好地了解牛γδ T细胞，对牛TRG基因座进行全面注释至关重要。测序技术的最新进展使得高质量的染色体水平基因组得以获取，从而能够更精确地注释TR基因座。在本研究中，通过使用LAST比对工具和比较基因组分析，我们在牛基因组中鉴定出先前未注释的TRG基因，包括1个新的TRGV基因、11个新的TRGJ基因和1个新的TRGC基因。我们比较并整合了来自牛基因组三个不同组装版本的信息，以提供牛TRG基因座的更新注释。通过下一代测序实验验证了一个新鉴定的TRGJ基因的表达。本研究通过改进TRG基因座注释和表达数据，扩展了我们对牛TRG基因座和库的认识，提供了更完整的牛γδ T细胞多样性和功能图景，这可能有助于解释牛独特的免疫生物学特性。
在线版本包含可在10.1186/s12864-025-12081-z获取的补充材料。
