From benchmarking alignment of genome assemblies to IMGT annotation: the paradigm of the bovine Bos taurus T cell receptor (TRG) locus

T cell receptors (TR) are essential components of the adaptive immune system, typically classified into αβ and γδ types. In humans and mice, αβ T cells predominate, with γδ T cells comprising only a small percentage of the total T cell population. γδ T cells are mainly distributed in peripheral tissues rather than lymphoid organs and have limited diversity. However, in ruminant species, the proportion of γδ T cells is significantly higher. To better understand bovine γδ 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 γδ T cell diversity and function, which may help explain the unique immunobiology of cattle.