A Comprehensive Analysis of the Genomic and Expressed Repertoire of the T-Cell Receptor Beta Chain in Equus caballus

In this paper, we report a comprehensive and consistent annotation of the locus encodingthe β-chain of the equine T-cell receptor (TRB), as inferred from recent genome assembly usingbioinformatics tools. The horse TRB locus spans approximately 1 Mb, making it the largest locusamong the mammalian species studied to date, with a signifi cantly higher number of genes related toextensive duplicative events. In the region, 136 TRBV (belonging to 29 subgroups), 2 TRBD, 13 TRBJ,and 2 TRBC genes, were identifi ed. The general genomic organization resembles that of othermammals, with a V cluster of 135 TRBV genes located upstream of two in-tandem aligned TRBD-J-Cclusters and an inverted TRBV gene at the 3′end of the last TRBC gene. However, the horse b-chainrepertoire would be affected by a high number of non-functional TRBV genes. Thus, we queried atranscriptomic dataset derived from splenic tissue of a healthy adult horse, using each TRBJ gene as aprobe to analyze clonotypes encompassing the V(D)J junction. This analysis provided insights intothe 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.