Characterization of the Cattle TCR β CDR3 Repertoire and Gene Rearrangement Bias Influenced by Recombination Signal Sequences and Physical Distance

Cattle exhibit distinct immune system features, including ultra-long IGH CDR3 regions, which are characteristic of their adaptive immunity. However, less is known about the diversity and functional aspects of their T cell receptor (TCR) β chain complementarity-determining region 3 (CDR3) repertoire. This study aimed to investigate the features of the TCR β chain CDR3 repertoire in cattle using high throughput sequencing. The spleen tissue samples were collected from cattle, and the TCR β CDR3 repertoires were constructed using high-throughput sequencing. Key attributes analyzed included CDR3 length distribution, V and J gene usage, sequence diversity, and specific amino acid enrichment. The analysis also incorporated the impact of recombination signal sequences (RSS) quality and the physical distance on the rearrangement of germline genes. Frequently utilized V and J genes included TRBV7, TRBV6, TRBV14, TRBV21, TRBV29, TRBV5, TRBJ2-2, and TRBJ1-2. A bias in TRBV gene rearrangement was identified, influenced by RSS quality, where genes with RSS information content (RIC) scores below -45 showed reduced rearrangement frequency. The CDR3 length distribution displayed a bell-shaped curve, with a preference for the amino acids serine (S), glycine (G), and alanine (A). Compared to humans and mice, cattle exhibited lower diversity in their TCR β CDR3 repertoire and a higher proportion of dominant clones. This study provides insights into the TCR β CDR3 repertoire in cattle, enhancing our understanding of the species' adaptive immune system. These findings offer valuable insights for future research on the immune repertoire in cattle.