Exploration of the differential expression patterns of immunoglobulin heavy chain genes in horses and donkeys

This study investigated the immunoglobulins (IG) gene locus structure and expression diversity in local Chinese horse and donkey breeds, including Ningqiang, Guanzhong horses, and varieties such as Guanzhong, Jiami, and Northern Shaanxi donkey using genome alignment and high-throughput sequencing. The aim was to expand understanding of IG expression patterns in horses, donkeys, and their different breeds. The results revealed that the donkey IGH locus contains 117 VH genes (23 functional), 44 DH genes, and 8 JH genes, arranged in a VH-DH-JH sequence on chromosome 7, spanning approximately 1189 kb. Both horses and donkeys exhibited high frequencies of the IGHV4-IGHD2-IGHJ6, IGHV4-IGHD4-IGHJ6, and IGHV4-IGHD2-IGHJ4 combinations during VDJ recombination. Significant differences in V, D, and J junctions between horses and donkeys, as well as among breeds, were observed, mainly due to variations in N-nucleotide insertion length. The CDR3H region in horses exhibited greater length diversity and a higher Cys content than that in donkeys, which may contribute to species-specific differences in IGH spatial structure. Both horses and donkeys showed a clear preference for A > G and G > A mutations during somatic hypermutation (SHM), with consistent trends across breeds and species. In conclusion, this study reveals that V(D)J recombination, junction diversity, and SHM are key mechanisms driving IGH diversity in horses and donkeys. While the basic mechanisms for IGH diversification are similar across species and breeds, their specific manifestations exhibit both distinct and consistent patterns, reflecting differences in immune system adaptations and providing a theoretical basis for understanding IGH expression diversity in equids.