The chromosome-level genome of Chinese indicine cattle breed provides insights into bovine adaptation and immunity

Genomic research is currently undergoing a paradigm shift from reliance on a single reference sequence to the use of breed-specific genomes. Chinese indicine cattle (Bos taurus indicus), characterized by their notable tick resistance and heat tolerance, display extensively genetic diversity than taurine. Here, we generated a chromosome level genome assembly of Chinese indicine cattle, achieving a contiguity N50 of 90.92 Mb and an overall size of 2.91 Gb, utilizing PacBio high-fidelity (HiFi) sequencing complemented by Hi-C sequencing technology. The assembly is characterized by near-complete chromosomes, telomeres, and less gaps. Utilizing this highly quality assembly, we explored the phylogenetic relationship and speciation time. The gene family and selection signatures analyses indicated that candidate genes and biosynthetic pathways potentially contributing to disease immunity and thermotolerance of indicine cattle. Altogether, this study enriches the bovine pangenome repository and advances our understanding of the complex evolutionary patterns and distinctive adaptation traits of Chinese indicine cattle.