Telomere-to-telomere yak genome: A high-quality reference for genetic diversity analyses and functional multi-omics studies

The yak (Bos grunniens) is a vital livestock species on the Qinghai-Tibetan and Pamir Plateaus, integral to the economy and culture of high-altitude regions. This study presents the first gap-free, telomere-to-telomere (T2T) genome assembly for the Pamir yak, a domestic yak (Bos grunniens domesticus) renowned for its adaptation to alpine desert steppes. The BosGru_T2T1.0, generated by integrating PacBio HiFi, Oxford Nanopore ultralong, and Hi-C sequencing data, spans 2.66 Gb with a contig N50 of 96.04 Mb. It comprises 30 chromosomes (29 autosomes and X), captures 30 centromeres, and exhibits high completeness (96.9% BUSCO score). A total of 28,596 protein-coding genes were annotated, representing a significant increase over previous assemblies. Comparative genomic and population structure analyses of various yak breeds revealed distinct phylogenetic lineages and genetic diversity. The T2T assembly demonstrated superior performance in variant calling, identifying more SNPs with a higher transition/transversion ratio compared to the previous classic BosGru3.0 reference genome. Furthermore, the BosGru_T2T1.0 assembly enabled more accurate characterizations of epigenetic modification landscape (CENP-A, H3K27ac, H3K27me3) and chromatin architecture (TADs, loops), and refined gene annotations and expressions. This high-quality reference genome serves as a crucial resource for performing genomic and multi-omics analysis and elucidating the genetic basis of transcriptional regulation, gene function, and even yak adaptation and biological diversity.