Abstract

Saussurea hypsipeta Diels, a perennial medicinal plant used in traditional Chinese medicine, is primarily distributed on the Qinghai-Tibet Plateau, where it serves as a key component of the alpine ecosystem. The lack of genetic information and high-quality genome assembly hinders in-depth research on this species as well as its conservation and further utilization. Here, we report the chromosome-level genome assembly of this diploid species, which was accomplished by integrating Illumina short-read, PacBio HiFi long-read, and Hi-C sequencing. The final assembly size was 3.18 Gb with excellent contiguity (contig N50 = 4.33 Mb; scaffold N50 = 182.60 Mb) and integrity (BUSCO score 97.46%). Among them, 98.91% of the sequences were anchored to 16 pairs of chromosomes, and the content of repetitive sequences was 87.15%. Furthermore, we predicted 70,374 genes, including 41,655 protein-coding genes, of which 94.13% were functionally annotated. This high-quality genomic resource provides a critical foundation for elucidating the molecular mechanisms of high-altitude adaptation, also offering genetic insights into its medicinal value.