Chromosome-level genome assembly and annotation files of Saussurea hypsipeta Diels

This dataset contains the chromosome-level genome assembly and corresponding annotation files for Saussurea hypsipeta Diels, a key alpine species endemic to the Qinghai–Tibet Plateau. Fresh leaf tissue was collected at 3,749.9 m in the Qilian Mountain Spur (E101°23', N37°20') in the northeastern part of the Qinghai-Tibet Plateau. Genomic DNA was extracted using a CTAB–PEG protocol and sequenced with Illumina short-read, PacBio HiFi long-read and Hi-C libraries. The final assembly spans 3.18 Gb, with a contig N50 of 4.33 Mb and scaffold N50 of 182.60 Mb; BUSCO analysis recovered 97.46 % of complete orthologs. Repetitive elements constitute 87.15 % of the genome, and 41,655 protein-coding genes were predicted and functionally annotated. The data package includes:Sahy.genome.fa – chromosome-level assemblySahy.cds.zip – coding sequencesSahy.gene.zip – gene model (gff3)Sahy.pep.zip – protein sequencesSahy.genome.repeat.TRF.zip – repeat sequences (gff3)Sahy.merged.ncRNA.zip – ncRNA (gff3)Raw reads have been deposited in NCBI BioProject PRJNA1293189. These resources facilitate comparative and evolutionary genomics of high-altitude plants.