A near telomere-to-telomere chromosome-level genome assembly of Rhodiola yunnanensis (Crassulaceae)

Rhodiola yunnanensis (Crassulaceae) is an endemic medicinal plant species distributed in the Hengduan Mountains of southwestern China. Here, we present a high-quality and near telomere-to-telomere chromosome-level genome assembly of R. yunnanensis generated using Oxford Nanopore long-read sequencing and Hi-C scaffolding. The assembled genome spans 643.28 Mb with a contig N50 of 51.92 Mb, and 98.46% of the sequence was anchored to 11 pseudo-chromosomes, eight of which contained no internal gaps in the current assembly. Benchmark analyses revealed a BUSCO completeness of 97.46%, while the LTR Assembly Index (LAI) score achieved 20.50, both suggesting a high level of assembly quality. Telomeric repeat motifs were detected at both ends of 10 pseudo-chromosomes, and centromeric regions were identified on all 11 chromosomes. We predicted 36,495 protein-coding genes, 94.16% of which were functionally annotated, together with 1,643 transcription factors and 6,429 non-coding RNAs. This high-quality genome provides a valuable resource for studying alpine adaptation, specialized metabolite biosynthesis, and evolutionary diversification in Rhodiola and other high-altitude plants.