A near telomere-to-telomere genome assembly of Rhodiola macrocarpa (Crassulaceae)

Rhodiola macrocarpa, a medicinal species of the family Crassulaceae, is distributed in regions of southwestern China and northern Myanmar. Here, we present a near telomere-to-telomere (T2T) chromosome-level genome assembly generated using Oxford Nanopore Technologies long reads in combination with Hi-C scaffolding. The final assembly spans 727.48 Mb and exhibits a contig N50 of 71.78 Mb. Notably, 99.80% of the assembled sequence was anchored to ten pseudo-chromosomes, six of which are gap-free, while the remaining four contain a single gap each. Assembly evaluation showed a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness of 97.71% and a Long Terminal Repeat Assembly Index (LAI) of 15.81, both indicating reference-level quality. Telomeric repeat motifs were identified at both ends of seven pseudo-chromosomes, and centromeric regions were identified across all ten chromosomes. Genome annotation predicted 37,627 protein-coding genes, of which 93.69% were functionally annotated, along with 1,753 transcription factors and 6,580 non-coding RNAs. This near T2T genome assembly provides a high-quality genomic resource for comparative studies and for investigating high-altitude adaptation, specialized metabolite biosynthesis, and the evolutionary history of the genus Rhodiola.