Chromosome-level genome assembly of the wild Chinese yam (Dioscorea opposita Thunb.)

Dioscorea opposita, a perennial dioecious vine endemic to East Asia, holds substantial economic value owing to its dual role as a source of both food and traditional medicine. In this study, we constructed a high-quality, chromosome-level reference genome for this species by integrating PacBio HiFi long reads, BGI short reads, and Hi-C sequencing technology. The assembled haploid genome is approximately 430.73 Mb in size, with a scaffold N50 of 19.82 Mb. A total of 94.33% of the sequences were anchored onto 20 pseudo-chromosomes, consistent with its karyotype (2n = 6x = 120). We annotated 24,960 protein-coding genes, of which 93.58% were functionally annotated. Repetitive sequences accounted for 65.93% of the genome, with LTR elements being the most abundant component (48.00% of the genome). BUSCO assessment confirmed high completeness of both the genome assembly and gene annotation. This high-resolution genomic resource not only serves as a crucial reference for studies on sex determination, adaptive evolution, and genomic diversity within D. opposita and its related species, but also provides a solid foundation for genetic improvement, germplasm conservation, and sustainable utilization of this economically and medicinally important plant.