Chromosome-level genome assembly of the wild Chinese yam Dioscorea opposita

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, BGI, and Hi-C sequencing technologies. The assembled haploid genome is approximately 430.73 Mb, 94.33% of the sequences were anchored onto 20 pseudochromosomes. Our analysis confirmed that this species not only underwent a recent hexaploidization event (2n = 6x = 120), but also carried genomic signatures originating from earlier polyploidization events. 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%). BUSCO confirmed high completeness of both the genome assembly and gene annotation. This genomic resource provides a crucial reference for studying sex determination, adaptive evolution, and genomic diversity within Dioscorea and lays a solid foundation for genetic improvement, germplasm conservation, and sustainable utilization of this key plant.