The <i>Dioscorea opposita</i> genome provides insights into anthocyanin biosynthesis in Tiegun yam

Tiegun yam (<italic>Dioscorea opposita</italic> Thunb., <italic>D. opposita</italic>) is the most widely cultivated variety and a premium product among Huai yams, which are considered one of the 'Four Huai Medicines' in China. The presence of 'Rusty spot' (Rs) on the rhizome epidermis of Tiegun yam is a characteristic feature indicative of its superior quality and authenticity. However, the mechanisms underlying the formation and regulation of Rs remain largely unexplored. This knowledge gap is primarily due to the absence of a reference genome for <italic>D. opposita</italic>, which hinders in-depth molecular research. In this study, we sequenced and assembled the genome of <italic>D. opposita</italic>, producing a 424.01 Mb high-quality reference genome anchored to 20 pseudochromosomes (n = 20) in haplotype. We identified 24,405 protein-coding genes. Metabolomic and transcriptomic analyses revealed that Rs is rich in anthocyanins, with up-regulated expression of genes involved in the biosynthesis, environment regulation, and signaling pathways of anthocyanins in Rs compared to other tissues. The genomic assembly of <italic>D. opposita</italic> provides valuable insights into its genetic background, facilitates the identification of genes controlling important agronomic traits, and supports the development of high-quality germplasm resources for Tiegun yam and potentially other yam species.