Haplotype-resolved genome assembly of a male Dioscorea alata cultivar reveals the structure and evolution of sex chromosomes

Dioscorea alata L., the most widely cultivated yam species, exhibits dioecy (XY system) and a strong male-biased sex ratio. These two major constraints limit parental combinations and hinder breeding progress. To get insight into the sex chromosome structure and evolution in D. alata , we present a haplotype-resolved, near-complete genome assembly of the male cultivar ‘Kabusa’, spanning 958 Mb across 40 chromosomes. DalaChr6A is identified as the Y chromosome which exhibits early signs of heteromorphism, including a slight reduction in size (∼400 Kb difference) and a potential centromere shift relative to the X chromosome. Our findings also reveal a sex chromosome turnover between D. alata and D. rotundata . The sex chromosomes of D. alata are evolutionarily young (~4.32 million year ago) and emerged after the divergence from the D. rotundata lineage. The sex-determining region (SDR) is refined to ∼7.6 Mb, representing ~44% of the Y chromosome. It contains several inversions and a divergence gradient was observed across these inversions. INV4 identified as the oldest pericentric inversion likely marks the early step in D. alata SDR evolution. Despite structural divergence, both X and Y chromosomes remain transcriptionally active. Among the 231 genes annotated in the SDR, 97 are sex-biased and enriched in functions associated with floral organ formation and hormonal signaling pathways. This study enhances our understanding of sex chromosome evolution and sex determination in dioecious plants. It provides a gold-standard reference genome for the Dioscorea genus and lays the foundation for accelerated breeding and genetic improvement in yam.