Haplotype-resolved telomere-to-telomere genome assembly of a male Dioscorea alata cultivar provides insights into sex determination mechanism

Background : Dioecy presents significant challenges in plant breeding and evolutionary biology. In Dioscorea alata L., the most widely cultivated yam species, dioecy (XY system) and a significant male-biased sex ratio hinder breeding efforts by restricting parental combinations and limiting genetic progress. To address these challenges, we present a high-quality, phased, telomere-to-telomere genome assembly of the male cultivar ‘Kabusa’, comprising 40 chromosomes and totaling 958 Mb. This resource facilitates detailed exploration of haplotype variation and the molecular basis of sex determination. Results : HaplotypeA includes the Y chromosome (DalaChr6A), which shows early-stage heteromorphism, characterized by a slight size reduction and a centromere shift compared to the X chromosome. Comparative genomic analysis revealed a sex chromosome turnover in Dioscorea . The sex-determination region (SDR) was refined to ~7.6 Mb, accounting for ~44% of the sex chromosomes. This region corresponds to a pericentric inversion enriched with male-specific variants and sex-specific genes. Among the 455 genes annotated in the SDR, 88 were identified as sex-linked candidates with sex-biased expression, many involved in flower organ development. Notably, a Y-encoded COI1 gene was identified as a potential regulator of jasmonic acid (JA) signaling. Male flowers exhibited JA-Ile concentrations three times higher than female flowers, and gene expression analyses implicated the JA biosynthesis and signaling pathway in sex phenotype determination. Conclusions : This study contributes to increase the knowledge on sex determination of dioecious plants, particularly in D. alata . It delivers a gold-standard genome reference for the Dioscorea genus that will accelerate genetic improvement and breeding initiatives.