Chromosome-scale genome of Woonyoungia septentrionalis provides insights into sex differentiation and genomic evolution in Magnoliaceae

The Magnoliaceae family represents one of the most ancient angiosperm lineage and provides key insights into early flowering plant evolution. Woonyoungia septentrionalis is an endangered dioecious tree endemic to the karst regions of Southwest China, with small and fragmented populations threatened by habitat loss and low reproductive success. Here, we generated a high-quality chromosome-scale genome assembly of W. septentrionalis with an assembled genome size of 2.62 Gb and 98.9 % completeness based on BUSCO. Repetitive elements occupy 81.23 % of the genome, dominated by long terminal repeat retrotransposons. Ks-based analysis revealed an ancestral whole-genome duplication event around 65 Mya shared with Magnolia species. Phylogenomic analyses indicated that W. septentrionalis represents the earliest diverging lineage within Magnolia sensu lato, reflecting its distinct evolutionary position. Comparative and transcriptomic analyses identified gene family expansions and sex-biased regulatory networks, including hub genes such as MCM2-MCM7, and transcription factors SPL, TCP, and ERF, which may be involved in floral organ differentiation and dioecy formation. This reference genome provides a valuable resource for exploring the molecular basis of reproductive specialization and evolutionary diversification in Magnoliaceae, and supports conservation efforts for this endangered species.