Chromosome-level genome of <i>Madhuca hainanensis</i> reveals genomic evolution and floral divergence in <i>Madhuca</i>

<i>Madhuca hainanensis</i> and <i>Madhuca pasquieri</i> are endangered species in China, classified as vulnerable on the IUCN red list. Compared to the fast-growing <i>Madhuca longifolia</i>, they exhibit lower fruit set and distinct floral morphology. Here, we present the chromosome-level genome assembly of <i>M. hainanensis</i> (760.86 Mb, 12 pseudochromosomes) using PacBio HiFi, Illumina, and Hi-C sequencing. Comparative genomics across floral developmental stages identified six key genes, including <i>ADO1</i> and <i>COL5</i>, associated with floral divergence. This study provides genomic insights critical for conservation efforts and elucidates molecular mechanisms contributing to the species' endangered status.