Abstract: Orchidantha, the sole genus in the family Lowiaceae (Zingiberales), exhibits distinctive, orchid-like flowers that emit a carrion-like scent, attracting dung beetles for pollination. Despite their ecological and ornamental value, many Orchidantha species are endangered and face an elevated risk of extinction. Here, we present the first chromosome-scale genome assembly of the endangered Orchidantha insularis from Hainan Island. The 2.24 Gb genome was assembled into nine pseudochromosomes, and 31,541 protein-coding genes were annotated. Phylogenomic analysis places O. insularis within the 'banana group' of Zingiberales and indicates divergence from Musaceae approximately 65 Ma, following a shared recent whole-genome duplication (WGD). We identify significant expansions in gene families related to photosynthesis and carbon fixation, consistent with adaptation to low-light tropical understory habitats. Our analysis uncovers the genetic basis of the carrion-like floral scent in O. insularis by revealing complete biosynthetic pathways for dimethyl disulfide (DMDS) and indole. In parallel, the expansions of FMO genes and signatures of positive selection reinforce indole metabolism, which links floral scent production to both adaptation and defense. Whole-genome resequencing of population samples revealed high genetic differentiation and low nucleotide diversity. Demographic inference indicates severe Pleistocene bottlenecks followed by continued population decline. Together, these results provide a genomic foundation for understanding genome evolution in early-diverging Zingiberales and inform conservation and horticultural use.

Key words: chromosome-scale genome, endangered species, floral scent biosynthesis, indole-derived volatiles, Lowiaceae, Orchidantha insularis