Genomic underpinnings of floral scent and ecological adaptation of the endangered Orchidantha insularis
Orchidantha, the sole genus in the Lowiaceae family (Zingiberales), exhibits distinctive, orchid-like flowers that emit a carrion-like scent, attracting dung beetles for pollination. Despite its ecological and ornamental value, many species are endangered and face elevated extinction risk. 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 annotated 31,541 protein-coding genes. Phylogenomic analysis places O. insularis within the Zingiberales 'banana group' and indicates its divergence from Musaceae approximately 65 Mya, supporting a shared recent whole-genome duplication. We identified significant expansions in gene families related to photosynthesis and carbon fixation, consistent with adaptation to its low-light tropical understory habitat. Our analysis uncovers the genetic basis of its carrion-like floral scent, involving complete dimethyl disulfide (DMDS) and indole pathways. In parallel, FMO gene expansion and positive selection reinforce indole metabolism, linking floral scent to both adaptation and defense. Whole-genome resequencing of 23 individuals from two populations revealed high genetic differentiation and low nucleotide diversity. Demographic inference indicates severe Pleistocene bottlenecks followed by continued decline. These results provide a genomic foundation for understanding early Zingiberales genome evolution and support future conservation and horticultural use.
Orchidantha, the sole genus in the Lowiaceae family (Zingiberales), exhibits distinctive, orchid-like flowers that emit a carrion-like scent, attracting dung beetles for pollination. Despite its ecological and ornamental value, many species are endangered and face elevated extinction risk. 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 annotated 31,541 protein-coding genes. Phylogenomic analysis places O. insularis within the Zingiberales 'banana group' and indicates its divergence from Musaceae approximately 65 Mya, supporting a shared recent whole-genome duplication. We identified significant expansions in gene families related to photosynthesis and carbon fixation, consistent with adaptation to its low-light tropical understory habitat. Our analysis uncovers the genetic basis of its carrion-like floral scent, involving complete dimethyl disulfide (DMDS) and indole pathways. In parallel, FMO gene expansion and positive selection reinforce indole metabolism, linking floral scent to both adaptation and defense. Whole-genome resequencing of 23 individuals from two populations revealed high genetic differentiation and low nucleotide diversity. Demographic inference indicates severe Pleistocene bottlenecks followed by continued decline. These results provide a genomic foundation for understanding early Zingiberales genome evolution and support future conservation and horticultural use.