Single-cell and haplotype-resolved transcriptomics reveal molecular signatures of orchid floral structures.

Orchidaceae is among the largest families of flowering plants, yet the cell heterogeneity and molecular basis underlying specialized orchid floral structures remain largely unknown. Here, we report a spatially resolved single-cell transcriptomic census of Dendrobium Chao Praya Smile flower buds, identifying 14 distinct cell types. Compared with the generation of conventional pollen grains, Dendrobium meiotic cells are uniquely enriched with specific enzymatic activities associated with mucilage-mediated pollinium formation. We identified specialized cell populations that drive tepal morphology, including lip-specialized cells, vascular cells that guide organ curvature, and pigment cells that direct localized coloration. By integrating haplotype-resolved genomes with single-cell transcriptomics, we further revealed that cis-regulatory structural variants favor alleles from the pigmented parent in pigment cells. These findings uncover cellular and molecular signatures of orchid floral specialization and demonstrate how parental genomes interact through cell-type- and allele-specific expression to shape interspecific hybrid traits, offering new insights into plant reproductive development and ornamental breeding.