Resolving floral development dynamics using genome and single-cell temporal transcriptome of Dendrobium devonianum

Dendrobium devonianum, a species of the Orchidaceae family, is notable for its unique floral characteristics, which include two yellow spots and purple tips on its labellum, as well as fringed edges. However, the molecular mechanisms underlying flower pattern formation in D. devonianum remain poorly understood, hindering advancements in its breeding process. Here, a chromosome-scale genome of D. devonianum was presented for the first time, revealing two significant polyploidization events. Additionally, a high-resolution single-cell transcriptomic atlas was constructed, capturing 11 distinct cell clusters. Expression patterns of MADS-box genes were identified through temporal and spatial bulk RNA-Seq, revealing alignment with the ABCDE model of flower formation. Meanwhile, mass spectrometry imaging and scRNA analyses showed that the yellow spots were primarily associated with carotenoid biosynthesis gene expression, while the purple colour is predominantly linked to anthocyanin biosynthesis gene expression. These genes were mainly expressed in the epidermis and vascular cells. Developmental trajectory analyses of epidermal cells further uncovered a gene regulatory network and several transcription factors likely responsible for fringes formation along the labellum margin. This study provides valuable insights into the molecular mechanisms driving floral colour differentiation and structural traits in D. devonianum, contributing to a deeper understanding of orchid evolution, diversification and breeding.