Developmental and regulatory logic of cannabis glandular trichomes resolved by single cell multiomics

Glandular trichomes of Cannabis sativa produce specialised metabolites including cannabinoids and terpenes, yet the cellular basis of trichome development and metabolic specialisation remains unresolved. Here we reconstruct the glandular trichome lineage within the C. sativa inflorescence using single-cell transcriptomics and chromatin accessibility profiling. We identify a continuous developmental trajectory from the protoderm, linking bulbous, sessile, and capitate-stalked trichomes, indicating that these morphologies represent sequential stages rather than distinct trichome types. We further identify a previously undescribed neck cell that shares a developmental origin with secretory disc cells before lineage bifurcation. Integration of chromatin accessibility with transcription factor (TF) binding reveals cell state specific regulatory programs coordinating neck cell development and specialised metabolism, redox homeostasis, and secretion in mature secretory disc cells. Methyl jasmonate elicitation induces extensive transcriptional and chromatin landscape reprogramming in mature secretory disc cells and transient repression of specialised metabolic pathways. Together, these findings provide a cell-resolved regulatory framework for glandular trichome development and function, revising prevailing models of trichome identity, maturation and defence associated metabolic regulation.