Integration of single-cell and spatial RNA sequencing uncovers spatiotemporal transition of fruit senescence trajectory from exocarp to mesocarp in Pitaya (Hylocereus undatus)

Senescence is the last critical stage of the fruit life cycle, which directly affects the maintenance of fruit quality and post harvest lifespan. The pericarp consists of various cell types, making it challenging to elucidate their roles in fruit senescence. In this study, an expression atlas of H. undatus pericarp was constructed using scRNA-seq profiles, encompassing data from thousands of individual cells. Five different algorithms, including deconvolution (SingleR and SciBet), supervised learning (RCTD and CARD), and multi-modal cross-analysis (MIA), were employed to assign 17 transcriptionally distinct cell clusters identified in single cells to four different cell types: exocarp, mesocarp, endocarp, and vascular bundles. Pseudotime trajectory analysis revealed a clear spatiotemporal transition from ROS-induced stress and disease resistance to senescence during the fruit ripening process, moving from the exocarp to the mesocarp. Previously unknown early response genes related to senescence and resistance were identified, providing novel tools for fruit senescence prediction based on mesocarp and enhancement of fruit resistance based on exocarp.