Spatiotemporal trajectory of senescence in mesocarp cell clusters of Hylocereus undatus based on single-cell and...

Fruit senescence is a complex physiological process. Single-cell RNA sequencing (scRNA-seq) analysis revealed the differentiation trajectories of 13 cell clusters during the senescence of Hylocereus undatus (H. undatus). The mesocarp of the fruit contained four cell clusters, but their precise localization and functional division remained unclear. This work documented mesocarp phenotypic alterations and elucidated the time courses of mesocarp flavonoid biosynthesis and superoxide anion generation. Additionally, overall ROS changes were observed using fluorescence microscopy. By combining the single-cell atlas with spatial transcriptomics data at resolutions of 0.2 and 0.8, and applying four computational algorithms (SingleR, SciBet, CARD, and RCTD), we accurately mapped the spatial distribution of the four cell populations in the two layers of the mesocarp from outer to inner regions. Furthermore, we identified highly correlated cells with cell-specific functions, which allowed us to perform a detailed analysis of the differentiation trajectories of these four cell clusters. We proposed a hypothesis that these four clusters in the mesocarp participate in the senescence process. Finally, using SCODE, we uncovered the gene regulatory networks of the pericarp's highly correlated cell clusters during fruit senescence. Through single-cell technology, the functional division of the four cell clusters in the mesocarp-responsible for stress responses, signal transduction, material preparation, and cell differentiation trajectories-has been revealed. These findings provide insights from a single-cell dimension and a spatiotemporal perspective, enhancing the understanding of the dynamic process of plant senescence.