Single-cell transcriptome sequencing (scRNA-seq) reveals dynamic gene expression trajectories regulating vascular cell senescence in Hylocereus undatus.

Abstract

Fruit is highly susceptible to postharvest quality deterioration, and changes at the cellular level in the vascular bundle, a key hub for substance transport within the fruit, have a significant impact on the senescence process. Single-cell transcriptome sequencing (scRNA-seq) enables the precise analysis of gene expression dynamics in vascular cells across different stages of postharvest freshness and senescence. Utilizing scRNA-seq, this study developed a cellular atlas of the Hylocereus undatus (H. undatus) pericarp. Among the 13 cell clusters identified in the pericarp, vascular cells were predominantly localized in cluster 10, and the cell number within this cluster showed a significant decline with senescence. At a resolution of 0.2, two subpopulations of vascular cells were subdivided and identified, and their dynamics during the senescence process were analysed. In addition, through pseudo-timing trajectory analysis, two senescence hub regulators, HuCEP and HuSCPL48, were screened out by the pericarp vascular senescence gene regulatory network constructed by SCODE based on connectivity. In particular, genes related to mass transport, such as HuAAE3, and related to energy metabolism, such as HuNAD7, were significantly upregulated. At the same time, in the later stages of senescence, genes related to specific subsets of vascular cell activation protein degradation such as HuATG8CL and oxidative stress such as HuPMA4 were significantly up-regulated, leading to a stress response to fruit physiological decline. This study explored the dynamic changes in gene expression during vascular cell senescence.