Abstract Asparagus stem blight, caused by the pathogenic fungus Phomopsis asparagi , is a highly destructive disease, yet the molecular mechanisms underlying resistance remain largely unexplored, with little known regarding immune responses across various cell types. In this study, we employed spatial transcriptome sequencing at two key stages of P. asparagi infection in asparagus stems to elucidate the pathogen-triggered transcriptomic reprogramming of distinct cell types. We identified 74 marker genes across five cell types and uncovered over 5303 genes that are differentially regulated during the early stages of infection. Our findings reveal the spatiotemporal heterogeneity of immune response gene expression and the key regulatory pathways functioning at both infection sites and distant areas regions. Notably, the analysis of co-upregulated immune response genes demonstrated that asparagus employs two distinct regulatory modules to mediate salicylic acid- and jasmonic acid-mediated responses against pathogens with different lifestyles. GO enrichment and cell trajectory analysis further linked each cell type to specific, yet partially shared transcriptional reprogramming patterns and regulatory factors. Collectively, this study provides a comprehensive perspective of the cellular landscape of asparagus stems during fungal pathogen infection, shedding light on the underlying mechanisms of immune response at both spatial and cellular levels.
Liping et al. (Wed,) studied this question.