single-cell RNA-seq to dessect fungal infection to plant leaves. undefined

Plant infection by microbial pathogens is a dynamic process. Here, we investigated the heterogeneity of plant responses in the context of pathogen location. A single cell atlas of Arabidopsis thaliana leaves challenged by the fungus Colletotrichum higginsianum revealed cell type-specific gene expression that highlights an enrichment of intracellular immune receptors in vasculature cells. Using trajectory inference, we assigned cells that directly interacted with the invasive hyphae. Further analysis of these infection site cells revealed transcriptional plasticity in a cell type-dependent manner. A reprogramming of abscisic acid signaling was specifically activated in guard cells. Consistently, a contact-dependent stomatal closure was observed, possibly representing a response that anticipates pathogen penetration. We also found different sets of genes were induced in different cell types to activate indole glucosinolate biosynthesis, which contributed to fungal resistance. This research highlights the spatial dynamics of plant response during infection and revealed cell type-specific processes and gene functions.