Dual Single-Nucleus Gene Expression Atlas of Grapevine and <i>Erysiphe necator</i> During Early Powdery Mildew Infection

We applied dual-organism single-nucleus transcriptomics to study the interaction between grapevine leaves and <i>Erysiphe necator</i>, the causal agent of powdery mildew, at 1 and 5 days postinfection, including controls and three biological replicates. We generated a grapevine leaf atlas encompassing over 100,000 nuclei and a pathogen atlas of more than 3,000 nuclei. We successfully annotated all major grapevine cell types, including mesophyll, epidermis, phloem and xylem parenchyma, companion cells, and guard cells. We identified key <i>E</i>. <i>necator</i> structures, including appressoria, haustoria, and hyphae and provided a list of novel cell type markers for both species. We reveal structure-specific gene expression programs in <i>E</i>. <i>necator</i>, laying a foundation for future studies of fungal development and virulence mechanisms. In the host, we identified spatially distinct expression patterns of defense-related genes. As the infection progressed, we observed the activation of a coordinated immune response involving multiple cell types, mainly epidermal and mesophyll cells. High-dimensional weighted gene co-expression network analysis identified key hubs and networks associated with cell type-specific signaling and defense response. We describe a spatial separation of pattern- and effector-triggered immunity, supporting a model in which pattern-triggered immunity is activated at the site of pathogen contact and effector-triggered immunity is induced in surrounding tissue. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.