Time-resolved single-cell and spatial gene regulatory atlas of plants under pathogen attack

Plant leaf apoplast provides a nutrient-rich and heterogeneous niche for microbes that critically impacts plant health. However, how individual plant cells respond to heterogeneous microbial colonization remains elusive. Here, by time-resolved simultaneous single-cell transcriptome and epigenome profiling of plants infected by bacterial pathogens, we present cell atlases with gene regulatory logic associated with disease and immunity. We also employ time-resolved spatial transcriptomics to reveal spatial heterogeneity of plant immune responses. Integrating our single-cell multiomics and spatial omics data enables spatiotemporal mapping of defense gene regulatory logic. Our study provides a molecularly-defined spatiotemporal map of plant-microbe interaction at the single-cell resolution.