Plants lack specialized and mobile immune cells. Consequently, any cell type that encounters pathogens must mount immune responses and communicate with surrounding cells for successful defence. However, the diversity, spatial organization and function of cellular immune states in pathogen-infected plants are poorly understood1. Here we infect Arabidopsis thaliana leaves with bacterial pathogens that trigger or supress immune responses and integrate time-resolved single-cell transcriptomic, epigenomic and spatial transcriptomic data to identify cell states. We describe cell-state-specific gene-regulatory logic that involves transcription factors, putative cis-regulatory elements and target genes associated with disease and immunity. We show that a rare cell population emerges at the nexus of immune-active hotspots, which we designate as primary immune responder (PRIMER) cells. PRIMER cells have non-canonical immune signatures, exemplified by the expression and genome accessibility of a previously uncharacterized transcription factor, GT-3A, which contributes to plant immunity against bacterial pathogens. PRIMER cells are surrounded by another cell state (bystander) that activates genes for long-distance cell-to-cell immune signalling. Together, our findings suggest that interactions between these cell states propagate immune responses across the leaf. Our molecularly defined single-cell spatiotemporal atlas provides functional and regulatory insights into immune cell states in plants.

Publication

Nobori, T., Monell, A., Lee, T.A., Sakata, Y., Shirahama, S., Zhou, J., Nery, J.R., Mine, A. and Ecker, J.R., (2025) A rare PRIMER cell state in plant immunity. Nature [Link]

Data Browser

GitHub (Single-cell multiomics)

GitHub (Spatial transcriptomic)

Image credit: Hsuan Pai

PHYTOMap (Plant HYbridization-based Targeted Observation of gene expression Map) is a method that can spatially map expression of dozens of genes at the single-molecule resolution in 3D whole-mount plant tissues. PHYTOMap dramatically accelerates and advances spatial gene expression analysis in plants compared to traditional transgenic reporter approaches. It does not require tissue sectioning, a major bottleneck in commercial spatial transcriptomics assays. PHYTOMap experiments can be done in a standard molecular biology lab at a low cost without requiring a transgenic line; thus, the method can be applied to many plant species, including non-model species.