Plant Immunity in High Resolution: Advances in Single-Cell and Spatial Transcriptomics in Plant-Pathogen Interactions.
Plant immune responses are shaped by cellular identity and tissue context. During interactions with pathogenic microbes, different plant cell types activate distinct defense-associated transcriptional programs that are not readily resolved using whole-tissue analyses. As a result, bulk transcriptomic approaches have limited our ability to capture spatial and cellular heterogeneity during immune responses. Recent advances in single-cell RNA sequencing and spatial transcriptomics have enabled the analysis of plant immune responses at cellular resolution while preserving spatial information. Studies using these approaches have revealed heterogeneous and coordinated transcriptional responses across cell types and tissue regions during pathogen attacks. In this review, we summarize recent single-cell and spatial transcriptomic studies across diverse plant-pathogen systems, highlighting how these methods contribute to a more refined understanding of cell-type-specific immune responses, intercellular communication, and spatial organization of defense responses within plant tissues. We also discuss current technical limitations and future directions for applying spatially resolved transcriptomic approaches in plant-pathogen interaction research.