A single nucleus atlas of transcriptional responses to growth altering stress: Drought, flooding, and salinity

Single-nuclear RNA-sequencing allows for in-depth characterization of transcriptome differences between plant cell types and states during cell fate specification and maturation. Here, we perturbed growth and development of emerging leaves in rice plants by applying different levels of water stress. We measured the transcriptomes of individual nuclei harvested from these tissues and identified transcriptome signatures of a developmental gradient of cell states for each of the major tissue systems across stress treatments. We show that there is extensive heterogeneity between cell types with respect to their responses to different stressors, and propose an analytical approach for distinguishing between cell states.