Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing

High-throughput single-cell RNA sequencing (scRNA-seq) is becoming a cornerstone of developmental research, providing unprecedented power in understanding dynamic processes. Here, we present a high-resolution scRNA-seq expression atlas of the Arabidopsis root composed of thousands of independently profiled cells. This atlas provides detailed spatiotemporal information, identifying defining expression features for all major cell types, including the scarce cells of the quiescent center. These reveal key developmental regulators and downstream genes that translate cell fate into distinctive cell shapes and functions. Developmental trajectories derived from pseudotime analysis depict a finely resolved cascade of cell progressions from the niche through differentiation that are supported by mirroring expression waves of highly interconnected transcription factors. This study demonstrates the power of applying scRNA-seq to plants and provides an unparalleled spatiotemporal perspective of root cell differentiation. [Display omitted] •scRNA-seq of Arabidopsis root cells captures precise spatiotemporal information•Defining expression features for cell types identify new developmental regulators•Cluster arrangement reflects developmental time with a centrally localized niche•Intricate waves of gene expression finely resolve developmental trajectories Denyer and Ma et al. generate a single-cell RNA expression atlas of the Arabidopsis root that captures spatiotemporal information for all major cell types and uncovers new regulators. Pseudotime-analysis-derived developmental trajectories depict a cascade of developmental progressions between stem cell and final differentiation mirrored by waves of transcription factor expression.