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

Abstract

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 precise spatiotemporal information, identifying defining expression features for all major cell types, including the scarce cells of the quiescent centre. These reveal new 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 a unique spatiotemporal perspective of root cell differentiation.