Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing.
IF: 13.417
Cited by: 289


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.


Temporal Gene Expression
Spatial reconstruction
gene regulatory network
quiescent center
root development
single-cell RNA sequencing
spatiotemporal gene expression
stem cell

MeSH terms

Cell Differentiation
Gene Expression Regulation, Plant
Gene Regulatory Networks
Genes, Plant
Genetic Markers
High-Throughput Nucleotide Sequencing
Plant Roots
Reproducibility of Results
Sequence Analysis, RNA
Single-Cell Analysis
Time Factors
Transcription Factors
Transcription, Genetic


Denyer, Tom
Ma, Xiaoli
Klesen, Simon
Scacchi, Emanuele
Nieselt, Kay
Timmermans, Marja C P

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