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

46 Pages Posted: 13 Dec 2018 Sneak Peek Status: Published

See all articles by Tom Denyer

Tom Denyer

University of Tuebingen - Center for Plant Molecular Biology

Xiaoli Ma

University of Tuebingen - Center for Plant Molecular Biology

Simon Klesen

University of Tuebingen - Center for Plant Molecular Biology

Emanuele Scacchi

University of Tuebingen - Center for Plant Molecular Biology

Kay Nieselt

University of Tuebingen - Center for Bioinformatics

Marja Timmermans

University of Tuebingen - Center for Plant Molecular Biology

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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.

Suggested Citation

Denyer, Tom and Ma, Xiaoli and Klesen, Simon and Scacchi, Emanuele and Nieselt, Kay and Timmermans, Marja, Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single Cell RNA Sequencing (December 12, 2018). Available at SSRN: https://ssrn.com/abstract=3300042 or http://dx.doi.org/10.2139/ssrn.3300042
This is a paper under consideration at Cell Press and has not been peer-reviewed.

Tom Denyer

University of Tuebingen - Center for Plant Molecular Biology

Wilhelmstr. 19
72074 Tuebingen, Baden Wuerttemberg
Germany

Xiaoli Ma

University of Tuebingen - Center for Plant Molecular Biology

Wilhelmstr. 19
72074 Tuebingen, Baden Wuerttemberg
Germany

Simon Klesen

University of Tuebingen - Center for Plant Molecular Biology

Wilhelmstr. 19
72074 Tuebingen, Baden Wuerttemberg
Germany

Emanuele Scacchi

University of Tuebingen - Center for Plant Molecular Biology

Wilhelmstr. 19
72074 Tuebingen, Baden Wuerttemberg
Germany

Kay Nieselt

University of Tuebingen - Center for Bioinformatics

Wilhelmstr. 19
72074 Tuebingen, Baden Wuerttemberg
Germany

Marja Timmermans (Contact Author)

University of Tuebingen - Center for Plant Molecular Biology ( email )

Wilhelmstr. 19
72074 Tuebingen, Baden Wuerttemberg
Germany

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