A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root

Abstract

Cells of eukaryotic multicellular organisms have inherent heterogeneity. Recent advances in single-cell gene expression studies enable us to explore transcriptional regulation in dynamic development processes and highly heterogeneous cell populations. In this study, using a high-throughput single-cell RNAsequencing assay, we found that the cells in Arabidopsis root are highly heterogeneous in their transcriptomes. A total of 24 putative cell clusters and the cluster-specific marker genes were identified. The spatial distribution and temporal ordering of the individual cells at different developmental stages illustrate their hierarchical structures and enable the reconstruction of continuous differentiation trajectory of root development. Moreover, we found that each root cell cluster exhibits distinct patterns of ion assimilation and hormonal responses. Collectively, our study reveals a high degree of heterogeneity of root cells and identifies the expression signatures of intermediate states during root cell differentiation at single-cell resolution. We also established a web server (http://wanglab.sippe.ac.cn/rootatlas/) to facilitate the use of the datasets generated in this study.

Single-cell transcriptome analyses recapitulate the cellular and developmental responses to abiotic stresses in rice

“…One of the strategies is to encapsulate cells into individual liquid droplets using a microfluidic device, and therefore, the transcriptomes of thousands of cells were obtained in a single experiment; identifies of individual cells are further recognized with following-up computational analyses (Klein et al, 2015;Macosko et al, 2015). Such strategy was mainly applied to animal tissues, although a growing number of applications in plants were implemented in the year of 2019 (Denyer et al, 2019;Jean-Baptiste et al, 2019;Rich-Griffin et al, 2019;Ryu et al, 2019;Shulse et al, 2019;Zhang et al, 2019). All these studies have been focused on the Arabidopsis root; the application of scRNA-seq to other plant cells remains absent, presumably because less prior knowledge on the cellular composition and developmental processes makes it technically more challenging.…”

Visualization of Protein Coding, Long Noncoding, and Nuclear RNAs by Fluorescence in Situ Hybridization in Sections of Shoot Apical Meristems and Developing Flowers

“…To further unravel the functions of coding and noncoding transcripts, it is necessary to resolve their distribution at the single cell and subcellular levels. Single-cell RNA sequencing has been recently applied in plants to resolve transcriptome dynamics in different root cell types (Denyer et al, 2019;Jean-Baptiste et al, 2019;Ryu et al, 2019;Shulse et al, 2019;Zhang et al, 2019). However, only some genes are expressed in a cell typespecific manner (consider cell cycle-expressed genes as a counterexample), and these methods do not yet, at least, resolve subcellular locations of RNA molecules.…”

Biological and Cellular Functions of the Microdomain-Associated FWL/CNR Protein Family in Plants

“…This statement is supported by microscopic studies conducted on plant plasma membranes [65]. The recent release of Arabidopsis root transcriptomes at a single-cell resolution now allows for a deeper exploration of gene expression and co-expression [66][67][68][69][70]. As a first attempt, we mined one of these Arabidopsis root single-cell transcriptomic datasets [68] to quantify the level of transcriptional activity of the twelve members of the AtFWL family.…”