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

First author: Tian-Qi Zhang; Affiliations: CAS Center for Excellence in Molecular Plant Sciences (中科院分子植物科学卓越创新中心): Shanghai, China

Corresponding author: Jia-Wei Wang

Cells have the inherent heterogeneity. Recent advances in the single-cell gene expression studies enable us to explore transcriptional regulation in dynamic development processes and highly heterogeneous cell populations. Using high-throughput single-cell RNA sequencing (scRNA-seq) assay, we found that the cells in Arabidopsis root are highly heterogeneous in their transcriptomes. A total of 24 putative cell clusters and their cluster-specific marker genes were identified. The spatial distribution and temporal ordering of the individual cell at different developmental stages illustrate their hierarchical structure and reconstructs continuous differentiation trajectory of root development. Moreover, we found that each root cell cluster exhibits distinct patterns in ion assimilation and hormone response. Our study thus reveals high degree of heterogeneity of root cells and identifies the expression signatures of intermediate states during root cell differentiation at the single-cell resolution. We have implemented a supplementary web server (http://wanglab.sippe.ac.cn/rootatlas/) to facilitate the use of the datasets generated in this study.

细胞存在固有的异质性。近来在单细胞RNA-seq技术方面的进展使得我们能够从单细胞水平研究动态发育过程的转录调控以及高度异质细胞群体。利用高通量scRNA-seq，作者发现拟南芥根中的细胞在转录组水平上是高度异质的。作者总共鉴定到了24种细胞群体，并鉴定每一类细胞群的标记基因。单个细胞在不同发育阶段空间上的分布和时间上的排列显示了他们的层次结构，重建了根发育的连续分化轨迹。此外，作者还发现每一个根细胞群在离子吸收和激素响应方面存在不同的模式。本文的研究揭示了拟南芥根细胞的高度异质性，并鉴定了根细胞分化中间状态的表达信号。作者还开发了一个网页方便研究人员使用本文的数据。

通讯：王佳伟（http://www.sippe.ac.cn/sourcedb_sippe/zw/zjrc/201812/t20181219_5218206.html）

个人简介：1995-1999年，上海交通大学，学士；1999-2005年，中科院植物生理生态研究所，博士；2005-2011年，Max Planck Institute for Developmental Biology，博士后。

研究方向：植物年龄途径的分子基础。

doi: https://doi.org/10.1016/j.molp.2019.04.004

Journal: Molecular Plant

Published date: April 17, 2019