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 RNA-sequencing 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.

真核多细胞生物的细胞具有固有的异质性。单细胞基因表达研究的最新进展使我们能够探索动态发育过程和高度异质性细胞群体中的转录调控。在这项研究中，使用高通量单细胞RNA测序测定，我们发现拟南芥中的细胞根在转录组中高度异质。总共确定了24个推定的细胞簇和簇特异性标记基因。各个细胞在不同发育阶段的空间分布和时间顺序说明了它们的层次结构，并能够重建根发育的连续分化轨迹。此外，我们发现每个根细胞簇表现出不同的离子同化和激素反应模式。总的来说，我们的研究揭示了根细胞高度的异质性，并以单细胞分辨率鉴定了根细胞分化过程中中间状态的表达特征。我们还建立了一个Web服务器（http://wanglab.sippe.ac.cn/rootatlas/），以方便使用本研究中生成的数据集。