Single-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells

被引:343
作者
Ryu, Kook Hui [1 ]
Huang, Ling [2 ]
Kang, Hyun Min [3 ]
Schiefelbein, John [1 ]
机构
[1] Univ Michigan, Dept Mol Cellular & Dev Biol, Ann Arbor, MI 48109 USA
[2] Salk Inst Biol Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037 USA
[3] Univ Michigan, Dept Biostat, Ann Arbor, MI 48109 USA
基金
美国国家科学基金会;
关键词
DIFFERENTIATION; ORGANIZATION; TRICHOME; GENES; MAP;
D O I
10.1104/pp.18.01482
中图分类号
Q94 [植物学];
学科分类号
071001 ;
摘要
Single-cell RNA sequencing (scRNA-seq) has been used extensively to study cell-specific gene expression in animals, but it has not been widely applied to plants. Here, we describe the use of a commercially available droplet-based microfluidics platform for high-throughput scRNA-seq to obtain single-cell transcriptomes from protoplasts of more than 10,000 Arabidopsis (Arabidopsis thaliana) root cells. We find that all major tissues and developmental stages are represented in this single-cell transcriptome population. Further, distinct subpopulations and rare cell types, including putative quiescent center cells, were identified. A focused analysis of root epidermal cell transcriptomes defined developmental trajectories for individual cells progressing from meristematic through mature stages of root-hair and nonhair cell differentiation. In addition, single-cell transcriptomes were obtained from root epidermis mutants, enabling a comparative analysis of gene expression at single-cell resolution and providing an unprecedented view of the impact of the mutated genes. Overall, this study demonstrates the feasibility and utility of scRNA-seq in plants and provides a first-generation gene expression map of the Arabidopsis root at single-cell resolution.
引用
收藏
页码:1444 / 1456
页数:13
相关论文
共 38 条
[1]   The bHLH genes GL3 and EGL3 participate in an intercellular regulatory circuit that controls cell patterning in the Arabidopsis root epidermis [J].
Bernhardt, C ;
Zhao, MZ ;
Gonzalez, A ;
Lloyd, A ;
Schiefelbein, J .
DEVELOPMENT, 2005, 132 (02) :291-298
[2]   Cell type-specific expression profiting in plants via cell sorting of protoplasts from fluorescent reporter lines [J].
Birnbaum, K ;
Jung, JW ;
Wang, JY ;
Lambert, GM ;
Hirst, JA ;
Galbraith, DW ;
Benfey, PN .
NATURE METHODS, 2005, 2 (08) :615-619
[3]   A high-resolution root spatiotemporal map reveals dominant expression patterns [J].
Brady, Siobhan M. ;
Orlando, David A. ;
Lee, Ji-Young ;
Wang, Jean Y. ;
Koch, Jeremy ;
Dinneny, Jose R. ;
Mace, Daniel ;
Ohler, Uwe ;
Benfey, Philip N. .
SCIENCE, 2007, 318 (5851) :801-806
[4]  
Brennecke P, 2013, NAT METHODS, V10, P1093, DOI [10.1038/nmeth.2645, 10.1038/NMETH.2645]
[5]   A Gene Regulatory Network for Root Epidermis Cell Differentiation in Arabidopsis [J].
Bruex, Angela ;
Kainkaryam, Raghunandan M. ;
Wieckowski, Yana ;
Kang, Yeon Hee ;
Bernhardt, Christine ;
Xia, Yang ;
Zheng, Xiaohua ;
Wang, Jean Y. ;
Lee, Myeong Min ;
Benfey, Philip ;
Woolf, Peter J. ;
Schiefelbein, John .
PLOS GENETICS, 2012, 8 (01)
[6]   Integrating single-cell transcriptomic data across different conditions, technologies, and species [J].
Butler, Andrew ;
Hoffman, Paul ;
Smibert, Peter ;
Papalexi, Efthymia ;
Satija, Rahul .
NATURE BIOTECHNOLOGY, 2018, 36 (05) :411-+
[7]   The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root [J].
DiLaurenzio, L ;
WysockaDiller, J ;
Malamy, JE ;
Pysh, L ;
Helariutta, Y ;
Freshour, G ;
Hahn, MG ;
Feldmann, KA ;
Benfey, PN .
CELL, 1996, 86 (03) :423-433
[8]  
DOLAN L, 1993, DEVELOPMENT, V119, P71
[9]   Root Regeneration Triggers an Embryo-like Sequence Guided by Hormonal Interactions [J].
Efroni, Idan ;
Mello, Alison ;
Nawy, Tal ;
Ip, Pui-Leng ;
Rahni, Ramin ;
DelRose, Nicholas ;
Powers, Ashley ;
Satija, Rahul ;
Birnbaum, Kenneth D. .
CELL, 2016, 165 (07) :1721-1733
[10]   The potential of single-cell profiling in plants [J].
Efroni, Idan ;
Birnbaum, Kenneth D. .
GENOME BIOLOGY, 2016, 17