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

Plant Physiol. 2019 Apr;179(4):1444-1456. doi: 10.1104/pp.18.01482. Epub 2019 Feb 4.


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.

Publication types

  • Evaluation Study
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Arabidopsis / cytology
  • Arabidopsis / metabolism*
  • Feasibility Studies
  • Plant Epidermis / metabolism
  • Plant Roots / cytology
  • Plant Roots / metabolism*
  • Protoplasts / metabolism
  • Sequence Analysis, RNA
  • Single-Cell Analysis*
  • Transcriptome*