High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types

Cell Rep. 2019 May 14;27(7):2241-2247.e4. doi: 10.1016/j.celrep.2019.04.054.


Single-cell transcriptome profiling of heterogeneous tissues can provide high-resolution windows into developmental dynamics and environmental responses, but its application to plants has been limited. Here, we used the high-throughput Drop-seq approach to profile >12,000 cells from Arabidopsis roots. This identified numerous distinct cell types, covering all major root tissues and developmental stages, and illuminated specific marker genes for these populations. In addition, we demonstrate the utility of this approach to study the impact of environmental conditions on developmental processes. Analysis of roots grown with or without sucrose supplementation uncovers changes in the relative frequencies of cell types in response to sucrose. Finally, we characterize the transcriptome changes that occur across endodermis development and identify nearly 800 genes with dynamic expression as this tissue differentiates. Collectively, we demonstrate that single-cell RNA-seq can be used to profile developmental processes in plants and show how they can be altered by external stimuli.

Keywords: Arabidopsis; development; endodermis; plant; root; single-cell RNA-seq; sucrose; transcriptomics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Arabidopsis / genetics
  • Arabidopsis / growth & development
  • Arabidopsis / metabolism*
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation, Plant / genetics
  • High-Throughput Nucleotide Sequencing
  • Plant Cells / metabolism
  • Plant Roots / cytology*
  • Plant Roots / genetics
  • Plant Roots / metabolism*
  • Single-Cell Analysis / methods*
  • Sucrose / metabolism
  • Transcriptome / genetics*


  • Sucrose