Single-cell RNA-sequencing analysis of Arabidopsis roots

We report the use of high-throughput single-cell RNA sequencing (scRNA-seq) to analyze gene expression in wild-type and mutant Arabidopsis root cells. We demonstrate that using a commercially available platform for droplet-based scRNA-seq (10X Genomics Chromium) enables transcriptional profiling of individual protoplasts representing all of the major cell/tissue types of the root. Furthermore, rare cell types and subtypes have been identified. These single-cell transcriptomes were also used to generate a pseudotime series for the root hair and non-hair cell differentiation pathways. In addition, scRNA-seq was used to define and compare transcriptomes from root epidermis mutants, which enabled a detailed molecular analysis of the mutant phenotype. This study demonstrates the feasibility and usefulness of scRNA-seq in plants and provides a gene expression map at single-cell resolution for the Arabidopsis root. Overall design: Analysis of gene expression among WT(Col-0), hairless mutant(rhd6-1) and hairy mutant(gl2) at the single cell level