Project description:Purpose: The root hair is a model for understanding evolution of individual cell differentiation programs in plants. We compare the expression of the genes that participate in root hair development between Arabidopsis and other vascular plants to assess the conservation/diversification of the root hair development programs in vascular plants. Methods: We used RNA-Seq, in triplicates, to measure the genome-wide transcription activity of the root-hair cells isolated by Fluorescence-activated cell sorting (FACS) in Arabidopsis (COBL9::GFP transgeneic line, AtRH) and rice (EXPA30::GFP transgenic line, OsRH). We also generated RNA-Seq data, in triplicates, on the Arabidopsis rhd6 WER::GFP and WT WER::GFP by FACS to identify the RHD6-regulating root hair morphogenesis genes (AtRHM). For Arabidopsis, rice, tomato, soybean, cucumber and maize, we used RNA-seq, in triplicates, to measure genome-wide transcription activity of root hair cells filtered by sieves after stirred in liquid nitrogen (HAIR genes). Each sample was trimmed to retain high-quality reads, mapped to the reference genome by TopHat, and quantified by Cufflinks. The number of raw reads of Arabidopsis rhd6 WER::GFP and WT WER::GFP sample was counted by HTSeq and analyzed by edgeR to identify the differentially expressed genes. Results: We defined the root-hair transcriptome in diverse vascular plant species and analyzed the relative conservation/divergence in the expression of a large set of gene families.
Project description: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.
2019-02-05 | GSE123013 | GEO
Project description:RNA-seq of Arabidopsis root under Pb stress