Abstract
Root hairs, tubular-shaped outgrowths from root epidermal cells, play important roles in the acquisition of nutrients and water, interaction with microbe, and in plant anchorage. As a specialized cell type, root hairs, especially in Arabidopsis, provide a pragmatic research system for various aspects of studies. Here, we re-analyzed the RNA-seq transcriptome profile of Arabidopsis root hair cells by Tophat software and used Cufflinks program to mine the differentially expressed genes. Results showed that ERD14, RIN4, AT5G64401 were among the most abundant genes in the root hair cells; while ATGSTU2, AT5G54940, AT4G30530 were highly expressed in non-root hair tissues. In total, 5409 genes, with a fold change greater than two-fold (FDR adjusted P < 0.05), showed differential expression between root hair cells and non-root hair tissues. Of which, 61 were expressed only in root hair cells. One hundred and thirty-six out of 5409 genes have been reported to be “core” root epidermal genes, which could be grouped into nine clusters according to expression patterns. Gene ontology (GO) analysis of the 5409 genes showed that processes of “response to salt stress,” “ribosome biogenesis,” “protein phosphorylation,” and “response to water deprivation” were enriched. Whereas only process of “intracellular signal transduction” was enriched in the subset of 61 genes expressed only in the root hair cells. One hundred and twenty-one unannotated transcripts were identified and 14 of which were shown to be differentially expressed between root hair cells and non-root hair tissues, with transcripts XLOC_000763, XLOC_031361, and XLOC_005665 being highly expressed in the root hair cells. The comprehensive transcriptomic analysis provides new information on root hair gene activity and sets the stage for follow-up experiments to certify the biological functions of the newly identified genes and novel transcripts in root hair cell morphogenesis.
Highlights
IntroductionRoot hairs provide a remarkably tractable system for various aspects of studies, such as development, cell biology, and physiology, in Arabidopsis thaliana (Dolan et al, 1998; Ryan et al, 2001; Grebe, 2012; Grierson et al, 2014)
Digital Information on Gene Expression in Root Hairs and Non-root Hair Tissues at Genome-wide Level In previous study, using transgenic plants carrying Expansin7 (EXP7) promoter fused to GFP as materials (Cho and Cosgrove, 2002), coupled with fluorescence-activated cell sorting (FACS) technique, Arabidopsis root hair protoplasts were harvested and the transcriptome profiling has been explored by RNA-seq from two biological repeats
The RNA-seq data were re-analyzed by aligning the paired-end reads to Arabidopsis Genome released in TAIR10 via Tophat program (Trapnell et al, 2009)
Summary
Root hairs provide a remarkably tractable system for various aspects of studies, such as development, cell biology, and physiology, in Arabidopsis thaliana (Dolan et al, 1998; Ryan et al, 2001; Grebe, 2012; Grierson et al, 2014). More than 45 genes including ROOT HAIR DEFECTIVE 6 (RHD6), ROOT HAIR DEFECTIVE 2 (RHD2), EXPANSIN A7 (EXPA7), and EXPANSIN A18 (EXPA18) have been proved to be involved in root hair morphogenesis by molecular genetics studies (Grierson et al, 2014) These genes coordinately regulate the processes of Rop-GTPase re-localization and subsequently mediated signaling, vesicle trafficking, cell wall reassembly, establishment of ion gradients, reorganization of cytoskeleton (actin and microtubule), and producing and homoeostasismaintaining of reactive oxygen species (Ishida et al, 2008; Grierson et al, 2014)
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