E-CURD-29
Ontology highlight
ABSTRACT:
PROVIDER: E-CURD-29 | ExpressionAtlas | 2020-04-03
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-CURD-29-analysis-methods.tsv | Tabular | |||
| E-CURD-29-analytics.tsv | Tabular | |||
| E-CURD-29-atlasExperimentSummary.Rdata | Rdata | |||
| E-CURD-29-configuration.xml | Xml | |||
| E-CURD-29-g4_g1-mvaPlot.png | Other |
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Project description:Diversification of Root Hair Development Genes in Vascular Plants - rice dataset
2020-04-03 | E-CURD-28 | ExpressionAtlas
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.
2017-05-11 | GSE85516 | GEO
Project description:Diversification of Root Hair Development Genes in Vascular Plants
| PRJNA338767 | ENA
Project description:Several fungi have been reported to form intimate bonds with plants. These close mutual relationships can provide physiological benefits to the interacting organisms, including the improvement of nutrient assimilation or enhanced stress tolerance. The root-colonizing fungus Fusarium sp. strain K-23 is known to successfully colonize tomato roots. Previous studies highlighted the promotion of plant biomass production and stress tolerance of tomato plants infected with the K-23. However, up to data, nothing is known about the effect of this fungus on the model plant Arabidopsis thaliana. We here report the comparative analysis of the effect of mock- and K-23-infected wild-type Arabidopsis plants (Col-0) in the abscence and presence of moderate salt stress conditions (50 mM NaCl). Our data provide evidence for a profound effect of K-23 on root hair elongation through the activation of a regulatory network that includes several plant hormones. Intriguingly, the fungus suppresses gibberellic acid biosynthesis which, in turn, promotes root hair elongation.
2024-03-20 | GSE260960 | GEO
Project description:There are two main types of root systems in flowering plants, which are taproot systems in dicot and fibrous root systems in monocot. The cellular and molecular mechanism involved in root development are mainly from the study of dicot model Arabidopsis thaliana. However, mechanisms of root development and their conservation and divergence in monocot, which including the major crops, remain largely elusive. Here we profile the transcriptomes of more than 20,000 single cells in the root tips of two rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica). Single-cell analysis coupled with in situ hybridization identify the cell type-specific marker genes and annotate all the clusters. Comparison of single-cell transcriptome and analysis of mark gene expression suggest well-conserved molecular landscape between rice Nip and 93-11. Moreover, our analysis suggests specific functions gene expression patterns for each cell type cluster, including the hormone genes. Comparison to Arabidopsis single-cell RNA-sequencing dataset reveals extensive differences between Arabidopsis and rice cell types, and species-specific features emphasize the importance of directly studying rice root. Our study reveals transcriptome landscape of major cell types of rice root in singe-cell resolution and provides molecular insight of the cell type morphology of cell type evolution in plants.
2020-12-25 | GSE146034 | GEO
Project description:There are two main types of root systems in flowering plants, which are taproot systems in dicot and fibrous root systems in monocot. The cellular and molecular mechanism involved in root development are mainly from the study of dicot model Arabidopsis thaliana. However, mechanisms of root development and their conservation and divergence in monocot, which including the major crops, remain largely elusive. Here we profile the transcriptomes of more than 20,000 single cells in the root tips of two rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica). Single-cell analysis coupled with in situ hybridization identify the cell type-specific marker genes and annotate all the clusters. Comparison of single-cell transcriptome and analysis of mark gene expression suggest well-conserved molecular landscape between rice Nip and 93-11. Moreover, our analysis suggests specific functions gene expression patterns for each cell type cluster, including the hormone genes. Comparison to Arabidopsis single-cell RNA-sequencing dataset reveals extensive differences between Arabidopsis and rice cell types, and species-specific features emphasize the importance of directly studying rice root. Our study reveals transcriptome landscape of major cell types of rice root in singe-cell resolution and provides molecular insight of the cell type morphology of cell type evolution in plants.
2020-12-25 | GSE146033 | GEO
Project description:This model is from the article:
The influence of cytokinin-auxin cross-regulation on cell-fate determination in Arabidopsis thaliana root development
Muraro D, Byrne H, King J, Voss U, Kieber J, Bennett M.
J Theor Biol.2011 Aug 21;283(1):152-67.
PMID: 21640126,
Abstract:
Root growth and development in Arabidopsis thaliana are sustained by a specialised zone termed the meristem, which contains a population of dividing and differentiating cells that are functionally analogous to a stem cell niche in animals. The hormones auxin and cytokinin control meristem size antagonistically. Local accumulation of auxin promotes cell division and the initiation of a lateral root primordium. By contrast, high cytokinin concentrations disrupt the regular pattern of divisions that characterises lateral root development, and promote differentiation. The way in which the hormones interact is controlled by a genetic regulatory network. In this paper, we propose a deterministic mathematical model to describe this network and present model simulations that reproduce the experimentally observed effects of cytokinin on the expression of auxin regulated genes. We show how auxin response genes and auxin efflux transporters may be affected by the presence of cytokinin. We also analyse and compare the responses of the hormones auxin and cytokinin to changes in their supply with the responses obtained by genetic mutations of SHY2, which encodes a protein that plays a key role in balancing cytokinin and auxin regulation of meristem size. We show that although shy2 mutations can qualitatively reproduce the effect of varying auxin and cytokinin supply on their response genes, some elements of the network respond differently to changes in hormonal supply and to genetic mutations, implying a different, general response of the network. We conclude that an analysis based on the ratio between these two hormones may be misleading and that a mathematical model can serve as a useful tool for stimulate further experimental work by predicting the response of the network to changes in hormone levels and to other genetic mutations.
2024-09-02 | BIOMD0000000416 | BioModels
Project description:Phosphate (Pi) deficiency alters root hair length and frequency as a means of increasing the absorptive surface area of roots. Three partly redundant single R3 MYB proteins, CAPRICE (CPC), ENHANCER OF TRY AND CPC1 (ETC1) and TRIPTYCHON (TRY), positively regulate the root hair cell fate by participating in a lateral inhibition mechanism. To identify putative targets and processes that are controlled by these three transcription factors (TFs), we conducted transcriptional profiling of roots from Arabidopsis thaliana wild-type plants, and cpc, etc1 and try mutants grown under Pi-replete and Pi-deficient conditions using RNA-seq.
2015-06-20 | E-MTAB-4396 | biostudies-arrayexpress
Project description:Physiological mechanisms involved in root hair development in response to magnesium (Mg) availability are unclear. This study investigated the influence of Mg availability on root hair development in arabidopsis grown in different Mg concentrations ranging from 0.5 μM to 10 mM. After 7-d treatment, root hair development was enhanced in roots exposed to low Mg but was inhibited severely in roots grown in high Mg. Low Mg (0.5 µM) enhanced many genes like LRX1, COW1, EXP7 and ROP2 that control root hair development. Low Mg supply also increased concentrations of total Ca2+ and ROS in roots, but application of either BAPTA or DPI to low Mg treatment blocked the enhanced development of root hairs. The opposite was true when the plants under high Mg (3 mM) were supplied with Ca2+ or PMS. Besides, in roots under low Mg and high Mg, the most significant biological function enrichment were in the ‘oxidation reduction’, ‘cell wall organization’, ‘ion response’. This study demonstrated that Ca2+ and ROS played critically in controlling the Mg-induced development of root hairs. Meanwhile, transcriptome analysis associated with Mg supply contributed to a better understanding of molecular events responsible for sensing Mg status. Roots were sampled from five-week-cultivated Arabidopsis after 7 d treatment of low Mg (supplied with 0.5 μM Mg2+) and high Mg (supplied with 10 mM Mg2+).
2012-12-14 | E-GEOD-42899 | biostudies-arrayexpress
Project description:A mutant previously isolated from a screen of EMS-mutagenized Arabidopsis lines, per1, showed normal root hair development under control conditions but displayed an inhibited root hair elongation phenotype upon Pi deficiency. Additionally, the per1 mutant exhibited a pleiotropic phenotype under control conditions, resembling Pi-deficient plants in several aspects. Under Pi deficiency, the accumulation of Pi and iron was increased in the mutant when compared to the wild-type. Inhibition of root hair elongation upon growth on low Pi media was reverted by treatment with the Pi analog phosphite, suggesting that the mutant phenotype is not the result of a defect in Pi sensing. Reciprocal grafting experiments revealed that the mutant rootstock is sufficient to cause the phenotype. Transcriptional profiling of per1 and wild-type plants subjected to short-term Pi starvation revealed genes that may be important for the signaling of Pi deficiency. We conclude that UBP14 function is crucial for adapting root development to the prevailing local availability of phosphate.
2009-04-14 | GSE15649 | GEO