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Expression data from rice leaves treated or not with fungal elicitors and high-throughput pyrosequencing of endogenous small RNAs from Oryza sativa

ABSTRACT: High-throughput sequencing of small RNAs from rice was used to identify distinct miRNAs that are responsive to elicitors from the fungal pathogen Magnaporthe oryzae. [Expression profiling by array] We used microarrays to determine the expression behaviour of target genes for elicitor-regulated miRNAs. [High throughput sequencing] High-throughput sequencing of rice small RNAs was performed in two different tissues, leaves and roots, and two different time point of elicitor treatment, 30' and 2h Amplicons were prepared by 5´and 3´adaptor ligation in which the 5'-adaptor contained a 'barcode' consisting of a 4-nucleotide identifier sequence for each sample. The libraries containing unique barcodes were combined and subjected to pyrosequencing (454 Life SciencesTM, Roche)

ORGANISM(S): Oryza sativa Oryza sativa Japonica Group

PROVIDER: GSE30583 | GEO | 2014/01/15

SECONDARY ACCESSION(S): PRJNA144497

REPOSITORIES: GEO

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Expression data from rice leaves treated or not with fungal elicitors and high-throughput pyrosequencing of endogenous small RNAs from Oryza sativa

Project description:High-throughput sequencing of small RNAs from rice was used to identify distinct miRNAs that are responsive to elicitors from the fungal pathogen Magnaporthe oryzae. [Expression profiling by array] We used microarrays to determine the expression behaviour of target genes for elicitor-regulated miRNAs. [High throughput sequencing] High-throughput sequencing of rice small RNAs was performed in two different tissues, leaves and roots, and two different time point of elicitor treatment, 30' and 2h Amplicons were prepared by 5M-BM-4and 3M-BM-4adaptor ligation in which the 5'-adaptor contained a 'barcode' consisting of a 4-nucleotide identifier sequence for each sample. The libraries containing unique barcodes were combined and subjected to pyrosequencing (454 Life SciencesTM, Roche) [Expression profiling by array] Leaves from rice plants were harvested at two time points after the onset of treatment (30' and 2h) with elicitors of Magnaporthe oryzae 18.1 and used for RNA extraction and hybridization on Affymetrix microarrays. Mock inoculations were performed with sterile water for control experiments. Three biological replicates were analyzed. Each sample represented a pool of approximately 150 rice plants. [High throughput sequencing] 8 samples examined: leaves and roots, treated or not with elicitors at two different time points, 30' and 2h (2x2x2)

2014-01-15 | E-GEOD-30583 | biostudies-arrayexpress

MicroRNA-mediated regulation of gene expression in the response of rice plants to fungal elicitors [degradome]

Project description:Elicitor-responsive miRNAs and their targets in rice

2016-03-06 | GSE66610 | GEO

MicroRNA-mediated regulation of gene expression in the response of rice plants to fungal elicitors [miRNA-Seq]

Project description:Elicitor-responsive miRNAs and their targets in rice

2016-03-06 | GSE66609 | GEO

The virulome of Streptomyces scabiei in response to cello-oligosaccharides elicitors

Project description:We provide a manually-curated genome mining analysis of the bacterial plant pathogen Streptomyces scabiei. The expression of the deduced biosynthetic gene clusters was assessed by a RNAseq approach, and their potential to be induced by the virulence elicitors cellobiose and cellotriose was estimated by comparing mRNA levels before and after elicitor addition. Finally, we performed metabolomic analyzes to evaluate how the production of known specialized metabolites responds to virulence elicitors, in correlation (or not) with the transcriptomic data

2021-08-08 | GSE181490 | GEO

Study of bacterial and fungal elicitors on rice plant

Project description:Study of bacterial and fungal elicitors on rice plant

| PRJEB36533 | ENA

Bacterial lipopolysaccharides induce defense responses associated with Programmed cell death in rice cell

Project description:PAMP (Pathogen-Associated Molecular Pattern) recognition plays an important role in innate immune responses both in plants and animals. Lipopolysaccharides (LPS) of gram-negative bacteria are a typical PAMP molecule and have been reported to induce defense-related responses such as suppression of hypersensitive responses, defense gene espression and systemic resistance in plant. However the detailed analysis of these cellular responses and the molecular machinery involved in the perception and transduction of LPS molecule largely remains to be studied. Furthermore, the biological activities of LPS on plants have so far been reported only for dicots and no information is available on the action of LPS on monocots. We report here that bacterial LPSs, both from plant pathogens and non-pathogens, could induce various defense responses in rice cells, including reactive oxygen generation and defense gene expression. Global analysis of gene expression induced by two PAMP elicitors, LPS and chitin oligosaccharide elicitor, showed a close correlation between the gene responses induced by these elicitors, indicating the convergence of signaling cascades downstream of corresponding receptors. Further, we show that the defense responses induced by LPS are associated with programmed cell death, a finding so far not reported for LPS action on plant cells. Keywords: elicitor, defense, LPS, rice cell

2006-09-28 | GSE5906 | GEO

Rice gene global expression analysis upon inoculation with different Magnaporthe isolates

Project description:Magnaporthe oryzae is the causative agent of the rice blast, the most relevant rice disease worldwide. To date expression analysis on rice infected with Magnaporthe oryzae have been carried out only with the strains FR13 (leaf) and Guy 11 (root). However different strains of Magnaporthe are present in the environment leading to different rice responses at molecular level. To gain more insight on the unknown molecular mechanisms activated by different Magnaporthe strains during rice defense, a global expression analysis was performed by using the GeneChip® Rice Genome Array. To identify rice genes differentially regulated upon infection by Magnaporthe isolates, inoculation with different strains were performed and samples were collected 24 hours post infection.

2012-03-27 | GSE30941 | GEO

Small RNA profiling of Arabidopsis in response to fungal elicitors

Project description:This experiment describes small RNA gene expression after treatment of Arabidopsis seedlings with elicitors obtained from the fungus F. oxysporum

2014-12-01 | GSE59978 | GEO

Proteomic changes in Oryza sativa leaves in response to MSP1 and flg22 treatments

Project description:Rice blast disease caused by Magnaporthe oryzae is one of the most damaging diseases affecting rice productivity. Previously, we reported a novel M. oryzae- secreted protein MSP1, which triggers cell death and pathogen-associated molecular pattern (PAMP)-triggered immune (PTI) responses in rice. To investigate the MSP1 induced defense response in rice at the protein level, we employed a label-free quantitative proteomic approach, in parallel with the flg22, which is a wellknown elicitor. Proteomics analysis using the MaxQuant-Perseus platform led to the identification of 4087 proteins of which 417 showed significant differences (multiple sample test, ANOVA p<0.05) in response to MSP1 and/or flg22 treatments. Functional annotation of the differential proteins showed that proteins related to the primary metabolism, secondary metabolism and lipid metabolism were strongly down-regulated, while elevated proteins were mainly associated with the stress response, chromatin remodeling, post-translational modification of proteins and signaling.

2018-07-06 | PXD008069 | Pride

RNAseq of wt and receptor mutant lines in response to 7 elicitor treatments over a 6-point time course

Project description:The degree to which plants discriminate among elicitors in early transcriptional responses is unknown. To test this, we selected a panel of seven elicitors recognized by the model plant Arabidopsis thaliana. Two-week old Arabidopsis seedlings in liquid culture were treated with each elicitor individually, and tissue flash-frozen at 0, 5, 10, 30, 90, and 180 min post-treatment. As a control, receptor mutants for each elicitor were treated and harvested in parallel with wt plants. The experiment was repeated four times. mRNA was extracted via pulldown of poly-A tail from bulk lysate, and libraries were prepared via tagmentation with custom Tn-5 adapter oligos. Libraries for each experiment were pooled, and sequenced across 2-3 flowcells of a NextSeq500 benchtop sequencer.

2021-01-29 | E-MTAB-9694 | biostudies-arrayexpress

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