Ontology highlight
ABSTRACT:
PROVIDER: PRJNA797929 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17642852_1.fastq.gz | Fastqsanger.gz | |||
| SRR17642852_2.fastq.gz | Fastqsanger.gz | |||
| SRR17642853_1.fastq.gz | Fastqsanger.gz | |||
| SRR17642853_2.fastq.gz | Fastqsanger.gz | |||
| SRR17642854_1.fastq.gz | Fastqsanger.gz |
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Project description:Next to their essential roles in plant growth and development, phytohormones play a central role in plant immunity against pathogens. In this study we examined the role of hormones in the antagonism of the plant-pathogenic oomycete Pythium arrhenomanes against the root-knot nematode Meloidogyne graminicola in rice roots. Hormone measurements and gene expression analyses showed that the jasmonate (JA) pathway is induced early upon P. arrhenomanes infection. Exogenous application of methyl-jasmonate (MeJA) on the plant confirmed that JA is needed for basal defence against both P. arrhenomanes and M. graminicola in rice. Whereas M. graminicola suppresses root JA levels to increase host susceptibility, Pythium inoculation boosts JA accumulation up to levels that can no longer be repressed by the nematode in double-inoculated plants. Exogenous MeJA supply phenocopied the defence-inducing capacity of P. arrhenomanes against the root-knot nematode, whereas the antagonism was weakened in JA-insensitive mutants. Transcriptome analysis confirmed upregulation of JA biosynthesis and signalling genes upon P. arrhenomanes infection, and additionally revealed induction of genes involved in biosynthesis of diterpenoid phytoalexins, consistent with strong activation of the gene encoding the JA-inducible transcriptional regulator DITERPENOID PHYTOALEXIN FACTOR. Next to that, our results provide evidence for induced expression of genes encoding ERF83, and related PR proteins, as well as auxin depletion in P. arrhenomanes infected rice roots, which potentially further contributes to the reduced nematode susceptibility seen in double-infected plants.
2019-10-21 | GSE133268 | GEO
Project description:MicroRNAs (miRNAs) are small non-coding RNAs that function as post-transcriptional regulators of gene expression in eukaryotes. In rice, miR7695 targets an alternatively spliced transcript of natural resistance-associated macrophage protein 6 (OsNramp6) encoding an iron transporter whose expression is regulated by infection with the rice blast fungus Magnaporthe oryzae. Rice plants grown under high iron supply showed blast resistance, which supports that iron is a factor in controlling blast resistance by still unknown mechanisms. Here, iron accumulated near M. oryzae appressoria, the sites of pathogen entry, and in cells surrounding infected regions of the rice leaf. Activation-tagged MIR7695 rice plants (MIR7695-Ac) exhibited enhanced resistance to M. oryzae infection. RNA-seq analysis revealed that blast resistance in MIR7695-Ac plants was associated with strong induction of defense-related genes, including pathogenesis-related and diterpenoid biosynthetic genes. Levels of phytoalexins during pathogen infection were higher in MIR7695-Ac than wild-type plants. Early phytoalexin biosynthetic genes, OsCPS2 and OsCSP4, were highly upregulated in rice plants grown under high iron supply. Our data indicate that miR7695 positively regulates rice immunity while establishing links between defense and iron signaling in rice. MiR7695-mediated regulation of OsNramp6 has great potential for the development of strategies to control rice blast disease.
2020-01-08 | GSE122258 | GEO
Project description:Double-strand break (DSB) damage are primarily repaired via homologous recombination (HR) and non-homologous end joining (NHEJ) in Eukaryotes. We reveals that HR subcomplex RAD51A1-RAD51C in rice (Oryza sativa L.) inhibits classic NHEJ pathway while acts as a transcriptional mediator underlying alternative NHEJ signaling. RAD51C hijacks the KU70 at DSBs, facilitated by the interacting partner RAD51A1 or TOP6B responding environmental cues (pathogens and 4℃). Consequently, the enhanced alternative NHEJ signaling generates the phosphorylated SOG1, which activates the regulatory network in diterpenoid phytoalexin biosynthesis and a group of genes in phenylpropanoid pathway. Intriguingly, SOG1-BRCA1-RAD51 associates with RAD51C-RAD51D-XRCC3 forming a transcription pre-initiation complex in this process. Phenotypically, chemical disease resistance and 4℃-conditioned stomatal closure are compromised in single mutants (atm-3, sog1, and rad51c-1), double mutants (rad51a1 rad51a2 and rad51d xrcc3). In summary, HR pathway integrates classic and alternative NHEJ pathways to orchestrate stress-activated specific metabolism in rice plants. Hierarchical functional collaboration of global DSB-repair machinerys enable plant adaptability to DSB-related environmental stresses.
2025-01-27 | GSE287659 | GEO
Project description:MicroRNAs (miRNAs) are small non-coding RNAs that act as post-transcriptional regulators of gene expression via sequence-specific cleavage or translational repression of target transcripts. They are transcribed as long single-stranded RNA precursors with unique stem-loop structures that are processed by a DICER-Like (DCL) ribonuclease, typically DCL1, to produce mature miRNA sequences. Here, we investigated the contribution of OsDCL1 to innate immunity in rice. Activation-tagged dcl1a mutants (dcl1a-Ac) showed enhanced susceptibility to infection by the fungal pathogens Magnaporthe oryzae and Fusarium fujikuroi. Susceptibility to pathogen infection in dcl1a-Ac plants was associated with weaker induction of defence gene expression. Plant growth and development were not affected in dcl1a-Ac plants in the absence of pathogen challenge. To analyse the impact of OsDCL1a activation on the host transcriptome, we compared the mRNA and miRNA transcriptomes of dcl1a-Ac and wild-type plants. OsDCL1a activation misregulated genes involved in detoxification of reactive oxygen species (ROS) and accumulation of O2•- in leaves. Consequently, dcl1a-Ac plants were more sensitive to oxidative stress caused by methyl viologen treatment. Notably, transcriptome analysis revealed downregulation of diterpenoid phytoalexin biosynthetic genes in dcl1a-Ac, the expression of these genes also being weakly induced during pathogen infection in these plants. Finally, OsDCL1a activation resulted in marked alterations in the rice miRNAome, including both upregulation and downregulation of miRNAs. Our findings support that OsDCL1a plays an important role in regulating innate immunity in rice.
2018-09-05 | GSE109303 | GEO
Project description:MicroRNAs (miRNAs) are small non-coding RNAs that act as post-transcriptional regulators of gene expression via sequence-specific cleavage or translational repression of target transcripts. They are transcribed as long single-stranded RNA precursors with unique stem-loop structures that are processed by a DICER-Like (DCL) ribonuclease, typically DCL1, to produce mature miRNA sequences. Here, we investigated the contribution of OsDCL1 to innate immunity in rice. Activation-tagged dcl1a mutants (dcl1a-Ac) showed enhanced susceptibility to infection by the fungal pathogens Magnaporthe oryzae and Fusarium fujikuroi. Susceptibility to pathogen infection in dcl1a-Ac plants was associated with weaker induction of defence gene expression. Plant growth and development were not affected in dcl1a-Ac plants in the absence of pathogen challenge. To analyse the impact of OsDCL1a activation on the host transcriptome, we compared the mRNA and miRNA transcriptomes of dcl1a-Ac and wild-type plants. OsDCL1a activation misregulated genes involved in detoxification of reactive oxygen species (ROS) and accumulation of O2•- in leaves. Consequently, dcl1a-Ac plants were more sensitive to oxidative stress caused by methyl viologen treatment. Notably, transcriptome analysis revealed downregulation of diterpenoid phytoalexin biosynthetic genes in dcl1a-Ac, the expression of these genes also being weakly induced during pathogen infection in these plants. Finally, OsDCL1a activation resulted in marked alterations in the rice miRNAome, including both upregulation and downregulation of miRNAs. Our findings support that OsDCL1a plays an important role in regulating innate immunity in rice.
2018-09-05 | GSE109299 | GEO
Project description:Double-strand break (DSB) damage are primarily repaired via homologous recombination (HR) and non-homologous end joining (NHEJ) in Eukaryotes. We reveals that HR subcomplex RAD51A1-RAD51C in rice (Oryza sativa L.) inhibits classic NHEJ pathway while acts as a transcriptional mediator underlying alternative NHEJ signaling. RAD51C hijacks the KU70 at DSBs, facilitated by its partner RAD51A1 or TOP6B responding environmental cues (pathogens and 4℃). Consequently, the enhanced alternative NHEJ signaling generates the phosphorylated SOG1, which activates the regulatory network in diterpenoid phytoalexin biosynthesis and a group of enzyme genes in phenylpropanoid pathway. Intriguingly, SOG1-BRCA1-RAD51 associates with RAD51C-RAD51D-XRCC3 to form a transcription pre-initiation complex in this process. Phenotypically, chemical disease resistance and 4℃-conditioned stomatal closure are compromised in single mutants (atm-3, sog1, and rad51c-1), double mutants (rad51a1 rad51a2 and rad51d xrcc3). In summary, HR pathway integrates classic and alternative NHEJ pathways to orchestrate stress-activated specific metabolism in rice. Hierarchical collaboration of global DSB-repair machinerys enable plant adaptability to DSB-related environmental stresses.
2025-01-30 | GSE288025 | GEO
Project description:We used mRNA sequencing to study the effects of foliar treatment with piperonylic acid, acibenzolar-S-methyl or beta-aminobutyric acid on the root transcriptome of rice plants (cv. Kitaake) in order to find conserved systemic responses to distinct resistance-inducing stimuli
2022-12-06 | GSE194400 | GEO
Project description:There is mounting evidence for the role of epigenetic processes in the regulation of plant responses to a wide range of external stimuli. Despite their importance, the significance of epigenetic processes in plant-pathogen interactions remain poorly understood. So far, the role of histone modifications has not been investigated at genome wide level in plant-nematode interactions, although their expression levels are altered in nematode-induced galls. In this study, we first applied chemical inhibitors of histone modifying enzymes on rice plants. Despite theirdistinct effects on histone modifications, application of different concentrations of Niconinamide, sulfamethazine and fumaric acid lead to reduced susceptibility to nematode infection. Similarly, two overexpression lines of histone lysine methyltransferases and one histone deacetylase were analyzed in an infection assay with nematodes, showing contrasting results in susceptibility. These data indicate that histone modifications can affect plant defence against nematodes in rice. To further investigate their effect, the genome-wide level of three histone marks namely H3K9ac, H3K9me2 and H3K27me3 was studied by chromatin-immunoprecipitation (ChIP)-sequencing on nematode-induced galls in comparison with control root tips.
2021-02-17 | GSE145501 | GEO
Project description:Rice (Oryza sativa L.) is one of the most important staple foods in the world, feeding more than 50% of the human population. One of its most damaging pathogens, with major impact on rice yield, is the migratory root rot nematode Hirschmanniella oryzae. In comparison with the existing knowledge on the infection process of dicots by sedentary nematodes, far less is known about the interaction between monocot plants and nematodes or plant interactions with migratory nematode species. Therefore, to gain deeper insight into the systemic transcriptional changes in rice after migratory root rot nematode infection we have performed mRNA-Seq on the shoots of root rot nematode infected rice plants. The observations were independently validated using qRT-PCR and biochemical analyses. This research reveals significant modifications in the metabolism of the plant, with a general suppression of chlorophyll biosynthesis, and primary metabolic processes involved in plant growth .
2015-05-18 | GSE57707 | GEO
Project description:WRKY45-overexpressing (WRKY45-ox) rice plants are extremely resistant to rice blast and bacterial leaf-blight diseases. To search for the genes that are potentially responsible for the strong resistance, we performed genome-wide gene expression analysis in WRKY45-ox rice. A microarray analysis using Agilent rice oligo microarray for approximately 42,000 rice genes identified 1,664 genes that are upregulated in WRKY45-ox rice compared with non-transformant rice cv. Nipponbare (NB). Analysis of the genes with altered expression in WRKY45-ox rice by a Gene ontology program (Agri GO; http://bioinfo.cau.edu.cn/agriGO/) revealed that several genes in the biosynthetic pathway for diterpenoid phytoalexins, for which anti-blast fungus activities have been reported, were upregulated in WRKY45-ox rice.
2013-12-31 | GSE48202 | GEO