Ontology highlight
ABSTRACT:
PROVIDER: PRJNA881284 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21604278_1.fastq.gz | Fastqsanger.gz | |||
| SRR21604278_2.fastq.gz | Fastqsanger.gz | |||
| SRR21604279_1.fastq.gz | Fastqsanger.gz | |||
| SRR21604279_2.fastq.gz | Fastqsanger.gz | |||
| SRR21604280_1.fastq.gz | Fastqsanger.gz |
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Project description:The cucumber mosaic virus (CMV) 2b counter-defense protein disrupts plant antiviral mechanisms mediated by RNA silencing and salicylic acid (SA). Using NASC ATH-1 microarrays to investigate defensive gene expression in 2b-transgenic Arabidopsis thaliana plants we found that, surprisingly, 2b inhibited expression of few SA-regulated genes and in some instances enhanced the effect of SA on certain genes. Strikingly, the 2b protein inhibited changes in the expression of 90% of genes regulated by jasmonic acid (NASCARRAYS-415: Lewsey et al. Molec. Plant-Microbe Interact. vol. 23, in press). We will extend this work to understand the effects of the 2b protein on plant gene expression during an authentic viral infection. By comparing the effects on the transcriptome of infection by wild-type CMV and the 2b gene deletion mutant, CMVâËâ 2b, we will reveal not only the influence of the 2b protein but also the effects of its interactions with other viral gene products (and the process of infection itself), on the host transcriptome. 9 samples were used in this experiment
2012-05-14 | E-GEOD-37921 | biostudies-arrayexpress
Project description:This study evaluates the transcriptome of Arabidopsis thaliana seedlings (Col-0 ecotype) treated with methyl jasmonate (MeJA) or with the salicylic acid analog benzothiadiazole (BTH).
2017-01-12 | GSE90077 | GEO
Project description:To study the effect of plant metabolites on M. oryzae, we selected salicylic acid (SA), abscisic acid (ABA), and sakuranetin to treat M. oryzae grown on the medium with the concentration of 100μM. After 10 days' treatment, the total RNA were extracted and detected the transcriptome.
2023-11-25 | GSE248232 | GEO
Project description:The cucumber mosaic virus (CMV) 2b counter-defense protein disrupts plant antiviral mechanisms mediated by RNA silencing and salicylic acid (SA). Using NASC ATH-1 microarrays to investigate defensive gene expression in 2b-transgenic Arabidopsis thaliana plants we found that, surprisingly, 2b inhibited expression of few SA-regulated genes and in some instances enhanced the effect of SA on certain genes. Strikingly, the 2b protein inhibited changes in the expression of 90% of genes regulated by jasmonic acid (NASCARRAYS-415: Lewsey et al. Molec. Plant-Microbe Interact. vol. 23, in press). We will extend this work to understand the effects of the 2b protein on plant gene expression during an authentic viral infection. By comparing the effects on the transcriptome of infection by wild-type CMV and the 2b gene deletion mutant, CMVâËâ 2b, we will reveal not only the influence of the 2b protein but also the effects of its interactions with other viral gene products (and the process of infection itself), on the host transcriptome.
2012-05-15 | GSE37921 | GEO
Project description:Purpose: The goals of this study are using RNA-seq to obtain cucumber and Botrytis cinerea transcriptome changes during infection Methods: mRNA profiles of anti-infection samples and interaction sample were generate by deep sequencing,using Illumina Hiseq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: BurrowsâWheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRTâPCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow,In total, 248,908,688 raw reads were generated; after removing low-quality reads and those containing adapter and poly-N, 238,341,648 clean reads remained to map the reference genome. There were 3,512 cucumber (differential expression genes) DEGs and 1,735 B. cinerea DEGs. GO enrichment and KEGG enrichment analysis were performed on these DEGs to study the interaction between cucumber and B. cinerea. To verify the reliability and accuracy of our transcriptome data, 5 cucumber DEGs and 5 B. cinerea DEGs were chosen for RT-PCR verification. Conclusions:To the best of our knowledge, this is the first analysis of large-scale transcriptome changes of cucumber during the infection of Botrytis cinerea. These results will increase our understanding of the molecular mechanisms of the cucumber defense Botrytis cinerea and may be used to protect plants against disasters caused by necrotrophic fungal pathogens. mRNA profiles of infection and anti-infection cucumber were generated by deep sequencing, using Illumina Hiseq 2500 .
2016-08-01 | E-GEOD-72191 | biostudies-arrayexpress
Project description:Background: Melatonin is considered to be a polyfunctional master regulator in animals and higher plants. Exogenous melatonin inhibits plant infection by multiple diseases; however, the role of melatonin in cucumber green mottle mosaic virus (CGMMV) infection remains unknown. Results: In this study, we demonstrated that exogenous melatonin treatment can effectively control CGMMV infection. The greatest control effect was achieved by 3 days of root irrigation at a melatonin concentration of 50 µM. Exogenous melatonin showed preventive and therapeutic effects against CGMMV infection at early stage in tobacco and cucumber. We utilized RNA sequencing technology to compare the expression profiles of mock-inoculated, CGMMV-infected, and melatonin+CGMMV-infected tobacco leaves. Defense-related gene CRISP1 was specifically upregulated in response to melatonin, but not to salicylic acid (SA). Silencing CRISP1 enhanced the preventive effects of melatonin on CGMMV infection, but had no effect on CGMMV infection. We also found exogenous melatonin has preventive effects against another Tobamovirus, pepper mild mottle virus (PMMoV) infection. Conclusions: Together, these results indicate that exogenous melatonin controls two Tobamovirus infection and inhibition of CRISP1 enhanced melatonin control effects against CGMMV infection, which may lead to the development of a novel melatonin treatment for Tobamovirus control.
2022-12-30 | GSE221904 | GEO
Project description:Purpose: The goals of this study are using RNA-seq to obtain cucumber and Botrytis cinerea transcriptome changes during infection Methods: mRNA profiles of anti-infection samples and interaction sample were generate by deep sequencing,using Illumina Hiseq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow,In total, 248,908,688 raw reads were generated; after removing low-quality reads and those containing adapter and poly-N, 238,341,648 clean reads remained to map the reference genome. There were 3,512 cucumber (differential expression genes) DEGs and 1,735 B. cinerea DEGs. GO enrichment and KEGG enrichment analysis were performed on these DEGs to study the interaction between cucumber and B. cinerea. To verify the reliability and accuracy of our transcriptome data, 5 cucumber DEGs and 5 B. cinerea DEGs were chosen for RT-PCR verification. Conclusions:To the best of our knowledge, this is the first analysis of large-scale transcriptome changes of cucumber during the infection of Botrytis cinerea. These results will increase our understanding of the molecular mechanisms of the cucumber defense Botrytis cinerea and may be used to protect plants against disasters caused by necrotrophic fungal pathogens.
2016-08-01 | GSE72191 | GEO
Project description:Plants often generate secondary metabolites with antifungal properties as defense mechanisms against parasites. Although some fungi may potentially overcome the barrier of antimicrobial compounds, only a limited number of examples and molecular mechanisms of resistance have been reported. Here, we found an Aglaia plant-parasitizing fungus that overcomes the toxicity of rocalgates, which are translation inhibitors synthesized by the plant, through an amino acid substitution in a translation initiation factor (eIF). De novo transcriptome assembly of the fungus revealed that eIF4A, a molecular target of rocaglates, replaces a critical amino acid in the rocaglate binding site. Moreover, genome-wide ribosome profiling harnessing a cucumber-infecting fungus, Colletotrichum orbiculare, demonstrated that the translational inhibitory effects of rocaglates were largely attenuated by the mutation found in the Aglaia parasite. The engineered Colletotrichum orbiculare showed a survival advantage on cucumber plants with rocaglates. Our study exemplifies a plant-fungus tug-of-war centered on secondary metabolites produced by host plants.
2023-02-20 | GSE200060 | GEO
Project description:Cucumber (Cucumis sativus L.) is one of the most important fruit vegetable crops and is widely grown worldwide (FAO STAT 2016, http://faostat3.fao.org). Astringency greatly affects the flavor quality of cucumber fruits and can be irritating due to the unpleasant oral sensation it causes. However, there are no available report addressing the molecular mechanisms driving the development of cucumber fruit astringency at the transcriptome level. A few relatively basic research efforts have been carried out in our previous studies. In this study, genome-wide analysis of gene expression in the highly astringent cucumber inbred line ‘YB’ was performed using RNA-seq. The aims of this research were to identify the genes responsible for fruit astringency development and to provide new insights into the mechanism underlying the synthesis of astringent compounds in cucumber fruits.
2018-12-01 | GSE112666 | GEO