Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1277283 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR33991771.fastq.gz | Fastqsanger.gz | |||
| SRR33991772.fastq.gz | Fastqsanger.gz | |||
| SRR33991773.fastq.gz | Fastqsanger.gz | |||
| SRR33991774.fastq.gz | Fastqsanger.gz | |||
| SRR33991775.fastq.gz | Fastqsanger.gz |
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Project description:40mer probes were designed to detect plant viroids infection at the genus level. This microarray platform is able to detect a wide spectrum of all the 8 reported viroid genera, including 37 known plant viroid species. Viroid samples were extracted from infected plant hosts and plasmids. Total RNA was extracted and hybridized to the microarray.
2013-12-31 | E-GEOD-44334 | biostudies-arrayexpress
Project description:40mer probes were designed to detect plant viroids infection at the genus level. This microarray platform is able to detect a wide spectrum of all the 8 reported viroid genera, including 37 known plant viroid species.
2013-12-31 | GSE44334 | GEO
Project description:Plant Viroid Detection Microarray
| PRJNA189479 | ENA
Project description:Potato (Solanum tuberosum L) is a natural host of Potato spindle tuber viroid (PSTVd) which can cause characteristic symptoms on developing plants including stunting phenotype and distortion of leaves and tubers. PSTVd is the type species of the family Pospiviroidae, it can replicate in the nucleus and the viroid RNA moves systemically in infected plants. Its KF440-2 strain can cause severe symptoms in potato. It is not well understood how the viroid can affect host genes for successful invasion and which genes show altered expression levels upon infection. In this study, we used a high-scale method to identify differentially expressed genes in potato. We have identified defence, stress and sugar metabolism related genes having altered expression levels upon infection. Additionally, hormone pathways connected genes showed up- or down-regulation. Our primary focus is on the identification of genes which can affect tuber formation as the viroid infection can strongly influence tuber development, especially tuber shape is affected. DWARF1/DIMINUTO, Gibberellin 7-oxidase and BEL5 protein were identified and validated which showed differential expression in viroid infected tissues suggesting that gibberellin and brassinosteroid pathways have a possible role in tuber development upon PSTVd infection.
2016-02-01 | E-MTAB-3869 | biostudies-arrayexpress
Project description:Using a high-throughput sequencing approach we quantitatively analyzed the content of viroid-derived siRNAs of an infected tree. Our results show that the entire PLMVd genome is found in the siRNA population. Also both polarities are susceptible to be targeted by the RNAi machinery but specific regions for each polarity are over represented. Those regions, that are not the same for each polarity, do not necessarily correlate with double stranded regions that could be substrate for Dicer-like enzymes. Finally the analysis of the first 5’ nucleotide revealed a bias toward a C or a U in viroid-derived siRNAs, indicating that at least AGO5 and AGO1 can recruit these small RNAs. Analysis of siRNAs population from RNA sample isolated from a viroid-infected tree
2010-02-20 | E-GEOD-18764 | biostudies-arrayexpress
Project description:The development of viroid-elimination technology is an important means to ensure the production of tomatoes. Viroid is an obligate pathogen that can infect the apical meristem cells. The combination of low-temperature therapy and meristem culture is a commonly used method for viroid eradication, but tomatoes cannot withstand long-term low-temperature treatment. This study identified a new HSVd genotype and measured the growth and physiological parameters of diseased tomato “Alisa Craig”. Five HSVd-targeting ds-sRNAs were synthesized to match different regions of the HSVd genome, and their permeability in plants was tested. By screening the types of ds-sRNA and processing duration, the optimal treatment for inhibiting HSVd in diseased tomato shoot terminal was obtained. miRNAs produced by HSVd genome were detected by using miRNA-seq and degradation-seq to verify the occurrence of the ds-sRNA induced HSVd gene silencing. Exogenous ds-sRNA can penetrate all cells including vascular bundles, thin-walled cells, and stem apical meristematic tissues and induced HSVd gene silencing in shoot terminals, leading to the accumulation of miRNAs produced by HSVd in plants.
2024-02-07 | GSE254910 | GEO
Project description:In order to verify the production of viroid specific small RNAs (vd-sRNA) by viroids upon infecting plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were inoculated with Potato spindle tuber viroid (PSTVd) variants. After 21-days of post inoculation, total RNA was extracted and subjected for deep-sequencing using Illumina platform. Obtained data was analyzed for the presence of PSTVd specific small RNAs.
2020-05-26 | GSE147577 | GEO
Project description:In order to analyze the production of small RNA (sRNA) by viroids upon infecting the plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were inoculated with the variants of Potato spindle tuber viroid (PSTVd). After 21-days of post inoculation, total RNA was extracted and subjected for deep-sequencing using Illumina platform. The primers were trimmed and only 21- to 24-nt long small RNAs were filtered after quality check of the raw data. The filtered 21- to 24-nt was mapped against the genomic and antigenomic strands of the respective PSTVd variants using standard pattern matching algorithm. The profiling of viroid derived sRNA (vd-sRNA) revealed that the viroids are susceptible to host RNA silencing mechanism.
2015-05-27 | GSE69225 | GEO
Project description:Using a high-throughput sequencing approach we quantitatively analyzed the content of viroid-derived siRNAs of an infected tree. Our results show that the entire PLMVd genome is found in the siRNA population. Also both polarities are susceptible to be targeted by the RNAi machinery but specific regions for each polarity are over represented. Those regions, that are not the same for each polarity, do not necessarily correlate with double stranded regions that could be substrate for Dicer-like enzymes. Finally the analysis of the first 5’ nucleotide revealed a bias toward a C or a U in viroid-derived siRNAs, indicating that at least AGO5 and AGO1 can recruit these small RNAs.
2010-02-20 | GSE18764 | GEO
Project description:Viroids are pathogenic non-coding RNAs that completely rely on their host molecular machinery to accomplish their life cycle. Several interactions between viroids and their host molecular machinery have been identified, including an interference with epigenetic mechanisms such as DNA methylation. Despite this, whether viroids influence changes in other epigenetic marks such as histone modifications remained unknown. Epigenetic regulation is particularly important during pathogenesis processes because it might be a key regulator of the dynamism of the defense response. Here we have analyzed the changes taking place in Cucumis sativus facultative and constitutive heterochromatin during hop stunt viroid (HSVd) infection using chromatin immunoprecipitation (ChIP) of the two main heterochromatic marks: H3K9me2 and H3K27me3. We find that HSVd infection is associated with changes in both H3K27me3 and H3K9me2, with a tendency to decrease the levels of repressive epigenetic marks through infection progression. These epigenetic changes are connected to the transcriptional regulation of their expected targets, genes and transposable elements. Indeed, several genes connected to the defense response are targets of both epigenetic marks. Our results highlight another host regulatory mechanism affected by viroid infection, providing further information about the complexity of the multiple layers of interactions between pathogens/viroids and hosts/plants.
2024-07-15 | GSE249651 | GEO