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Plant Viroid Detection Microarray

ABSTRACT: 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.

ORGANISM(S): Pelamoviroid Apscaviroid Citrus dwarfing viroid Hop stunt viroid Avocado sunblotch viroid Avsunviroid Hostuviroid Citrus exocortis viroid Elaviroid Apscaviroid cicatricimali Hop latent viroid Pospiviroid Coleviroid Chrysanthemum chlorotic mottle viroid Peach latent mosaic viroid Cocadviroid Columnea latent viroid Coleus blumei viroid 1 Potato spindle tuber viroid unclassified viroids Tomato apical stunt viroid Tomato planta macho viroid Chrysanthemum stunt viroid

PROVIDER: GSE44334 | GEO | 2013/12/31

SECONDARY ACCESSION(S): PRJNA189479

REPOSITORIES: GEO

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Plant Viroid Detection Microarray

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

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Plant virus detection microarray

Project description:70mer probes were designed to detect plant viruses infection in genus level. This microarray platform is able to detect 169 plant virus species of 13 virus genera. Virus sampels were extracted from infected plant hosts. Genomic RNA was extracted and hybridized to the microarray.

2010-06-30 | E-GEOD-15837 | biostudies-arrayexpress

Plant Viroid Detection Microarray

Project description:Plant Viroid Detection Microarray

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Large scale sequencing of viroid derived small RNA in Potato spindle tuber viroid infected tomato plants

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. Evaluation of the vd-sRNA production in PSTVd infected tomato plants by high-throughput sequencing of small RNAs.

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Large scale sequencing of viroid derived small RNA in Potato spindle tuber viroid infected tomato plants

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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.

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Evolution of Potato spindle tuber viroid quasi-species during the course of disease in tomato plants

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.

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In depth sequencing of the siRNAs associated with peach latent mosaic viroid infection

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

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