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

ABSTRACT: 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.

ORGANISM(S): Solanum lycopersicum

PROVIDER: GSE69225 | GEO | 2015/05/27

SECONDARY ACCESSION(S): PRJNA284925

REPOSITORIES: GEO

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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.

2015-05-27 | E-GEOD-69225 | biostudies-arrayexpress

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.

2020-05-26 | GSE147577 | GEO

Large scale sequencing of PSTVd-RG1 sRNA in tomato plants

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2017-09-20 | GSE70166 | GEO

Large scale sequencing of PSTVd-I sRNA in tomato plants

Project description:In order to analyze the production of small RNA (sRNA) by Potato spindle tuber viroid-intermediate strain (PSTVd-I) upon infecting the plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were inoculated with the PSTVd-I. After 21-days of post inoculation, total RNA was extracted and subjected for deep-sequencing using Illumina MiSeq platform. The primers were trimmed and the 21- to 24-nt long small RNA species were filtered after quality check of the raw data.

2017-09-20 | GSE70096 | GEO

Large scale sequencing of small RNAs in tomato plants

Project description:In order to compare the small RNA (sRNA) population between the control and Potato spindle tuber viroid (PSTVd) upon infecting the plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were mock inoculated. At 21 dpi,tTotal RNA was extracted and subjected for deep-sequencing using Illumina MiSeq platform. The primers were trimmed and the 21- to 24-nt long small RNA species were filtered after quality check of the raw data.

2017-09-20 | GSE70256 | GEO

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.

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Plant Viroid Detection Microarray

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Insight on genes affecting tuber development in potato upon Potato spindle tuber viroid (PSTVd) infection

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

Revisiting non-coding nature of viroids

Project description:Viroids are small circular highly structured pathogens infecting a broad range of plants, caus-ing economic losses. Since their discovery in the 70s, they have been considered as non-coding pathogens. In the last few years the discovery of other RNA entities, similar in terms of size and structure, that where shown to be translated (e.g cirRNAs, precursors of miRNA, RNA sat-ellites) as well as studies showing that some viroids are located in ribosomes, have reemerged the idea that viroids may be translated. In this study we used advanced bioinformatic analy-sis, in vitro experiments and LC-MS/MS to search for small viroid peptides of the Pospiviroidae PSTVd. Our results suggest that in our experimental conditions, even though the circular form of PSTVd is found in ribosomes, no produced peptides were identified. This indicates that the presence of PSTVd in ribosomes is most probably not related to peptide pro-duction but rather to another unknown function that requires further study

2022-02-17 | PXD030755 | Pride

Hop stunt viroid infection alters heterochromatin in Cucumis sativus

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

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