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Potato spindle tuber viroid strain:intermediate strain

ABSTRACT: Potato spindle tuber viroid strain:intermediate strain Raw sequence reads

PROVIDER: PRJNA1050043 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27144335_1.fastq.gz	Fastqsanger.gz
	SRR27144335_2.fastq.gz	Fastqsanger.gz
	SRR27144336_1.fastq.gz	Fastqsanger.gz
	SRR27144336_2.fastq.gz	Fastqsanger.gz
	SRR27144337_1.fastq.gz	Fastqsanger.gz

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Potato spindle tuber viroid strain:intermediate

Project description:Potato spindle tuber viroid strain:intermediate

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Project description:Potato spindle tuber viroid strain:Intermediate strain Raw sequence reads

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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.

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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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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.

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