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Comparative analysis of gene expression in tomato roots during mild and severe potato spindle tuber viroid infection. [roots RNA-seq]

ABSTRACT: Comparative analysis of gene expression in tomato roots during mild and severe potato spindle tuber viroid infection.

ORGANISM(S): Solanum lycopersicum

PROVIDER: GSE125228 | GEO | 2019/12/31

REPOSITORIES: GEO

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

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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. 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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Comparative analysis of gene expression in tomato leaves during mild and severe potato spindle tuber viroid infection.

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Comparative analysis of gene expression in tomato roots during mild and severe potato spindle tuber viroid infection.

Project description:Comparative analysis of gene expression in tomato roots during mild and severe potato spindle tuber viroid infection.

| PRJNA437993 | ENA

Comparative analysis of gene expression in tomato roots during mild and severe potato spindle tuber viroid infection. [roots RNA-seq]

Project description:Comparative analysis of gene expression in tomato roots during mild and severe potato spindle tuber viroid infection. [roots RNA-seq]

| PRJNA515609 | ENA

Comparative analysis of gene expression in tomato leaves during mild and severe potato spindle tuber viroid infection.

Project description:Comparative analysis of gene expression in tomato leaves during mild and severe potato spindle tuber viroid infection.

| PRJNA418441 | ENA