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Analysis of small RNA production patterns among the two potato spindle tuber viroid variants in tomato plants

In order to analyze the production of small RNA (sRNA) by viroids upon infecting the plants, the tomato plants (Solanum lycopersicum cultivar Rutgers) were inoculated with the variants of Potato spindle tuber viroid (PSTVd). After 21-days of postinoculation, total RNA was extracted and subjected for...

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Autores principales: Adkar-Purushothama, Charith Raj, Perreault, Jean-Pierre, Sano, Teruo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4664692/
https://www.ncbi.nlm.nih.gov/pubmed/26697336
http://dx.doi.org/10.1016/j.gdata.2015.08.008
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author Adkar-Purushothama, Charith Raj
Perreault, Jean-Pierre
Sano, Teruo
author_facet Adkar-Purushothama, Charith Raj
Perreault, Jean-Pierre
Sano, Teruo
author_sort Adkar-Purushothama, Charith Raj
collection PubMed
description In order to analyze the production of small RNA (sRNA) by viroids upon infecting the plants, the tomato plants (Solanum lycopersicum cultivar Rutgers) were inoculated with the variants of Potato spindle tuber viroid (PSTVd). After 21-days of postinoculation, total RNA was extracted and subjected for deep-sequencing using Illumina HiSeq platform. The primers were trimmed and only 21- to 24-nt long sRNAs were filtered after quality check of the raw data. The filtered sRNA population was then mapped against both 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. High-throughput sequence data linked to this project have been deposited in the Gene Expression Omnibus (GEO) database under accession number GSE69225.
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spelling pubmed-46646922015-12-22 Analysis of small RNA production patterns among the two potato spindle tuber viroid variants in tomato plants Adkar-Purushothama, Charith Raj Perreault, Jean-Pierre Sano, Teruo Genom Data Data in Brief In order to analyze the production of small RNA (sRNA) by viroids upon infecting the plants, the tomato plants (Solanum lycopersicum cultivar Rutgers) were inoculated with the variants of Potato spindle tuber viroid (PSTVd). After 21-days of postinoculation, total RNA was extracted and subjected for deep-sequencing using Illumina HiSeq platform. The primers were trimmed and only 21- to 24-nt long sRNAs were filtered after quality check of the raw data. The filtered sRNA population was then mapped against both 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. High-throughput sequence data linked to this project have been deposited in the Gene Expression Omnibus (GEO) database under accession number GSE69225. Elsevier 2015-08-12 /pmc/articles/PMC4664692/ /pubmed/26697336 http://dx.doi.org/10.1016/j.gdata.2015.08.008 Text en © 2015 The Authors http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Data in Brief
Adkar-Purushothama, Charith Raj
Perreault, Jean-Pierre
Sano, Teruo
Analysis of small RNA production patterns among the two potato spindle tuber viroid variants in tomato plants
title Analysis of small RNA production patterns among the two potato spindle tuber viroid variants in tomato plants
title_full Analysis of small RNA production patterns among the two potato spindle tuber viroid variants in tomato plants
title_fullStr Analysis of small RNA production patterns among the two potato spindle tuber viroid variants in tomato plants
title_full_unstemmed Analysis of small RNA production patterns among the two potato spindle tuber viroid variants in tomato plants
title_short Analysis of small RNA production patterns among the two potato spindle tuber viroid variants in tomato plants
title_sort analysis of small rna production patterns among the two potato spindle tuber viroid variants in tomato plants
topic Data in Brief
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4664692/
https://www.ncbi.nlm.nih.gov/pubmed/26697336
http://dx.doi.org/10.1016/j.gdata.2015.08.008
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