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...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2015-12-01
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| Series: | Genomics Data |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2213596015300027 |
| _version_ | 1818539119373975552 |
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| author | Charith Raj Adkar-Purushothama Jean-Pierre Perreault Teruo Sano |
| author_facet | Charith Raj Adkar-Purushothama Jean-Pierre Perreault Teruo Sano |
| author_sort | Charith Raj Adkar-Purushothama |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-11T21:37:50Z |
| format | Article |
| id | doaj.art-a3e07cc46be4453884719aa54a202b22 |
| institution | Directory Open Access Journal |
| issn | 2213-5960 |
| language | English |
| last_indexed | 2024-12-11T21:37:50Z |
| publishDate | 2015-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Genomics Data |
| spelling | doaj.art-a3e07cc46be4453884719aa54a202b222022-12-22T00:49:57ZengElsevierGenomics Data2213-59602015-12-016C656610.1016/j.gdata.2015.08.008Analysis of small RNA production patterns among the two potato spindle tuber viroid variants in tomato plantsCharith Raj Adkar-Purushothama0Jean-Pierre Perreault1Teruo Sano2RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, Québec J1E 4K8, CanadaRNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, Québec J1E 4K8, CanadaFaculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, JapanIn 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.http://www.sciencedirect.com/science/article/pii/S2213596015300027ViroidsPotato spindle tuber viroidViroid derived small RNARNA silencing |
| spellingShingle | Charith Raj Adkar-Purushothama Jean-Pierre Perreault Teruo Sano Analysis of small RNA production patterns among the two potato spindle tuber viroid variants in tomato plants Genomics Data Viroids Potato spindle tuber viroid Viroid derived small RNA RNA silencing |
| 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 | Viroids Potato spindle tuber viroid Viroid derived small RNA RNA silencing |
| url | http://www.sciencedirect.com/science/article/pii/S2213596015300027 |
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