title: Analysis of small RNA production patterns among the two potato spindle tuber viroid variants in tomato plants.
abstract: 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.
authors.affiliation: RNA 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, Canada.
authors.forename: Charith Raj
authors.initials: CR
authors.lastname: Adkar-Purushothama
authors.affiliation: RNA 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, Canada.
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Perreault
authors.affiliation: Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan.
authors.forename: Teruo
authors.initials: T
authors.lastname: Sano
keywords: Potato spindle tuber viroid; RNA silencing; Viroid derived small RNA; Viroids