title: Small RNA profiles of wild-type and silencing suppressor-deficient tomato spotted wilt virus infected Nicotiana benthamiana.
abstract: Tospoviruses are plant-infecting viruses belonging to the family Bunyaviridae. We used a collection of wild-type, phylogenetically distinct tomato spotted wilt virus isolates and related silencing-suppressor defective mutants to study the effects on the small RNA (sRNA) accumulation during infection of Nicotiana benthamiana. Our data showed that absence of a functional silencing suppressor determined a marked increase of the total amount of viral sRNAs (vsRNAs), and specifically of the 21 nt class. We observed a common under-representation of vsRNAs mapping to the intergenic region of S and M genomic segments, and preferential mapping of the reads against the viral sense open reading frames, with the exception of the NSs gene. The NSs-mutant strains showed enrichment of NSm-derived vsRNA compared to the expected amount based on gene size. Analysis of 5' terminal nucleotide preference evidenced a significant enrichment in U for the 21 nt- and in A for 24 nt-long endogenous sRNAs in all the samples. Hotspot analysis revealed a common abundant accumulation of reads at the 5' end of the L segment, mostly in the antiviral sense, for the NSs-defective isolates, suggesting that absence of the silencing suppressor can influence preferential targeting of the viral genome.
authors.affiliation: Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy; Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Paolo
authors.initials: P
authors.lastname: Margaria
authors.affiliation: Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy.
authors.forename: Laura
authors.initials: L
authors.lastname: Miozzi
authors.affiliation: Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Cristina
authors.initials: C
authors.lastname: Rosa
authors.affiliation: Department of Biology, and The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Axtell
authors.affiliation: Department of Plant Pathology, Washington State University, PO Box 646430, Pullman, WA 99164, USA.
authors.forename: Hanu R
authors.initials: HR
authors.lastname: Pappu
authors.affiliation: Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy. Electronic address: massimo.turina@ipsp.cnr.it.
authors.forename: Massimo
authors.initials: M
authors.lastname: Turina
mesh_terms: D015967:Gene Expression Regulation, Viral; D020868:Gene Silencing; D016679:Genome, Viral; D010935:Plant Diseases / Q000821:virology*; D058727:RNA, Small Untranslated / Q000235:genetics* / Q000378:metabolism; D012367:RNA, Viral / Q000235:genetics* / Q000378:metabolism; D014026:Nicotiana / Q000821:virology*; D017865:Tospovirus / Q000235:genetics* / Q000378:metabolism; D014764:Viral Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D058727:RNA, Small Untranslated; D012367:RNA, Viral; D014764:Viral Proteins
keywords: RNA interference; Silencing suppressor; Tospovirus