Small RNA profiles of wild-type and silencing suppressor-deficient tomato spotted wilt virus infected Nicotiana benthamiana

Paolo Margaria, Laura Miozzi, Cristina Rosa, Michael J. Axtell, Hanu R. Pappu, Massimo Turina

Research output: Contribution to journalArticlepeer-review

21 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)30-38
Number of pages9
JournalVirus Research
Volume208
DOIs
StatePublished - Oct 2 2015

All Science Journal Classification (ASJC) codes

  • Cancer Research
  • Virology
  • Infectious Diseases

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