Analysis of small RNAs derived from tomato yellow leaf curl Sardinia virus reveals a cross reaction between the major viral hotspot and the plant host genome

Laura Miozzi, Vitantonio Pantaleo, J. Burgyán, Gian Paolo Accotto, Emanuela Noris

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

RNA silencing is a defense mechanism exploited by plants against viruses. Upon infection, viral genomes and their transcripts are processed by Dicer-like (DCL) ribonucleases into viral small interfering RNAs (vsRNAs) of 21-24 nucleotides that further guide silencing of viral transcripts. To get an insight into the molecular interaction between tomato and the monopartite phloem-limited begomovirus tomato yellow leaf curl Sardinia virus (TYLCSV), a pathogen inducing a devastating disease of tomato in the Mediterranean region, we characterized by deep sequencing the vsRNA population in virus-infected tomato plants, using a Solexa/Illumina platform. TYLCSV-sRNAs spanned the entire viral genome but were discontinuously distributed throughout it, with a prevalence from the transcribed regions. TYLCSV-sRNAs were mainly 21-22 nucleotides in length and their polarity was asymmetrically distributed along the genome. The most abundant vsRNAs originated from a narrow region overlapping the Rep/C4 genes and from a broader region including the end of the V2 and the beginning of the coat protein genes. Deep sequencing results were validated by different hybridization techniques. Comparisons with the data available on vsRNAs for other begomoviruses highlighted both similarities and differences. Host-derived RNA species cross-reacting with a portion of the viral genome corresponding to the most abundant vsRNAs hotspot were detected. Bioinformatics analyses were carried out to investigate the nature of these host molecules.

Original languageEnglish
Pages (from-to)287-296
Number of pages10
JournalVirus Research
Volume178
Issue number2
DOIs
Publication statusPublished - Dec 26 2013

Fingerprint

Plant Genome
Cross Reactions
Lycopersicon esculentum
Italy
Viral RNA
RNA
Viruses
Small Interfering RNA
Viral Genome
Begomovirus
High-Throughput Nucleotide Sequencing
Nucleotides
Mediterranean Region
Phloem
Plant Viruses
Capsid Proteins
Ribonucleases
RNA Interference
Computational Biology
Genes

Keywords

  • Deep sequencing
  • Geminiviruses
  • RNA silencing
  • Tomato
  • Viral small RNAs

ASJC Scopus subject areas

  • Virology
  • Infectious Diseases
  • Cancer Research

Cite this

Analysis of small RNAs derived from tomato yellow leaf curl Sardinia virus reveals a cross reaction between the major viral hotspot and the plant host genome. / Miozzi, Laura; Pantaleo, Vitantonio; Burgyán, J.; Accotto, Gian Paolo; Noris, Emanuela.

In: Virus Research, Vol. 178, No. 2, 26.12.2013, p. 287-296.

Research output: Contribution to journalArticle

Miozzi, Laura ; Pantaleo, Vitantonio ; Burgyán, J. ; Accotto, Gian Paolo ; Noris, Emanuela. / Analysis of small RNAs derived from tomato yellow leaf curl Sardinia virus reveals a cross reaction between the major viral hotspot and the plant host genome. In: Virus Research. 2013 ; Vol. 178, No. 2. pp. 287-296.
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