Use of siRNAs for diagnosis of viruses associated to woody plants in nurseries and stock collections

Nikoletta Czotter, János Molnár, Réka Pesti, Emese Demián, Dániel Baráth, Tünde Varga, E. Várallyay

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Citations (Scopus)

Abstract

Woody perennial plants like grapevine and fruit trees can be infected by several viruses even as multiple infections. Since they are propagated vegetatively, the phytosanitary status of the propagation material (both the rootstock and the variety) can have a profound effect on the lifetime and health of the new plantations. The fast evolution of sequencing techniques provides a new opportunity for metagenomics-based viral diagnostics. Viral derived small RNAs produced by the host immune system during viral infection can be sequenced by next-generation techniques and analyzed for the presence of viruses, revealing the presence of all known viral pathogens in the sample. This method is based on Illumina sequencing of short RNAs and bioinformatics analysis of virus-derived small RNAs in the host. Here we describe a protocol for this challenging technique step by step with notes, in order to ensure success for every user.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages115-130
Number of pages16
DOIs
Publication statusPublished - Jan 1 2018

Publication series

NameMethods in Molecular Biology
Volume1746
ISSN (Print)1064-3745

Fingerprint

Nurseries
Viruses
RNA
RNA Sequence Analysis
Metagenomics
Virus Diseases
Computational Biology
Immune System
Fruit
Health
Infection

Keywords

  • Diagnostics
  • Next-generation sequencing
  • Small RNA
  • Virus

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Czotter, N., Molnár, J., Pesti, R., Demián, E., Baráth, D., Varga, T., & Várallyay, E. (2018). Use of siRNAs for diagnosis of viruses associated to woody plants in nurseries and stock collections. In Methods in Molecular Biology (pp. 115-130). (Methods in Molecular Biology; Vol. 1746). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-7683-6_9

Use of siRNAs for diagnosis of viruses associated to woody plants in nurseries and stock collections. / Czotter, Nikoletta; Molnár, János; Pesti, Réka; Demián, Emese; Baráth, Dániel; Varga, Tünde; Várallyay, E.

Methods in Molecular Biology. Humana Press Inc., 2018. p. 115-130 (Methods in Molecular Biology; Vol. 1746).

Research output: Chapter in Book/Report/Conference proceedingChapter

Czotter, N, Molnár, J, Pesti, R, Demián, E, Baráth, D, Varga, T & Várallyay, E 2018, Use of siRNAs for diagnosis of viruses associated to woody plants in nurseries and stock collections. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 1746, Humana Press Inc., pp. 115-130. https://doi.org/10.1007/978-1-4939-7683-6_9
Czotter N, Molnár J, Pesti R, Demián E, Baráth D, Varga T et al. Use of siRNAs for diagnosis of viruses associated to woody plants in nurseries and stock collections. In Methods in Molecular Biology. Humana Press Inc. 2018. p. 115-130. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-7683-6_9
Czotter, Nikoletta ; Molnár, János ; Pesti, Réka ; Demián, Emese ; Baráth, Dániel ; Varga, Tünde ; Várallyay, E. / Use of siRNAs for diagnosis of viruses associated to woody plants in nurseries and stock collections. Methods in Molecular Biology. Humana Press Inc., 2018. pp. 115-130 (Methods in Molecular Biology).
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