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Small RNA sequencing and multiplex RT-PCR for diagnostics of grapevine viruses and virus-like organisms
ID Miljanić, Vanja (Author), ID Jakše, Jernej (Author), ID Rusjan, Denis (Author), ID Škvarč, Andreja (Author), ID Štajner, Nataša (Author)

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Abstract
Metagenomic approaches used for virus diagnostics allow for rapid and accurate detection of all viral pathogens in the plants. In order to investigate the occurrence of viruses and virus-like organisms infecting grapevine from the Ampelographic collection Kromberk in Slovenia, we used Ion Torrent small RNA sequencing (sRNA-seq) and the VirusDetect pipeline to analyze the sRNA-seq data. The used method revealed the presence of: Grapevine leafroll-associated virus 1 (GLRaV-1), Grapevine leafroll-associated virus 2 (GLRaV-2), Grapevine leafroll-associated virus 3 (GLRaV-3), Grapevine rupestris stem pitting-associated virus (GRSPaV), Grapevine fanleaf virus (GFLV) and its satellite RNA (satGFLV), Grapevine fleck virus (GFkV), Grapevine rupestris vein feathering virus (GRVFV), Grapevine Pinot gris virus (GPGV), Grapevine satellite virus (GV-Sat), Hop stunt viroid (HSVd), and Grapevine yellow speckle viroid 1 (GYSVd-1). Multiplex reverse transcription-polymerase chain reaction (mRT-PCR) was developed for validation of sRNA-seq predicted infections, including various combinations of viruses or viroids and satellite RNA. mRT-PCR could further be used for rapid and cost-effective routine molecular diagnosis, including widespread, emerging, and seemingly rare viruses, as well as viroids which testing is usually overlooked.

Language:English
Keywords:Vitis vinifera L., grapevine, virome, metagenomic analysis, viruses, sRNA-seq, molecular diagnostics, mRT-PCR
Work type:Article
Typology:1.01 - Original Scientific Article
Organization:BF - Biotechnical Faculty
Publication status:Published
Publication version:Version of Record
Year:2022
Number of pages:11 str.
Numbering:Vol. 14, iss. 5, art. 921
PID:20.500.12556/RUL-136449 This link opens in a new window
UDC:577.2
ISSN on article:1999-4915
DOI:10.3390/v14050921 This link opens in a new window
COBISS.SI-ID:106521859 This link opens in a new window
Publication date in RUL:04.05.2022
Views:592
Downloads:107
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Record is a part of a journal

Title:Viruses
Shortened title:Viruses
Publisher:MDPI
ISSN:1999-4915
COBISS.SI-ID:517597977 This link opens in a new window

Licences

License:CC BY 4.0, Creative Commons Attribution 4.0 International
Link:http://creativecommons.org/licenses/by/4.0/
Description:This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

Language:Slovenian
Keywords:vinska trta, virusne bolezni, virusi, viroidi, molekularna diagnostika, metagenomska analiza

Projects

Funder:ARRS - Agencija za raziskovalno dejavnost Republike Slovenije
Project number:P4-0077
Name:Kmetijske rastline - genetika in sodobne tehnologije

Funder:Drugi - Drug financer ali več financerjev
Funding programme:Public Scholarship, Development, Disability and Maintenance Fund of the Republic of Slovenia, Scholarship for nationals of the Western Balkans for postgraduate study in Slovenia

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