Small RNA sequencing and multiplex RT-PCR for diagnostics of grapevine viruses and virus-like organisms

Miljanić, Vanja (author), Jakše, Jernej (author), Rusjan, Denis (author), Škvarč, Andreja (author), Štajner, Nataša (author)

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
• UDC: 577.2
• ISSN on article: 1999-4915
• DOI: 10.3390/v14050921
• COBISS.SI-ID: 106521859
• Publication date in RUL: 04.05.2022

Record is a part of a journal

• Title: Viruses
• Shortened title: Viruses
• Publisher: MDPI
• ISSN: 1999-4915
• COBISS.SI-ID: 517597977

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 - Slovenian Research Agency
• Project number: P4-0077
• Name: Kmetijske rastline - genetika in sodobne tehnologije

• Funder: Other - Other funder or multiple funders
• 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