NGS of virus-derived small RNAs as a diagnostic method used to determine viromes of Hungarian Vineyards

Nikoletta Czotter, Janos Molnar, Emese Szabó, Emese Demian, Levente Kontra, Ivett Baksa, Gyorgy Szittya, Laszlo Kocsis, Tamas Deak, Gyorgy Bisztray, G. Tusnády, J. Burgyán, E. Várallyay

Research output: Article

7 Citations (Scopus)

Abstract

As virus diseases cannot be controlled by traditional plant protection methods, the risk of their spread have to be minimized on vegetatively propagated plants, such as grapevine. Metagenomic approaches used for virus diagnostics offer a unique opportunity to reveal the presence of all viral pathogens in the investigated plant, which is why their application can reduce the risk of using infected material for a new plantation. Here we used a special branch, deep sequencing of virus-derived small RNAs, of this high-throughput method for virus diagnostics, and determined viromes of vineyards in Hungary. With NGS of virus-derived small RNAs we could detect not only the viruses tested routinely, but also new ones, which had never been described in Hungary before. Virus presence did not correlate with the age of the plantation, moreover phylogenetic analysis of the identified virus isolates suggests that infections are mostly caused by the use of infected propagating material. Our results, validated by other molecular methods, raised further questions to be answered before this method can be introduced as a routine, reliable test for grapevine virus diagnostics.

Original languageEnglish
Article number122
JournalFrontiers in Microbiology
Volume9
Issue numberFEB
DOIs
Publication statusPublished - febr. 6 2018

Fingerprint

RNA
Viruses
Hungary
High-Throughput Nucleotide Sequencing
Metagenomics
Farms
Virus Diseases
Infection

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)

Cite this

NGS of virus-derived small RNAs as a diagnostic method used to determine viromes of Hungarian Vineyards. / Czotter, Nikoletta; Molnar, Janos; Szabó, Emese; Demian, Emese; Kontra, Levente; Baksa, Ivett; Szittya, Gyorgy; Kocsis, Laszlo; Deak, Tamas; Bisztray, Gyorgy; Tusnády, G.; Burgyán, J.; Várallyay, E.

In: Frontiers in Microbiology, Vol. 9, No. FEB, 122, 06.02.2018.

Research output: Article

Czotter, N, Molnar, J, Szabó, E, Demian, E, Kontra, L, Baksa, I, Szittya, G, Kocsis, L, Deak, T, Bisztray, G, Tusnády, G, Burgyán, J & Várallyay, E 2018, 'NGS of virus-derived small RNAs as a diagnostic method used to determine viromes of Hungarian Vineyards', Frontiers in Microbiology, vol. 9, no. FEB, 122. https://doi.org/10.3389/fmicb.2018.00122
Czotter, Nikoletta ; Molnar, Janos ; Szabó, Emese ; Demian, Emese ; Kontra, Levente ; Baksa, Ivett ; Szittya, Gyorgy ; Kocsis, Laszlo ; Deak, Tamas ; Bisztray, Gyorgy ; Tusnády, G. ; Burgyán, J. ; Várallyay, E. / NGS of virus-derived small RNAs as a diagnostic method used to determine viromes of Hungarian Vineyards. In: Frontiers in Microbiology. 2018 ; Vol. 9, No. FEB.
@article{e17375b463cc45e09ff557bd88f05111,
title = "NGS of virus-derived small RNAs as a diagnostic method used to determine viromes of Hungarian Vineyards",
abstract = "As virus diseases cannot be controlled by traditional plant protection methods, the risk of their spread have to be minimized on vegetatively propagated plants, such as grapevine. Metagenomic approaches used for virus diagnostics offer a unique opportunity to reveal the presence of all viral pathogens in the investigated plant, which is why their application can reduce the risk of using infected material for a new plantation. Here we used a special branch, deep sequencing of virus-derived small RNAs, of this high-throughput method for virus diagnostics, and determined viromes of vineyards in Hungary. With NGS of virus-derived small RNAs we could detect not only the viruses tested routinely, but also new ones, which had never been described in Hungary before. Virus presence did not correlate with the age of the plantation, moreover phylogenetic analysis of the identified virus isolates suggests that infections are mostly caused by the use of infected propagating material. Our results, validated by other molecular methods, raised further questions to be answered before this method can be introduced as a routine, reliable test for grapevine virus diagnostics.",
keywords = "Diagnostics, Grapevine, Metagenomics, NGS, Small RNA, Vineyard, Virome, Virus",
author = "Nikoletta Czotter and Janos Molnar and Emese Szab{\'o} and Emese Demian and Levente Kontra and Ivett Baksa and Gyorgy Szittya and Laszlo Kocsis and Tamas Deak and Gyorgy Bisztray and G. Tusn{\'a}dy and J. Burgy{\'a}n and E. V{\'a}rallyay",
year = "2018",
month = "2",
day = "6",
doi = "10.3389/fmicb.2018.00122",
language = "English",
volume = "9",
journal = "Frontiers in Microbiology",
issn = "1664-302X",
publisher = "Frontiers Media S. A.",
number = "FEB",

}

TY - JOUR

T1 - NGS of virus-derived small RNAs as a diagnostic method used to determine viromes of Hungarian Vineyards

AU - Czotter, Nikoletta

AU - Molnar, Janos

AU - Szabó, Emese

AU - Demian, Emese

AU - Kontra, Levente

AU - Baksa, Ivett

AU - Szittya, Gyorgy

AU - Kocsis, Laszlo

AU - Deak, Tamas

AU - Bisztray, Gyorgy

AU - Tusnády, G.

AU - Burgyán, J.

AU - Várallyay, E.

PY - 2018/2/6

Y1 - 2018/2/6

N2 - As virus diseases cannot be controlled by traditional plant protection methods, the risk of their spread have to be minimized on vegetatively propagated plants, such as grapevine. Metagenomic approaches used for virus diagnostics offer a unique opportunity to reveal the presence of all viral pathogens in the investigated plant, which is why their application can reduce the risk of using infected material for a new plantation. Here we used a special branch, deep sequencing of virus-derived small RNAs, of this high-throughput method for virus diagnostics, and determined viromes of vineyards in Hungary. With NGS of virus-derived small RNAs we could detect not only the viruses tested routinely, but also new ones, which had never been described in Hungary before. Virus presence did not correlate with the age of the plantation, moreover phylogenetic analysis of the identified virus isolates suggests that infections are mostly caused by the use of infected propagating material. Our results, validated by other molecular methods, raised further questions to be answered before this method can be introduced as a routine, reliable test for grapevine virus diagnostics.

AB - As virus diseases cannot be controlled by traditional plant protection methods, the risk of their spread have to be minimized on vegetatively propagated plants, such as grapevine. Metagenomic approaches used for virus diagnostics offer a unique opportunity to reveal the presence of all viral pathogens in the investigated plant, which is why their application can reduce the risk of using infected material for a new plantation. Here we used a special branch, deep sequencing of virus-derived small RNAs, of this high-throughput method for virus diagnostics, and determined viromes of vineyards in Hungary. With NGS of virus-derived small RNAs we could detect not only the viruses tested routinely, but also new ones, which had never been described in Hungary before. Virus presence did not correlate with the age of the plantation, moreover phylogenetic analysis of the identified virus isolates suggests that infections are mostly caused by the use of infected propagating material. Our results, validated by other molecular methods, raised further questions to be answered before this method can be introduced as a routine, reliable test for grapevine virus diagnostics.

KW - Diagnostics

KW - Grapevine

KW - Metagenomics

KW - NGS

KW - Small RNA

KW - Vineyard

KW - Virome

KW - Virus

UR - http://www.scopus.com/inward/record.url?scp=85041811755&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85041811755&partnerID=8YFLogxK

U2 - 10.3389/fmicb.2018.00122

DO - 10.3389/fmicb.2018.00122

M3 - Article

AN - SCOPUS:85041811755

VL - 9

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

SN - 1664-302X

IS - FEB

M1 - 122

ER -