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High-Throughput Sequencing of Small RNAs for Diagnostics of Grapevine Viruses and Viroids in Russia

The use of high-throughput sequencing (HTS) technology has led to significant progress in the identification of many viruses and their genetic variants. In this study, we used the HTS platform to sequence small RNAs (sRNAs) of grapevine to study the virome. Isolation of RNA was performed using sympt...

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Autores principales: Navrotskaya, Emiliya, Porotikova, Elena, Yurchenko, Eugeniya, Galbacs, Zsuzsanna Nagyne, Varallyay, Eva, Vinogradova, Svetlana
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8709451/
https://www.ncbi.nlm.nih.gov/pubmed/34960701
http://dx.doi.org/10.3390/v13122432
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author Navrotskaya, Emiliya
Porotikova, Elena
Yurchenko, Eugeniya
Galbacs, Zsuzsanna Nagyne
Varallyay, Eva
Vinogradova, Svetlana
author_facet Navrotskaya, Emiliya
Porotikova, Elena
Yurchenko, Eugeniya
Galbacs, Zsuzsanna Nagyne
Varallyay, Eva
Vinogradova, Svetlana
author_sort Navrotskaya, Emiliya
collection PubMed
description The use of high-throughput sequencing (HTS) technology has led to significant progress in the identification of many viruses and their genetic variants. In this study, we used the HTS platform to sequence small RNAs (sRNAs) of grapevine to study the virome. Isolation of RNA was performed using symptomatic grapevines collected from commercial vineyards in Krasnodar Krai in 2017–2018. To determine the viromes of vineyards, we used an integrated approach that included a bioinformatic analysis of the results of sRNA HTS and the molecular method RT-PCR, which made it possible to identify 13 viruses and 4 viroids. Grapevine leafroll-associated virus 4 (GLRaV-4), Grapevine Syrah Virus-1 (GSyV-1), Raspberry bushy dwarf virus (RBDV), Australian grapevine viroid (AGVd), and Grapevine yellow speckle viroid 2 (GYSVd-2) were identified for the first time in Russia. Out of 38 samples analyzed, 37 had mixed infections with 4–11 viruses, indicating a high viral load. Analysis of the obtained sequences of fragments of virus genomes made it possible to identify recombination events in GLRaV-1, GLRaV-2, GLRaV-3, GLRaV-4, GVT, GPGV, GRSPaV, GVA, and GFLV. The obtained results indicate a wide spread of the viruses and a high genetic diversity in the vineyards of Krasnodar Krai and emphasize the urgent need to develop and implement long-term strategies for the control of viral grapevine diseases.
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spelling pubmed-87094512021-12-25 High-Throughput Sequencing of Small RNAs for Diagnostics of Grapevine Viruses and Viroids in Russia Navrotskaya, Emiliya Porotikova, Elena Yurchenko, Eugeniya Galbacs, Zsuzsanna Nagyne Varallyay, Eva Vinogradova, Svetlana Viruses Article The use of high-throughput sequencing (HTS) technology has led to significant progress in the identification of many viruses and their genetic variants. In this study, we used the HTS platform to sequence small RNAs (sRNAs) of grapevine to study the virome. Isolation of RNA was performed using symptomatic grapevines collected from commercial vineyards in Krasnodar Krai in 2017–2018. To determine the viromes of vineyards, we used an integrated approach that included a bioinformatic analysis of the results of sRNA HTS and the molecular method RT-PCR, which made it possible to identify 13 viruses and 4 viroids. Grapevine leafroll-associated virus 4 (GLRaV-4), Grapevine Syrah Virus-1 (GSyV-1), Raspberry bushy dwarf virus (RBDV), Australian grapevine viroid (AGVd), and Grapevine yellow speckle viroid 2 (GYSVd-2) were identified for the first time in Russia. Out of 38 samples analyzed, 37 had mixed infections with 4–11 viruses, indicating a high viral load. Analysis of the obtained sequences of fragments of virus genomes made it possible to identify recombination events in GLRaV-1, GLRaV-2, GLRaV-3, GLRaV-4, GVT, GPGV, GRSPaV, GVA, and GFLV. The obtained results indicate a wide spread of the viruses and a high genetic diversity in the vineyards of Krasnodar Krai and emphasize the urgent need to develop and implement long-term strategies for the control of viral grapevine diseases. MDPI 2021-12-03 /pmc/articles/PMC8709451/ /pubmed/34960701 http://dx.doi.org/10.3390/v13122432 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Navrotskaya, Emiliya
Porotikova, Elena
Yurchenko, Eugeniya
Galbacs, Zsuzsanna Nagyne
Varallyay, Eva
Vinogradova, Svetlana
High-Throughput Sequencing of Small RNAs for Diagnostics of Grapevine Viruses and Viroids in Russia
title High-Throughput Sequencing of Small RNAs for Diagnostics of Grapevine Viruses and Viroids in Russia
title_full High-Throughput Sequencing of Small RNAs for Diagnostics of Grapevine Viruses and Viroids in Russia
title_fullStr High-Throughput Sequencing of Small RNAs for Diagnostics of Grapevine Viruses and Viroids in Russia
title_full_unstemmed High-Throughput Sequencing of Small RNAs for Diagnostics of Grapevine Viruses and Viroids in Russia
title_short High-Throughput Sequencing of Small RNAs for Diagnostics of Grapevine Viruses and Viroids in Russia
title_sort high-throughput sequencing of small rnas for diagnostics of grapevine viruses and viroids in russia
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8709451/
https://www.ncbi.nlm.nih.gov/pubmed/34960701
http://dx.doi.org/10.3390/v13122432
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