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Grapevine Virology in the Third-Generation Sequencing Era: From Virus Detection to Viral Epitranscriptomics

Among all economically important plant species in the world, grapevine (Vitis vinifera L.) is the most cultivated fruit plant. It has a significant impact on the economies of many countries through wine and fresh and dried fruit production. In recent years, the grape and wine industry has been facin...

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Autores principales: Javaran, Vahid Jalali, Moffett, Peter, Lemoyne, Pierre, Xu, Dong, Adkar-Purushothama, Charith Raj, Fall, Mamadou Lamine
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8623739/
https://www.ncbi.nlm.nih.gov/pubmed/34834718
http://dx.doi.org/10.3390/plants10112355
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author Javaran, Vahid Jalali
Moffett, Peter
Lemoyne, Pierre
Xu, Dong
Adkar-Purushothama, Charith Raj
Fall, Mamadou Lamine
author_facet Javaran, Vahid Jalali
Moffett, Peter
Lemoyne, Pierre
Xu, Dong
Adkar-Purushothama, Charith Raj
Fall, Mamadou Lamine
author_sort Javaran, Vahid Jalali
collection PubMed
description Among all economically important plant species in the world, grapevine (Vitis vinifera L.) is the most cultivated fruit plant. It has a significant impact on the economies of many countries through wine and fresh and dried fruit production. In recent years, the grape and wine industry has been facing outbreaks of known and emerging viral diseases across the world. Although high-throughput sequencing (HTS) has been used extensively in grapevine virology, the application and potential of third-generation sequencing have not been explored in understanding grapevine viruses and their impact on the grapevine. Nanopore sequencing, a third-generation technology, can be used for the direct sequencing of both RNA and DNA with minimal infrastructure. Compared to other HTS methods, the MinION nanopore platform is faster and more cost-effective and allows for long-read sequencing. Due to the size of the MinION device, it can be easily carried for field viral disease surveillance. This review article discusses grapevine viruses, the principle of third-generation sequencing platforms, and the application of nanopore sequencing technology in grapevine virus detection, virus–plant interactions, as well as the characterization of viral RNA modifications.
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spelling pubmed-86237392021-11-27 Grapevine Virology in the Third-Generation Sequencing Era: From Virus Detection to Viral Epitranscriptomics Javaran, Vahid Jalali Moffett, Peter Lemoyne, Pierre Xu, Dong Adkar-Purushothama, Charith Raj Fall, Mamadou Lamine Plants (Basel) Review Among all economically important plant species in the world, grapevine (Vitis vinifera L.) is the most cultivated fruit plant. It has a significant impact on the economies of many countries through wine and fresh and dried fruit production. In recent years, the grape and wine industry has been facing outbreaks of known and emerging viral diseases across the world. Although high-throughput sequencing (HTS) has been used extensively in grapevine virology, the application and potential of third-generation sequencing have not been explored in understanding grapevine viruses and their impact on the grapevine. Nanopore sequencing, a third-generation technology, can be used for the direct sequencing of both RNA and DNA with minimal infrastructure. Compared to other HTS methods, the MinION nanopore platform is faster and more cost-effective and allows for long-read sequencing. Due to the size of the MinION device, it can be easily carried for field viral disease surveillance. This review article discusses grapevine viruses, the principle of third-generation sequencing platforms, and the application of nanopore sequencing technology in grapevine virus detection, virus–plant interactions, as well as the characterization of viral RNA modifications. MDPI 2021-10-31 /pmc/articles/PMC8623739/ /pubmed/34834718 http://dx.doi.org/10.3390/plants10112355 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 Review
Javaran, Vahid Jalali
Moffett, Peter
Lemoyne, Pierre
Xu, Dong
Adkar-Purushothama, Charith Raj
Fall, Mamadou Lamine
Grapevine Virology in the Third-Generation Sequencing Era: From Virus Detection to Viral Epitranscriptomics
title Grapevine Virology in the Third-Generation Sequencing Era: From Virus Detection to Viral Epitranscriptomics
title_full Grapevine Virology in the Third-Generation Sequencing Era: From Virus Detection to Viral Epitranscriptomics
title_fullStr Grapevine Virology in the Third-Generation Sequencing Era: From Virus Detection to Viral Epitranscriptomics
title_full_unstemmed Grapevine Virology in the Third-Generation Sequencing Era: From Virus Detection to Viral Epitranscriptomics
title_short Grapevine Virology in the Third-Generation Sequencing Era: From Virus Detection to Viral Epitranscriptomics
title_sort grapevine virology in the third-generation sequencing era: from virus detection to viral epitranscriptomics
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8623739/
https://www.ncbi.nlm.nih.gov/pubmed/34834718
http://dx.doi.org/10.3390/plants10112355
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