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

Among all economically important plant species in the world, grapevine (<i>Vitis vinifera</i> 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 indu...

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Autores principales:	Vahid Jalali Javaran, Peter Moffett, Pierre Lemoyne, Dong Xu, Charith Raj Adkar-Purushothama, Mamadou Lamine Fall
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	grapevine viral disease diagnostic methods RNA sequencing nanopore sequencing technology RNA modifications Botany QK1-989
Acceso en línea:	https://doaj.org/article/630e59c5e3f84a168777146ecaf02b79
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spelling	oai:doaj.org-article:630e59c5e3f84a168777146ecaf02b792021-11-25T18:45:44ZGrapevine Virology in the Third-Generation Sequencing Era: From Virus Detection to Viral Epitranscriptomics10.3390/plants101123552223-7747https://doaj.org/article/630e59c5e3f84a168777146ecaf02b792021-10-01T00:00:00Zhttps://www.mdpi.com/2223-7747/10/11/2355https://doaj.org/toc/2223-7747Among all economically important plant species in the world, grapevine (<i>Vitis vinifera</i> 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.Vahid Jalali JavaranPeter MoffettPierre LemoyneDong XuCharith Raj Adkar-PurushothamaMamadou Lamine FallMDPI AGarticlegrapevineviral diseasediagnostic methodsRNA sequencingnanopore sequencing technologyRNA modificationsBotanyQK1-989ENPlants, Vol 10, Iss 2355, p 2355 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	grapevine viral disease diagnostic methods RNA sequencing nanopore sequencing technology RNA modifications Botany QK1-989
spellingShingle	grapevine viral disease diagnostic methods RNA sequencing nanopore sequencing technology RNA modifications Botany QK1-989 Vahid Jalali Javaran Peter Moffett Pierre Lemoyne Dong Xu Charith Raj Adkar-Purushothama Mamadou Lamine Fall Grapevine Virology in the Third-Generation Sequencing Era: From Virus Detection to Viral Epitranscriptomics
description	Among all economically important plant species in the world, grapevine (<i>Vitis vinifera</i> 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.
format	article
author	Vahid Jalali Javaran Peter Moffett Pierre Lemoyne Dong Xu Charith Raj Adkar-Purushothama Mamadou Lamine Fall
author_facet	Vahid Jalali Javaran Peter Moffett Pierre Lemoyne Dong Xu Charith Raj Adkar-Purushothama Mamadou Lamine Fall
author_sort	Vahid Jalali Javaran
title	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_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_sort	grapevine virology in the third-generation sequencing era: from virus detection to viral epitranscriptomics
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/630e59c5e3f84a168777146ecaf02b79
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Grapevine Virology in the Third-Generation Sequencing Era: From Virus Detection to Viral Epitranscriptomics

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