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NanoViromics: long-read sequencing of dsRNA for plant virus and viroid rapid detection

There is a global need for identifying viral pathogens, as well as for providing certified clean plant materials, in order to limit the spread of viral diseases. A key component of management programs for viral-like diseases is having a diagnostic tool that is quick, reliable, inexpensive, and easy...

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Autores principales: Javaran, Vahid J., Poursalavati, Abdonaser, Lemoyne, Pierre, Ste-Croix, Dave T., Moffett, Peter, Fall, Mamadou L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10320856/
https://www.ncbi.nlm.nih.gov/pubmed/37415816
http://dx.doi.org/10.3389/fmicb.2023.1192781
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author Javaran, Vahid J.
Poursalavati, Abdonaser
Lemoyne, Pierre
Ste-Croix, Dave T.
Moffett, Peter
Fall, Mamadou L.
author_facet Javaran, Vahid J.
Poursalavati, Abdonaser
Lemoyne, Pierre
Ste-Croix, Dave T.
Moffett, Peter
Fall, Mamadou L.
author_sort Javaran, Vahid J.
collection PubMed
description There is a global need for identifying viral pathogens, as well as for providing certified clean plant materials, in order to limit the spread of viral diseases. A key component of management programs for viral-like diseases is having a diagnostic tool that is quick, reliable, inexpensive, and easy to use. We have developed and validated a dsRNA-based nanopore sequencing protocol as a reliable method for detecting viruses and viroids in grapevines. We compared our method, which we term direct-cDNA sequencing from dsRNA (dsRNAcD), to direct RNA sequencing from rRNA-depleted total RNA (rdTotalRNA), and found that it provided more viral reads from infected samples. Indeed, dsRNAcD was able to detect all of the viruses and viroids detected using Illumina MiSeq sequencing (dsRNA-MiSeq). Furthermore, dsRNAcD sequencing was also able to detect low-abundance viruses that rdTotalRNA sequencing failed to detect. Additionally, rdTotalRNA sequencing resulted in a false-positive viroid identification due to the misannotation of a host-driven read. Two taxonomic classification workflows, DIAMOND & MEGAN (DIA & MEG) and Centrifuge & Recentrifuge (Cent & Rec), were also evaluated for quick and accurate read classification. Although the results from both workflows were similar, we identified pros and cons for both workflows. Our study shows that dsRNAcD sequencing and the proposed data analysis workflows are suitable for consistent detection of viruses and viroids, particularly in grapevines where mixed viral infections are common.
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spelling pubmed-103208562023-07-06 NanoViromics: long-read sequencing of dsRNA for plant virus and viroid rapid detection Javaran, Vahid J. Poursalavati, Abdonaser Lemoyne, Pierre Ste-Croix, Dave T. Moffett, Peter Fall, Mamadou L. Front Microbiol Microbiology There is a global need for identifying viral pathogens, as well as for providing certified clean plant materials, in order to limit the spread of viral diseases. A key component of management programs for viral-like diseases is having a diagnostic tool that is quick, reliable, inexpensive, and easy to use. We have developed and validated a dsRNA-based nanopore sequencing protocol as a reliable method for detecting viruses and viroids in grapevines. We compared our method, which we term direct-cDNA sequencing from dsRNA (dsRNAcD), to direct RNA sequencing from rRNA-depleted total RNA (rdTotalRNA), and found that it provided more viral reads from infected samples. Indeed, dsRNAcD was able to detect all of the viruses and viroids detected using Illumina MiSeq sequencing (dsRNA-MiSeq). Furthermore, dsRNAcD sequencing was also able to detect low-abundance viruses that rdTotalRNA sequencing failed to detect. Additionally, rdTotalRNA sequencing resulted in a false-positive viroid identification due to the misannotation of a host-driven read. Two taxonomic classification workflows, DIAMOND & MEGAN (DIA & MEG) and Centrifuge & Recentrifuge (Cent & Rec), were also evaluated for quick and accurate read classification. Although the results from both workflows were similar, we identified pros and cons for both workflows. Our study shows that dsRNAcD sequencing and the proposed data analysis workflows are suitable for consistent detection of viruses and viroids, particularly in grapevines where mixed viral infections are common. Frontiers Media S.A. 2023-06-21 /pmc/articles/PMC10320856/ /pubmed/37415816 http://dx.doi.org/10.3389/fmicb.2023.1192781 Text en Copyright © 2023 Javaran, Poursalavati, Lemoyne, Ste-Croix, Moffett and Fall. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Javaran, Vahid J.
Poursalavati, Abdonaser
Lemoyne, Pierre
Ste-Croix, Dave T.
Moffett, Peter
Fall, Mamadou L.
NanoViromics: long-read sequencing of dsRNA for plant virus and viroid rapid detection
title NanoViromics: long-read sequencing of dsRNA for plant virus and viroid rapid detection
title_full NanoViromics: long-read sequencing of dsRNA for plant virus and viroid rapid detection
title_fullStr NanoViromics: long-read sequencing of dsRNA for plant virus and viroid rapid detection
title_full_unstemmed NanoViromics: long-read sequencing of dsRNA for plant virus and viroid rapid detection
title_short NanoViromics: long-read sequencing of dsRNA for plant virus and viroid rapid detection
title_sort nanoviromics: long-read sequencing of dsrna for plant virus and viroid rapid detection
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10320856/
https://www.ncbi.nlm.nih.gov/pubmed/37415816
http://dx.doi.org/10.3389/fmicb.2023.1192781
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