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Nanopore Sequencing Is a Credible Alternative to Recover Complete Genomes of Geminiviruses

Next-generation sequencing (NGS), through the implementation of metagenomic protocols, has led to the discovery of thousands of new viruses in the last decade. Nevertheless, these protocols are still laborious and costly to implement, and the technique has not yet become routine for everyday virus c...

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Autores principales: Ben Chehida, Selim, Filloux, Denis, Fernandez, Emmanuel, Moubset, Oumaima, Hoareau, Murielle, Julian, Charlotte, Blondin, Laurence, Lett, Jean-Michel, Roumagnac, Philippe, Lefeuvre, Pierre
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8147096/
https://www.ncbi.nlm.nih.gov/pubmed/33922452
http://dx.doi.org/10.3390/microorganisms9050903
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author Ben Chehida, Selim
Filloux, Denis
Fernandez, Emmanuel
Moubset, Oumaima
Hoareau, Murielle
Julian, Charlotte
Blondin, Laurence
Lett, Jean-Michel
Roumagnac, Philippe
Lefeuvre, Pierre
author_facet Ben Chehida, Selim
Filloux, Denis
Fernandez, Emmanuel
Moubset, Oumaima
Hoareau, Murielle
Julian, Charlotte
Blondin, Laurence
Lett, Jean-Michel
Roumagnac, Philippe
Lefeuvre, Pierre
author_sort Ben Chehida, Selim
collection PubMed
description Next-generation sequencing (NGS), through the implementation of metagenomic protocols, has led to the discovery of thousands of new viruses in the last decade. Nevertheless, these protocols are still laborious and costly to implement, and the technique has not yet become routine for everyday virus characterization. Within the context of CRESS DNA virus studies, we implemented two alternative long-read NGS protocols, one that is agnostic to the sequence (without a priori knowledge of the viral genome) and the other that use specific primers to target a virus (with a priori). Agnostic and specific long read NGS-based assembled genomes of two capulavirus strains were compared to those obtained using the gold standard technique of Sanger sequencing. Both protocols allowed the detection and accurate full genome characterization of both strains. Globally, the assembled genomes were very similar (99.5–99.7% identity) to the Sanger sequences consensus, but differences in the homopolymeric tracks of these sequences indicated a specific lack of accuracy of the long reads NGS approach that has yet to be improved. Nevertheless, the use of the bench-top sequencer has proven to be a credible alternative in the context of CRESS DNA virus study and could offer a new range of applications not previously accessible.
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spelling pubmed-81470962021-05-26 Nanopore Sequencing Is a Credible Alternative to Recover Complete Genomes of Geminiviruses Ben Chehida, Selim Filloux, Denis Fernandez, Emmanuel Moubset, Oumaima Hoareau, Murielle Julian, Charlotte Blondin, Laurence Lett, Jean-Michel Roumagnac, Philippe Lefeuvre, Pierre Microorganisms Article Next-generation sequencing (NGS), through the implementation of metagenomic protocols, has led to the discovery of thousands of new viruses in the last decade. Nevertheless, these protocols are still laborious and costly to implement, and the technique has not yet become routine for everyday virus characterization. Within the context of CRESS DNA virus studies, we implemented two alternative long-read NGS protocols, one that is agnostic to the sequence (without a priori knowledge of the viral genome) and the other that use specific primers to target a virus (with a priori). Agnostic and specific long read NGS-based assembled genomes of two capulavirus strains were compared to those obtained using the gold standard technique of Sanger sequencing. Both protocols allowed the detection and accurate full genome characterization of both strains. Globally, the assembled genomes were very similar (99.5–99.7% identity) to the Sanger sequences consensus, but differences in the homopolymeric tracks of these sequences indicated a specific lack of accuracy of the long reads NGS approach that has yet to be improved. Nevertheless, the use of the bench-top sequencer has proven to be a credible alternative in the context of CRESS DNA virus study and could offer a new range of applications not previously accessible. MDPI 2021-04-23 /pmc/articles/PMC8147096/ /pubmed/33922452 http://dx.doi.org/10.3390/microorganisms9050903 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
Ben Chehida, Selim
Filloux, Denis
Fernandez, Emmanuel
Moubset, Oumaima
Hoareau, Murielle
Julian, Charlotte
Blondin, Laurence
Lett, Jean-Michel
Roumagnac, Philippe
Lefeuvre, Pierre
Nanopore Sequencing Is a Credible Alternative to Recover Complete Genomes of Geminiviruses
title Nanopore Sequencing Is a Credible Alternative to Recover Complete Genomes of Geminiviruses
title_full Nanopore Sequencing Is a Credible Alternative to Recover Complete Genomes of Geminiviruses
title_fullStr Nanopore Sequencing Is a Credible Alternative to Recover Complete Genomes of Geminiviruses
title_full_unstemmed Nanopore Sequencing Is a Credible Alternative to Recover Complete Genomes of Geminiviruses
title_short Nanopore Sequencing Is a Credible Alternative to Recover Complete Genomes of Geminiviruses
title_sort nanopore sequencing is a credible alternative to recover complete genomes of geminiviruses
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8147096/
https://www.ncbi.nlm.nih.gov/pubmed/33922452
http://dx.doi.org/10.3390/microorganisms9050903
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