Cargando…
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...
Autores principales: | , , , , , , , , , |
---|---|
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 |
_version_ | 1783697551115943936 |
---|---|
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. |
format | Online Article Text |
id | pubmed-8147096 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT benchehidaselim nanoporesequencingisacrediblealternativetorecovercompletegenomesofgeminiviruses AT fillouxdenis nanoporesequencingisacrediblealternativetorecovercompletegenomesofgeminiviruses AT fernandezemmanuel nanoporesequencingisacrediblealternativetorecovercompletegenomesofgeminiviruses AT moubsetoumaima nanoporesequencingisacrediblealternativetorecovercompletegenomesofgeminiviruses AT hoareaumurielle nanoporesequencingisacrediblealternativetorecovercompletegenomesofgeminiviruses AT juliancharlotte nanoporesequencingisacrediblealternativetorecovercompletegenomesofgeminiviruses AT blondinlaurence nanoporesequencingisacrediblealternativetorecovercompletegenomesofgeminiviruses AT lettjeanmichel nanoporesequencingisacrediblealternativetorecovercompletegenomesofgeminiviruses AT roumagnacphilippe nanoporesequencingisacrediblealternativetorecovercompletegenomesofgeminiviruses AT lefeuvrepierre nanoporesequencingisacrediblealternativetorecovercompletegenomesofgeminiviruses |