Nanopore Sequencing Is a Credible Alternative to Recover Complete Genomes of Geminiviruses
In: ISSN: 2076-2607 ; Microorganisms ; https://hal.inrae.fr/hal-03276551 ; Microorganisms, 2021, 9 (5), pp.903. ⟨10.3390/microorganisms9050903⟩ ; https://www.mdpi.com/2076-2607/9/5/903, 2021
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International audience ; 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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Nanopore Sequencing Is a Credible Alternative to Recover Complete Genomes of Geminiviruses
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Autor/in / Beteiligte Person: | Ben Chehida, Selim ; Filloux, Denis ; Fernandez, Emmanuel ; Moubset, Oumaima ; Hoareau, Murielle ; Julian, Charlotte ; Blondin, Laurence ; Lett, Jean-Michel ; Roumagnac, Philippe ; Lefeuvre, Pierre ; Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) ; Département Systèmes Biologiques (Cirad-BIOS) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad) ; Plant Health Institute of Montpellier (UMR PHIM) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro ; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro) ; This study was funded by the European Union (ERDF, contract GURDT I2016-1731-0006632), the Conseil Régional de la Réunion and CIRAD. SBC is a recipient of a PhD fellowship from CIRAD and ANR (Phytovirus project number: ANR-19-CE35-0008). ; ANR-20-CE35-0008,SPADYVA,Dynamique spatio-temporelle des populations virales associées au riz en Afrique de l'Ouest(2020) |
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Zeitschrift: | ISSN: 2076-2607 ; Microorganisms ; https://hal.inrae.fr/hal-03276551 ; Microorganisms, 2021, 9 (5), pp.903. ⟨10.3390/microorganisms9050903⟩ ; https://www.mdpi.com/2076-2607/9/5/903, 2021 |
Veröffentlichung: | HAL CCSD ; MDPI, 2021 |
Medientyp: | academicJournal |
DOI: | 10.3390/microorganisms9050903 |
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