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Ben Chehida S, Filloux D, Fernandez E, Moubset O, Hoareau M, Julian C, Blondin L, Lett JM, Roumagnac P, Lefeuvre P. Nanopore Sequencing Is a Credible Alternative to Recover Complete Genomes of Geminiviruses. Microorganisms 2021; 9:903. [PMID: 33922452 PMCID: PMC8147096 DOI: 10.3390/microorganisms9050903] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 01/23/2023] Open
Abstract
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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Affiliation(s)
- Selim Ben Chehida
- CIRAD, UMR PVBMT, F-97410 St Pierre, La Réunion, France; (S.B.C.); (M.H.); (J.-M.L.)
| | - Denis Filloux
- CIRAD, PHIM, F-34398 Montpellier, France; (D.F.); (E.F.); (O.M.); (C.J.); (L.B.); (P.R.)
- PHIM Plant Health Institute, University Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34398 Montpellier, France
| | - Emmanuel Fernandez
- CIRAD, PHIM, F-34398 Montpellier, France; (D.F.); (E.F.); (O.M.); (C.J.); (L.B.); (P.R.)
- PHIM Plant Health Institute, University Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34398 Montpellier, France
| | - Oumaima Moubset
- CIRAD, PHIM, F-34398 Montpellier, France; (D.F.); (E.F.); (O.M.); (C.J.); (L.B.); (P.R.)
- PHIM Plant Health Institute, University Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34398 Montpellier, France
| | - Murielle Hoareau
- CIRAD, UMR PVBMT, F-97410 St Pierre, La Réunion, France; (S.B.C.); (M.H.); (J.-M.L.)
| | - Charlotte Julian
- CIRAD, PHIM, F-34398 Montpellier, France; (D.F.); (E.F.); (O.M.); (C.J.); (L.B.); (P.R.)
- PHIM Plant Health Institute, University Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34398 Montpellier, France
| | - Laurence Blondin
- CIRAD, PHIM, F-34398 Montpellier, France; (D.F.); (E.F.); (O.M.); (C.J.); (L.B.); (P.R.)
- PHIM Plant Health Institute, University Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34398 Montpellier, France
| | - Jean-Michel Lett
- CIRAD, UMR PVBMT, F-97410 St Pierre, La Réunion, France; (S.B.C.); (M.H.); (J.-M.L.)
| | - Philippe Roumagnac
- CIRAD, PHIM, F-34398 Montpellier, France; (D.F.); (E.F.); (O.M.); (C.J.); (L.B.); (P.R.)
- PHIM Plant Health Institute, University Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34398 Montpellier, France
| | - Pierre Lefeuvre
- CIRAD, UMR PVBMT, F-97410 St Pierre, La Réunion, France; (S.B.C.); (M.H.); (J.-M.L.)
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