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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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Souza TA, Silva JMF, Nagata T, Martins TP, Nakasu EYT, Inoue-Nagata AK. A Temporal Diversity Analysis of Brazilian Begomoviruses in Tomato Reveals a Decrease in Species Richness between 2003 and 2016. Front Plant Sci 2020; 11:1201. [PMID: 32849745 PMCID: PMC7424291 DOI: 10.3389/fpls.2020.01201] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 07/23/2020] [Indexed: 06/11/2023]
Abstract
Understanding the molecular evolution and diversity changes of begomoviruses is crucial for predicting future outbreaks of the begomovirus disease in tomato crops. Thus, a molecular diversity study using high-throughput sequencing (HTS) was carried out on samples of infected tomato leaves collected between 2003 and 2016 from Central Brazil. DNA samples were subjected to rolling circle amplification and pooled in three batches, G1 (2003-2005, N = 107), G2 (2009-2011, N = 118), and G3 (2014-2016, N = 129) prior to HTS. Nineteen genome-sized geminivirus sequences were assembled, but only 17 were confirmed by PCR. In the G1 library, five begomoviruses and one capula-like virus were detected, but the number of identified viruses decreased to three begomoviruses in the G2 and G3 libraries. The bipartite begomovirus tomato severe rugose virus (ToSRV) and the monopartite tomato mottle leaf curl virus (ToMoLCV) were found to be the most prevalent begomoviruses in this survey. Our analyses revealed a significant increase in both relative abundance and genetic diversity of ToMoLCV from G1 to G3, and ToSRV from G1 to G2; however, both abundance and diversity decreased from G2 to G3. This suggests that ToMoLCV and ToSRV outcompeted other begomoviruses from G1 to G2 and that ToSRV was being outcompeted by ToMoLCV from G2 to G3. The possible evolutionary history of begomoviruses that were likely transferred from wild native plants and weeds to tomato crops after the introduction of the polyphagous vector Bemisia tabaci MEAM1 and the wide use of cultivars carrying the Ty-1 resistance gene are discussed, as well as the strengths and limitations of the use of HTS in identification and diversity analysis of begomoviruses.
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Affiliation(s)
- Tadeu Araujo Souza
- Department of Plant Pathology, University of Brasilia, Brasilia, Brazil
- Laboratory of Virology, Embrapa Vegetables, Brasilia, Brazil
| | | | - Tatsuya Nagata
- Department of Cell Biology, University of Brasilia, Brasilia, Brazil
| | - Thaís Pereira Martins
- Laboratory of Virology, Embrapa Vegetables, Brasilia, Brazil
- Department of Cell Biology, University of Brasilia, Brasilia, Brazil
| | | | - Alice Kazuko Inoue-Nagata
- Department of Plant Pathology, University of Brasilia, Brasilia, Brazil
- Laboratory of Virology, Embrapa Vegetables, Brasilia, Brazil
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