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Daugrois JH, Filloux D, Julian C, Claude L, Ferdinand R, Fernandez E, Fontes H, Rott PC, Roumagnac P. Comparison of the Virome of Quarantined Sugarcane Varieties and the Virome of Grasses Growing near the Quarantine Station. Viruses 2021; 13:922. [PMID: 34065683 PMCID: PMC8157134 DOI: 10.3390/v13050922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 04/28/2021] [Accepted: 05/10/2021] [Indexed: 11/16/2022] Open
Abstract
Visacane is a sugarcane quarantine station located in the South of France, far away from sugarcane growing areas. Visacane imports up to 100 sugarcane varieties per year, using safe control and confinement measures of plants and their wastes to prevent any risk of pathogen spread outside of the facilities. Viruses hosted by the imported material are either known or unknown to cause disease in cultivated sugarcane. Poaceae viruses occurring in plants surrounding the quarantine glasshouse are currently unknown. These viruses could be considered as a source of new sugarcane infections and potentially cause new sugarcane diseases in cases of confinement barrier failure. The aim of this study was to compare the plant virome inside and outside of the quarantine station to identify potential confinement failures and risks of cross infections. Leaves from quarantined sugarcane varieties and from wild Poaceae growing near the quarantine were collected and processed by a metagenomics approach based on virion-associated nucleic acids extraction and library preparation for Illumina sequencing. While viruses belonging to the same virus genus or family were identified in the sugarcane quarantine and its surroundings, no virus species was detected in both environments. Based on the data obtained in this study, no virus movement between quarantined sugarcane and nearby grassland has occurred so far, and the confinement procedures of Visacane appear to be properly implemented.
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Affiliation(s)
- Jean H. Daugrois
- CIRAD, UMR PHIM, 34090 Montpellier, France; (J.H.D.); (D.F.); (C.J.); (L.C.); (R.F.); (E.F.); (P.C.R.)
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| | - Denis Filloux
- CIRAD, UMR PHIM, 34090 Montpellier, France; (J.H.D.); (D.F.); (C.J.); (L.C.); (R.F.); (E.F.); (P.C.R.)
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| | - Charlotte Julian
- CIRAD, UMR PHIM, 34090 Montpellier, France; (J.H.D.); (D.F.); (C.J.); (L.C.); (R.F.); (E.F.); (P.C.R.)
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| | - Lisa Claude
- CIRAD, UMR PHIM, 34090 Montpellier, France; (J.H.D.); (D.F.); (C.J.); (L.C.); (R.F.); (E.F.); (P.C.R.)
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| | - Romain Ferdinand
- CIRAD, UMR PHIM, 34090 Montpellier, France; (J.H.D.); (D.F.); (C.J.); (L.C.); (R.F.); (E.F.); (P.C.R.)
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| | - Emmanuel Fernandez
- CIRAD, UMR PHIM, 34090 Montpellier, France; (J.H.D.); (D.F.); (C.J.); (L.C.); (R.F.); (E.F.); (P.C.R.)
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| | - Hugo Fontes
- Tour du Valat, Research Institute for the Conservation of Mediterranean Wetlands, 13200 Arles, France;
- Institut Méditerranéen de Biodiversité et Ecologie, UMR CNRS-IRD, Avignon Université, Aix-Marseille Université, IUT d’Avignon, 337 chemin des Meinajariés, Site Agroparc BP 61207, 84911 Avignon, France
| | - Philippe C. Rott
- CIRAD, UMR PHIM, 34090 Montpellier, France; (J.H.D.); (D.F.); (C.J.); (L.C.); (R.F.); (E.F.); (P.C.R.)
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, 34090 Montpellier, France; (J.H.D.); (D.F.); (C.J.); (L.C.); (R.F.); (E.F.); (P.C.R.)
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
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Analysis of complete genomes of isolates of the Wheat dwarf virus from new geographical locations and descriptions of their defective forms. Virus Genes 2014; 48:133-9. [PMID: 24122067 DOI: 10.1007/s11262-013-0989-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 09/25/2013] [Indexed: 10/26/2022]
Abstract
Recently, the importance of the Geminiviruses infecting cereal crops has been appreciated, and they are now being studied in detail. Barley and wheat strains of Wheat dwarf virus are recorded in most European countries. Information on complete sequences of isolates from the United Kingdom, Spain, and Austria are reported here for the first time. Analysis revealed that their sequences are very stable. Recombination between strains was recorded only for the barley strain. We identified several defective forms of the barley strain from barley and wheat, which do not influence symptom expression. Sequences of barley isolates infecting wheat were obtained that did not differ from the isolates from barley. Based on specific features of the SIR of the barley strains, it is suggested that they are assigned to one of the two proposed new clusters, A1 or A2.
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Rosario K, Padilla-Rodriguez M, Kraberger S, Stainton D, Martin DP, Breitbart M, Varsani A. Discovery of a novel mastrevirus and alphasatellite-like circular DNA in dragonflies (Epiprocta) from Puerto Rico. Virus Res 2013; 171:231-7. [DOI: 10.1016/j.virusres.2012.10.017] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 10/14/2012] [Accepted: 10/18/2012] [Indexed: 11/28/2022]
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Kraberger S, Thomas JE, Geering AD, Dayaram A, Stainton D, Hadfield J, Walters M, Parmenter KS, van Brunschot S, Collings DA, Martin DP, Varsani A. Australian monocot-infecting mastrevirus diversity rivals that in Africa. Virus Res 2012; 169:127-36. [DOI: 10.1016/j.virusres.2012.07.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 07/14/2012] [Accepted: 07/17/2012] [Indexed: 11/26/2022]
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Martin DP, Briddon RW, Varsani A. Recombination patterns in dicot-infecting mastreviruses mirror those found in monocot-infecting mastreviruses. Arch Virol 2011; 156:1463-9. [PMID: 21484422 DOI: 10.1007/s00705-011-0994-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Accepted: 03/28/2011] [Indexed: 11/28/2022]
Abstract
Recombination has profoundly shaped the evolution of viruses in the family Geminiviridae and has been studied extensively in the two best characterised geminivirus lineages: the dicotyledonous plant infecting begomoviruses and the monocotyledonous plant infecting mastreviruses. Here, we demonstrate that the sizes and distributions of recombination events detectable within the members of a third major geminivirus lineage--the dicotyledonous plant infecting mastreviruses--are very similar to those of the monocot-infecting mastreviruses. This suggests that, despite host range differences, very similar biochemical, ecological and evolutionary factors must underlie recombination patterns in the dicot- and monocot-infecting mastreviruses.
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Affiliation(s)
- Darren P Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa
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