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Claverie S, Hoareau M, Chéhida SB, Filloux D, Varsani A, Roumagnac P, Martin DP, Lett JM, Lefeuvre P. Metagenomics reveals the structure of Mastrevirus-host interaction network within an agro-ecosystem. Virus Evol 2023; 9:vead043. [PMID: 37475836 PMCID: PMC10354507 DOI: 10.1093/ve/vead043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/24/2023] [Accepted: 07/04/2023] [Indexed: 07/22/2023] Open
Abstract
As highly pervasive parasites that sometimes cause disease, viruses are likely major components of all natural ecosystems. An important step towards both understanding the precise ecological roles of viruses and determining how natural communities of viral species are assembled and evolve is obtaining full descriptions of viral diversity and distributions at ecosystem scales. Here, we focused on obtaining such 'community-scale' data for viruses in a single genus. We chose the genus Mastrevirus (family Geminiviridae), members of which have predominantly been found infecting uncultivated grasses (family Poaceae) throughout the tropical and sub-tropical regions of the world. We sampled over 3 years, 2,884 individual Poaceae plants belonging to thirty different species within a 2-ha plot which included cultivated and uncultivated areas on the island of Reunion. Mastreviruses were found in ∼8 per cent of the samples, of which 96 per cent did not have any discernible disease symptoms. The multitude of host-virus associations that we uncovered reveals both the plant species that most commonly host mastreviruses and the mastrevirus species (such as maize streak virus and maize streak Reunion virus) that have especially large host ranges. Our findings are consistent with the hypothesis that perennial plant species capable of hosting years-long mixed mastrevirus infections likely play a disproportionately important role in the generation of inter-species and inter-strain mastrevirus recombinants.
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Affiliation(s)
- Sohini Claverie
- CIRAD, UMR PVBMT, F-97410 St Pierre, La Réunion, France
- Université de La Réunion, UMR PVBMT, F-97410 St Pierre, La Réunion, France
| | | | | | - Denis Filloux
- CIRAD, UMR PHIM, Montpellier F-34090, France
- PHIM Plant Health Institute, Université de Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier 34090, France
| | | | - Philippe Roumagnac
- CIRAD, UMR PHIM, Montpellier F-34090, France
- PHIM Plant Health Institute, Université de Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier 34090, France
| | - Darren P Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa
| | | | - Pierre Lefeuvre
- CIRAD, UMR PVBMT, F-97410 St Pierre, La Réunion, France
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, Cape Town 7700, South Africa
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2
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Monjane AL, Dellicour S, Hartnady P, Oyeniran KA, Owor BE, Bezuidenhout M, Linderme D, Syed RA, Donaldson L, Murray S, Rybicki EP, Kvarnheden A, Yazdkhasti E, Lefeuvre P, Froissart R, Roumagnac P, Shepherd DN, Harkins GW, Suchard MA, Lemey P, Varsani A, Martin DP. Symptom evolution following the emergence of maize streak virus. eLife 2020; 9:51984. [PMID: 31939738 PMCID: PMC7034976 DOI: 10.7554/elife.51984] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/14/2020] [Indexed: 11/24/2022] Open
Abstract
For pathogens infecting single host species evolutionary trade-offs have previously been demonstrated between pathogen-induced mortality rates and transmission rates. It remains unclear, however, how such trade-offs impact sub-lethal pathogen-inflicted damage, and whether these trade-offs even occur in broad host-range pathogens. Here, we examine changes over the past 110 years in symptoms induced in maize by the broad host-range pathogen, maize streak virus (MSV). Specifically, we use the quantified symptom intensities of cloned MSV isolates in differentially resistant maize genotypes to phylogenetically infer ancestral symptom intensities and check for phylogenetic signal associated with these symptom intensities. We show that whereas symptoms reflecting harm to the host have remained constant or decreased, there has been an increase in how extensively MSV colonizes the cells upon which transmission vectors feed. This demonstrates an evolutionary trade-off between amounts of pathogen-inflicted harm and how effectively viruses position themselves within plants to enable onward transmission.
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Affiliation(s)
- Adérito L Monjane
- Fish Health Research Group, Norwegian Veterinary Institute, Oslo, Norway.,Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven - University of Leuven, Leuven, Belgium.,Spatial Epidemiology Laboratory (SpELL), Université Libre de Bruxelles, Brussels, Belgium
| | - Penelope Hartnady
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
| | - Kehinde A Oyeniran
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
| | - Betty E Owor
- Department of Agricultural Production, School of Agricultural Sciences, Makerere University, Kampala, Uganda
| | - Marion Bezuidenhout
- Molecular and Cell Biology Department, University of Cape Town, Cape Town, South Africa
| | - Daphné Linderme
- Molecular and Cell Biology Department, University of Cape Town, Cape Town, South Africa
| | - Rizwan A Syed
- Molecular and Cell Biology Department, University of Cape Town, Cape Town, South Africa
| | - Lara Donaldson
- Molecular and Cell Biology Department, University of Cape Town, Cape Town, South Africa
| | - Shane Murray
- Molecular and Cell Biology Department, University of Cape Town, Cape Town, South Africa
| | - Edward P Rybicki
- Molecular and Cell Biology Department, University of Cape Town, Cape Town, South Africa
| | - Anders Kvarnheden
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Elham Yazdkhasti
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Rémy Froissart
- University of Montpellier, Centre National de la Recherche Scientifique (CNRS), Institut de recherche pour le développement (IRD), UMR 5290, Maladie Infectieuses & Vecteurs: Écologie, Génétique Évolution & Contrôle" (MIVEGEC), Montpellier, France
| | - Philippe Roumagnac
- CIRAD, BGPI, Montpellier, France.,BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, Montpellier, France
| | - Dionne N Shepherd
- Molecular and Cell Biology Department, University of Cape Town, Cape Town, South Africa.,Research Office, University of Cape Town, Cape Town, South Africa
| | - Gordon W Harkins
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, United States
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven - University of Leuven, Leuven, Belgium
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, United States.,Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Darren P Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
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3
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Kraberger S, Saumtally S, Pande D, Khoodoo MHR, Dhayan S, Dookun-Saumtally A, Shepherd DN, Hartnady P, Atkinson R, Lakay FM, Hanson B, Redhi D, Monjane AL, Windram OP, Walters M, Oluwafemi S, Michel-Lett J, Lefeuvre P, Martin DP, Varsani A. Molecular diversity, geographic distribution and host range of monocot-infecting mastreviruses in Africa and surrounding islands. Virus Res 2017; 238:171-178. [PMID: 28687345 DOI: 10.1016/j.virusres.2017.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 06/28/2017] [Accepted: 07/01/2017] [Indexed: 10/19/2022]
Abstract
Maize streak virus (MSV), an important pathogen of maize in Africa, is the most extensively studied member of the Mastrevirus genus in the family Geminiviridae. Comparatively little is known about other monocot-infecting African mastreviruses, most of which infect uncultivated grasses. Here we determine the complete sequences of 134 full African mastrevirus genomes from predominantly uncultivated Poaceae species. Based on established taxonomic guidelines for the genus Mastrevirus, these genomes could be classified as belonging to the species Maize streak virus, Eragrostis minor streak virus, Maize streak Reunion virus, Panicum streak virus, Sugarcane streak Reunion virus and Sugarcane streak virus. Together with all other publicly available African monocot-infecting mastreviruses, the 134 new isolates extend the known geographical distributions of many of these species, including MSV which we found infecting Digitaria sp. on the island of Grand Canaria: the first definitive discovery of any African monocot-infecting mastreviruses north-west of the Saharan desert. These new isolates also extend the known host ranges of both African mastrevirus species and the strains within these. Most notable was the discovery of MSV-C isolates infecting maize which suggests that this MSV strain, which had previously only ever been found infecting uncultivated species, may be in the process of becoming adapted to this important staple crop.
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Affiliation(s)
- Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life sciences, Arizona State University, Tempe, AZ 85287-5001, USA; School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Salem Saumtally
- Mauritius Sugarcane Industry Research Institute, Réduit, Mauritius
| | - Daniel Pande
- Department of Botany, Maseno University, P.O. Box 333, Maseno, Kenya; Department of Biological and Biomedical Science and Technology, Laikipia University, P.O. Box 1100-20300, Nyahururu, Kenya
| | | | - Sonalall Dhayan
- Mauritius Sugarcane Industry Research Institute, Réduit, Mauritius
| | | | - Dionne N Shepherd
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
| | - Penelope Hartnady
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7925, South Africa
| | - Richard Atkinson
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
| | - Francisco M Lakay
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
| | - Britt Hanson
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
| | - Devasha Redhi
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
| | - Adérito L Monjane
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa; Department of Immunology, Norwegian Veterinary Institute, Pb 750 Sentrum, N-0106 Oslo, Norway
| | - Oliver P Windram
- Grand Challenges in Ecosystems & the Environment, Imperial College London, Silwood Park Campus, Buckhurst Road, SL5 7PY Ascot, Berks, UK
| | - Matthew Walters
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Sunday Oluwafemi
- Department of Crop Production, Soil and Environmental Management, Bowen University, P.M.B. 284, Iwo, Osun State, Nigeria
| | - Jean Michel-Lett
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410 Saint-Pierre, Ile de La Réunion, France
| | - Pierre Lefeuvre
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410 Saint-Pierre, Ile de La Réunion, France
| | - Darren P Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7925, South Africa.
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life sciences, Arizona State University, Tempe, AZ 85287-5001, USA; School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand; Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa.
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4
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Pande D, Madzokere E, Hartnady P, Kraberger S, Hadfield J, Rosario K, Jäschke A, Monjane AL, Owor BE, Dida MM, Shepherd DN, Martin DP, Varsani A, Harkins GW. The role of Kenya in the trans-African spread of maize streak virus strain A. Virus Res 2017; 232:69-76. [PMID: 28192163 DOI: 10.1016/j.virusres.2017.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/07/2017] [Accepted: 02/08/2017] [Indexed: 10/20/2022]
Abstract
Maize streak virus (MSV), the causal agent of maize streak disease (MSD), is the most important viral pathogen of Africa's staple food crop, maize. Previous phylogeographic analyses have revealed that the most widely-distributed and common MSV variant, MSV-A1, has been repeatedly traversing Africa over the past fifty years with long-range movements departing from either the Lake Victoria region of East Africa, or the region around the convergence of Zimbabwe, South Africa and Mozambique in southern Africa. Despite Kenya being the second most important maize producing country in East Africa, little is known about the Kenyan MSV population and its contribution to the ongoing diversification and trans-continental dissemination of MSV-A1. We therefore undertook a sampling survey in this country between 2008 and 2011, collecting MSD prevalence data in 119 farmers' fields, symptom severity data for 170 maize plants and complete MSV genome sequence data for 159 MSV isolates. We then used phylogenetic and phylogeographic analyses to show that whereas the Kenyan MSV population is likely primarily derived from the MSV population in neighbouring Uganda, it displays considerably more geographical structure than the Ugandan population. Further, this geographical structure likely confounds apparent associations between virus genotypes and both symptom severity and MSD prevalence in Kenya. Finally, we find that Kenya is probably a sink rather than a source of MSV diversification and movement, and therefore, unlike Uganda, Kenya probably does not play a major role in the trans-continental dissemination of MSV-A1.
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Affiliation(s)
- Daniel Pande
- Department of Applied Plant Sciences, School of Agriculture and Food Security, Maseno, Kenya; Biological and Biomedical Science and Technology, Laikipia University, P.O. Box 1100-20300, Nyahururu, Kenya
| | - Eugene Madzokere
- South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa
| | - Penelope Hartnady
- Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town 7001, South Africa
| | - Simona Kraberger
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - James Hadfield
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA
| | - Anja Jäschke
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Department of Infectious Diseases, University of Heidelberg, D-69120 Heidelberg, Germany
| | - Adérito L Monjane
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa; Department of Immunology, Norwegian Veterinary Institute, Pb 750 Sentrum, N-0106 Oslo, Norway
| | - Betty E Owor
- Department of Agricultural Production, School of Agricultural Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Mathews M Dida
- Department of Applied Plant Sciences, School of Agriculture and Food Security, Maseno, Kenya
| | - Dionne N Shepherd
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa
| | - Darren P Martin
- Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town 7001, South Africa
| | - Arvind Varsani
- Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town 7001, South Africa; School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
| | - Gordon W Harkins
- South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa.
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5
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Monjane AL, Harkins GW, Martin DP, Lemey P, Lefeuvre P, Shepherd DN, Oluwafemi S, Simuyandi M, Zinga I, Komba EK, Lakoutene DP, Mandakombo N, Mboukoulida J, Semballa S, Tagne A, Tiendrébéogo F, Erdmann JB, van Antwerpen T, Owor BE, Flett B, Ramusi M, Windram OP, Syed R, Lett JM, Briddon RW, Markham PG, Rybicki EP, Varsani A. Reconstructing the history of maize streak virus strain a dispersal to reveal diversification hot spots and its origin in southern Africa. J Virol 2011; 85:9623-36. [PMID: 21715477 PMCID: PMC3165777 DOI: 10.1128/jvi.00640-11] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 06/21/2011] [Indexed: 01/11/2023] Open
Abstract
Maize streak virus strain A (MSV-A), the causal agent of maize streak disease, is today one of the most serious biotic threats to African food security. Determining where MSV-A originated and how it spread transcontinentally could yield valuable insights into its historical emergence as a crop pathogen. Similarly, determining where the major extant MSV-A lineages arose could identify geographical hot spots of MSV evolution. Here, we use model-based phylogeographic analyses of 353 fully sequenced MSV-A isolates to reconstruct a plausible history of MSV-A movements over the past 150 years. We show that since the probable emergence of MSV-A in southern Africa around 1863, the virus spread transcontinentally at an average rate of 32.5 km/year (95% highest probability density interval, 15.6 to 51.6 km/year). Using distinctive patterns of nucleotide variation caused by 20 unique intra-MSV-A recombination events, we tentatively classified the MSV-A isolates into 24 easily discernible lineages. Despite many of these lineages displaying distinct geographical distributions, it is apparent that almost all have emerged within the past 4 decades from either southern or east-central Africa. Collectively, our results suggest that regular analysis of MSV-A genomes within these diversification hot spots could be used to monitor the emergence of future MSV-A lineages that could affect maize cultivation in Africa.
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Affiliation(s)
- Adérito L. Monjane
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
| | - Gordon W. Harkins
- South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Darren P. Martin
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, 7925, Cape Town, South Africa
- Centre for High-Performance Computing, Rosebank, Cape Town, South Africa
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, K.U. Leuven, Leuven, Belgium
| | - Pierre Lefeuvre
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, 7925, Cape Town, South Africa
- CIRAD, UMR 53 PVBMT CIRAD-Université de la Réunion, Pôle de Protection des Plantes, 97410, Saint Pierre, La Réunion, France
| | - Dionne N. Shepherd
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
| | - Sunday Oluwafemi
- Department of Crop Production, Soil and Environmental Management, Bowen University, Iwo, Osun State, P.M.B. 284, Nigeria
| | | | - Innocent Zinga
- LASBAD Laboratory, Faculty of Sciences, University of Bangui, BP 908 Bangui, Central African Republic
| | - Ephrem K. Komba
- LASBAD Laboratory, Faculty of Sciences, University of Bangui, BP 908 Bangui, Central African Republic
| | - Didier P. Lakoutene
- LASBAD Laboratory, Faculty of Sciences, University of Bangui, BP 908 Bangui, Central African Republic
| | - Noella Mandakombo
- LASBAD Laboratory, Faculty of Sciences, University of Bangui, BP 908 Bangui, Central African Republic
| | - Joseph Mboukoulida
- LASBAD Laboratory, Faculty of Sciences, University of Bangui, BP 908 Bangui, Central African Republic
| | - Silla Semballa
- LASBAD Laboratory, Faculty of Sciences, University of Bangui, BP 908 Bangui, Central African Republic
| | - Appolinaire Tagne
- Cereals Research Program, Institute of Agricultural Research for Development, Box 2067 Messa, Yaounde, Cameroon
| | - Fidèle Tiendrébéogo
- Centre de Recherche en Sciences Biologiques Alimentaires et Nutritionnelles (CRSBAN), UFR/SVT Université de Ouagadougou, 03 BP 7131 Ouagadougou 03, Burkina Faso
| | - Julia B. Erdmann
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
- Institute of Biology, Department of Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany
| | - Tania van Antwerpen
- South African Sugarcane Research Institute, Mount Edgecombe, KwaZulu Natal, South Africa
| | - Betty E. Owor
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom, CB2 3EA
| | - Bradley Flett
- Crop Protection, ARC-Grain Crops Institute, Potchefstroom 2520, South Africa
| | - Moses Ramusi
- Crop Protection, ARC-Grain Crops Institute, Potchefstroom 2520, South Africa
| | - Oliver P. Windram
- Warwick HRI Biology Centre, University of Warwick, Wellesbourne, CV35 9EF, England
| | - Rizwan Syed
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
| | - Jean-Michel Lett
- CIRAD, UMR 53 PVBMT CIRAD-Université de la Réunion, Pôle de Protection des Plantes, 97410, Saint Pierre, La Réunion, France
| | - Rob W. Briddon
- National Institute for Biotechnology and Genetic Engineering, Jhang Road, P.O. Box 577, Faisalabad, Pakistan
| | - Peter G. Markham
- Department of Disease and Stress Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Edward P. Rybicki
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Arvind Varsani
- Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
- Electron Microscope Unit, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
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6
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Varsani A, Monjane AL, Donaldson L, Oluwafemi S, Zinga I, Komba EK, Plakoutene D, Mandakombo N, Mboukoulida J, Semballa S, Briddon RW, Markham PG, Lett JM, Lefeuvre P, Rybicki EP, Martin DP. Comparative analysis of Panicum streak virus and Maize streak virus diversity, recombination patterns and phylogeography. Virol J 2009; 6:194. [PMID: 19903330 PMCID: PMC2777162 DOI: 10.1186/1743-422x-6-194] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Accepted: 11/10/2009] [Indexed: 11/10/2022] Open
Abstract
Background Panicum streak virus (PanSV; Family Geminiviridae; Genus Mastrevirus) is a close relative of Maize streak virus (MSV), the most serious viral threat to maize production in Africa. PanSV and MSV have the same leafhopper vector species, largely overlapping natural host ranges and similar geographical distributions across Africa and its associated Indian Ocean Islands. Unlike MSV, however, PanSV has no known economic relevance. Results Here we report on 16 new PanSV full genome sequences sampled throughout Africa and use these together with others in public databases to reveal that PanSV and MSV populations in general share very similar patterns of genetic exchange and geographically structured diversity. A potentially important difference between the species, however, is that the movement of MSV strains throughout Africa is apparently less constrained than that of PanSV strains. Interestingly the MSV-A strain which causes maize streak disease is apparently the most mobile of all the PanSV and MSV strains investigated. Conclusion We therefore hypothesize that the generally increased mobility of MSV relative to other closely related species such as PanSV, may have been an important evolutionary step in the eventual emergence of MSV-A as a serious agricultural pathogen. The GenBank accession numbers for the sequences reported in this paper are GQ415386-GQ415401
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Affiliation(s)
- Arvind Varsani
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town 7925, South Africa
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7
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Varsani A, Shepherd DN, Monjane AL, Owor BE, Erdmann JB, Rybicki EP, Peterschmitt M, Briddon RW, Markham PG, Oluwafemi S, Windram OP, Lefeuvre P, Lett JM, Martin DP. Recombination, decreased host specificity and increased mobility may have driven the emergence of maize streak virus as an agricultural pathogen. J Gen Virol 2008; 89:2063-2074. [PMID: 18753214 PMCID: PMC2886952 DOI: 10.1099/vir.0.2008/003590-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Accepted: 06/17/2008] [Indexed: 01/20/2023] Open
Abstract
Maize streak virus (MSV; family Geminiviridae, genus Mastrevirus), the causal agent of maize streak disease, ranks amongst the most serious biological threats to food security in subSaharan Africa. Although five distinct MSV strains have been currently described, only one of these - MSV-A - causes severe disease in maize. Due primarily to their not being an obvious threat to agriculture, very little is known about the 'grass-adapted' MSV strains, MSV-B, -C, -D and -E. Since comparing the genetic diversities, geographical distributions and natural host ranges of MSV-A with the other MSV strains could provide valuable information on the epidemiology, evolution and emergence of MSV-A, we carried out a phylogeographical analysis of MSVs found in uncultivated indigenous African grasses. Amongst the 83 new MSV genomes presented here, we report the discovery of six new MSV strains (MSV-F to -K). The non-random recombination breakpoint distributions detectable with these and other available mastrevirus sequences partially mirror those seen in begomoviruses, implying that the forces shaping these breakpoint patterns have been largely conserved since the earliest geminivirus ancestors. We present evidence that the ancestor of all MSV-A variants was the recombinant progeny of ancestral MSV-B and MSV-G/-F variants. While it remains unknown whether recombination influenced the emergence of MSV-A in maize, our discovery that MSV-A variants may both move between and become established in different regions of Africa with greater ease, and infect more grass species than other MSV strains, goes some way towards explaining why MSV-A is such a successful maize pathogen.
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Affiliation(s)
- Arvind Varsani
- Electron Microscope Unit, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Dionne N. Shepherd
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Adérito L. Monjane
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Betty E. Owor
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Julia B. Erdmann
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
- Institute of Biology, Department of Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany
| | - Edward P. Rybicki
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
| | - Michel Peterschmitt
- CIRAD, UMR BGPI, TA A54/K, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France
| | - Rob W. Briddon
- National Institute for Biotechnology and Genetic Engineering, Jhang Road, PO Box 577, Faisalabad, Pakistan
| | - Peter G. Markham
- Department of Disease and Stress Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Sunday Oluwafemi
- Department of Crop, Soil and Environmental Management, Bowen University, PMB 284, Iwo, Osun State, Nigeria
| | - Oliver P. Windram
- Warwick HRI Biology Centre, University of Warwick, Wellesbourne CV35 9EF, UK
| | - Pierre Lefeuvre
- CIRAD, UMR 53 PVBMT CIRAD-Université de la Réunion, Pôle de Protection des Plantes, Ligne Paradis, 97410 Saint Pierre, La Réunion, France
| | - Jean-Michel Lett
- CIRAD, UMR 53 PVBMT CIRAD-Université de la Réunion, Pôle de Protection des Plantes, Ligne Paradis, 97410 Saint Pierre, La Réunion, France
| | - Darren P. Martin
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
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8
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Schubert J, Habekuss A, Kazmaier K, Jeske H. Surveying cereal-infecting geminiviruses in Germany--diagnostics and direct sequencing using rolling circle amplification. Virus Res 2007; 127:61-70. [PMID: 17449126 DOI: 10.1016/j.virusres.2007.03.018] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Revised: 03/20/2007] [Accepted: 03/20/2007] [Indexed: 11/18/2022]
Abstract
Geminiviruses have spread in German cereal crops during the last few years. In order to identify and classify them, we have compared conventional techniques (enzyme-linked immunosorbent assays, polymerase chain reaction, bacterial cloning, and sequencing) with a newly developed method which uses rolling circle amplification (RCA), restriction fragment length polymorphism (RFLP), and direct sequencing without a bacterial cloning step. Whereas immunological methods utilising polyclonal antibodies were reliable for detection of geminiviruses, they did not discriminate between different German mastrevirus species, in contrast to RCA/RFLP. Direct sequencing gave high fidelity results with the same quality as conventional cloning and sequencing but with significantly reduced effort and costs. Based on a survey of field-derived cereal samples and on DNA sequences of distinct virus isolates we propose two new mastrevirus species, to be named Barley dwarf virus (BDV), and Oat dwarf virus (ODV) according to sequence differences and host range studies. The results show the applicability of RCA-based techniques for field studies and the possibility of sequencing a geminiviral genome without cloning. This approach will accelerate genomics studies of all viruses with small circular DNA genomes. In addition, RCA proves to be a reliable technique allowing for the detection of new geminivirus species as it does not depend on the knowledge of specific primers.
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Affiliation(s)
- Jörg Schubert
- Institute of Resistance Research and Pathogen Diagnostics, Federal Centre for Breeding Research on Cultivated Plants, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
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9
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Köklü G, Ramsell JNE, Kvarnheden A. The complete genome sequence for a Turkish isolate of Wheat dwarf virus (WDV) from barley confirms the presence of two distinct WDV strains. Virus Genes 2006; 34:359-66. [PMID: 16927119 DOI: 10.1007/s11262-006-0029-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2006] [Accepted: 07/11/2006] [Indexed: 11/29/2022]
Abstract
The complete genome for a barley isolate of Wheat dwarf virus (WDV) from Tekirdağ, Turkey, WDV-Bar[TR], was isolated and sequenced. The genome was found to be 2739 nucleotides long, which is shorter than wheat-infecting WDV isolates, and with a genome organization typical for mastreviruses. The complete genome of WDV-Bar[TR] showed 83-84% nucleotide identity to wheat isolates of WDV, with the non-coding regions SIR and LIR least conserved (72-74% identity). The deduced amino acid sequences for Rep and RepA were most conserved (92-93%), while CP and MP were less conserved (87% and 79-80%, respectively). The identity to other mastrevirus species was significantly lower. In phylogenetic analyses, the WDV isolates formed a distinct clade, well separated from the other mastreviruses with the wheat isolates grouping closely together. Phylogenetic analyses of WDV-Bar[TR], the partial sequence for another Turkish barley isolate (WDV-Bar[TR2]) and published WDV sequences further supported the division of WDV into two distinct strains. The barley strain could also be divided into three subtypes based on relationships and geographic origin. This study shows the first complete published sequence for a barley isolate of WDV.
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Affiliation(s)
- Gassan Köklü
- Department of Plant Protection, Trakya University, Tekirdağ Faculty of Agriculture, 59030 Tekirdağ, Turkey.
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10
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Abu Ahmad Y, Rassaby L, Royer M, Borg Z, Braithwaite KS, Mirkov TE, Irey MS, Perrier X, Smith GR, Rott P. Yellow leaf of sugarcane is caused by at least three different genotypes of sugarcane yellow leaf virus, one of which predominates on the Island of Réunion. Arch Virol 2006; 151:1355-71. [PMID: 16453082 DOI: 10.1007/s00705-005-0712-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2005] [Accepted: 12/14/2005] [Indexed: 10/25/2022]
Abstract
The genetic diversity of sugarcane yellow leaf virus (SCYLV) was analyzed with 43 virus isolates from Réunion Island and 17 isolates from world-wide locations. We attempted to amplify by reverse-transcription polymerase chain reaction (RT-PCR), clone, and sequence four different fragments covering 72% of the genome of these virus isolates. The number of amplified isolates and useful sequence information varied according to each fragment, whereas an amplicon was obtained with diagnostic primers for 59 out of 60 isolates (98%). Phylogenetic analyses of the sequences determined here and additional sequences of 11 other SCYLV isolates available from GenBank showed that SCYLV isolates were distributed in different phylogenetic groups or belonged to single genotypes. The majority of isolates from Réunion Island were grouped in phylogenetic clusters that did not contain any isolates from other origins. The complete six ORFs (5612 bp) of five SCYLV isolates (two from Réunion Island, one from Brazil, one from China, and one from Peru) were amplified, cloned, and sequenced. The existence of at least three distinct genotypes of SCYLV was shown by phylogenetic analysis of the sequences of these isolates and additional published sequences of three SCYLV isolates (GenBank accessions). The biological significance of these genotypes and of the origin of the distinct lineage of SCYLV in Réunion Island remains to be determined.
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Affiliation(s)
- Y Abu Ahmad
- UMR 385 AGRO.M-CIRAD-INRA Biologie et Génétique des Interactions Plante-Parasite, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
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11
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Fargette D, Konaté G, Fauquet C, Muller E, Peterschmitt M, Thresh JM. Molecular ecology and emergence of tropical plant viruses. ANNUAL REVIEW OF PHYTOPATHOLOGY 2006; 44:235-60. [PMID: 16784403 DOI: 10.1146/annurev.phyto.44.120705.104644] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
An appreciation of the risks caused by emergent plant viruses is critical in tropical areas that rely heavily on agriculture for subsistence and rural livelihood. Molecular ecology, within 10 years, has unraveled the factors responsible for the emergence of several of the economically most important tropical plant viruses: Rice yellow mottle virus (RYMV), Cassava mosaic geminiviruses (CMGs), Maize streak virus (MSV), and Banana streak virus (BSV). A large range of mechanisms--most unsuspected until recently--were involved: recombination and synergism between virus species, new vector biotypes, genome integration of the virus, host adaptation, and long-distance dispersal. A complex chain of molecular and ecological events resulted in novel virus-vector-plant-environment interactions that led to virus emergence. It invariably involved a major agricultural change: crop introduction, cultural intensification, germplasm movement, and new genotypes. A current challenge is now to complement the analysis of the causes by an assessment of the risks of emergence. Recent attempts to assess the risks of emergence of virulent virus strains are described.
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Affiliation(s)
- D Fargette
- IRD BP 64501, 34394 Montpellier Cedex 5, France.
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12
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Willment JA, Martin DP, Van der Walt E, Rybicki EP. Biological and Genomic Sequence Characterization of Maize streak virus Isolates from Wheat. PHYTOPATHOLOGY 2002; 92:81-86. [PMID: 18944143 DOI: 10.1094/phyto.2002.92.1.81] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
ABSTRACT Maize streak virus (MSV) is best known as the causal agent of maize streak disease. However, only a genetically uniform subset of the viruses within this diverse species is actually capable of producing severe symptoms in maize. Whereas these "maize-type" viruses all share greater than 95% sequence identity, MSV strains isolated from grasses may share as little as 79% sequence identity with the maize-type viruses. Here, we present the complete genome sequences and biological characterization of two MSV isolates from wheat that share approximately 89% sequence identity with the maize-type viruses. Clonal populations of these two isolates, named MSV-Tas and MSV-VW, were leafhopper-transmitted to Digitaria sanguinalis and a range of maize, wheat, and barley genotypes. Whereas the two viruses showed some differences in their pathogenicity in maize, they were both equally pathogenic in D. sanguinalis and the various wheat and barley genotypes tested. Phylogenetic analyses involving the genome sequences of MSV-Tas and MSV-VW, a new maize-type virus also fully sequenced in this study (MSV-VM), and all other available African streak virus sequences, indicated that MSV-Tas and MSV-VW are close relatives that together represent a distinct MSV strain. Sequence analyses revealed that MSV-VM has a recombinant genome containing MSV-Tas/VW-like sequences within its movement protein gene.
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13
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Martin DP, Willment JA, Billharz R, Velders R, Odhiambo B, Njuguna J, James D, Rybicki EP. Sequence diversity and virulence in Zea mays of Maize streak virus isolates. Virology 2001; 288:247-55. [PMID: 11601896 DOI: 10.1006/viro.2001.1075] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Full genomic sequences were determined for 12 Maize streak virus (MSV) isolates obtained from Zea mays and wild grass species. These and 10 other publicly available full-length sequences were used to classify a total of 66 additional MSV isolates that had been characterized by PCR-restriction fragment length polymorphism and/or partial nucleotide sequence analysis. A description is given of the host and geographical distribution of the MSV strain and subtype groupings identified. The relationship between the genotypes of 21 fully sequenced virus isolates and their virulence in differentially MSV-resistant Z. mays genotypes was examined. Within the only MSV strain grouping that produced severe symptoms in maize, highly virulent and widely distributed genotypes were identified that are likely to pose the most serious threat to maize production in Africa. Evidence is presented that certain of the isolates investigated may be the products of either intra- or interspecific recombination.
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Affiliation(s)
- D P Martin
- Department of Moleculare Cell Biology, University of Cape Town, Cape Town, South Africa, 7701
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14
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Willment JA, Martin DP, Rybicki EP. Analysis of the diversity of African streak mastreviruses using PCR-generated RFLPs and partial sequence data. J Virol Methods 2001; 93:75-87. [PMID: 11311346 DOI: 10.1016/s0166-0934(00)00299-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Maize streak virus (MSV) is the most economically significant member of a diverse group of African grass-infecting Mastrevirus species in the family Geminiviridae. We designed a single set of degenerate primers which enables the PCR amplification of an approximately 1300 bp DNA fragment spanning both conserved (the RepA gene) and variable (the long intergenic region and MP gene) portions of these viruses' genomes. Using restriction fragment length polymorphism (RFLP) analysis of PCR products obtained from 39 MSV, one SSV, and two PanSV isolates, it was possible to both identify the different virus species, which differ in nucleotide sequence by up to 40%, and to differentiate between MSV isolates sharing up to 99% sequence identity. The reliability of the RFLP data for typing the MSV isolates was verified by the phylogenetic analysis of the partial genomic nucleotide sequences of a representative subset of the MSV isolates. Based on both the RFLP and sequence data, the MSV isolates could be clearly differentiated into the four groups: these were a group of predominantly maize-infecting isolates, and three groups containing grass/wheat-infecting isolates. RFLP analysis also revealed a number of mixed virus infections in which, in certain instances, it was possible to identify individual population members.
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Affiliation(s)
- J A Willment
- Department of Microbiology, University of Cape Town, Private Bag, Rondebosch 7701, Western Cape, South Africa
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15
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Affiliation(s)
- E P Rybicki
- Department of Microbiology, University of Cape Town, South Africa
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16
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Affiliation(s)
- K E Palmer
- Department of Microbiology, University of Cape Town, Western Cape, South Africa
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