1
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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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Lin Y, Ali N, Hajimorad MR, Zhang L, Qi X, Zhou L, Wen R, Chen B. Incidence, Geographical Distribution, and Genetic Diversity of Sugarcane Striate Virus in Saccharum Species in China. PLANT DISEASE 2021; 105:3531-3537. [PMID: 34042497 DOI: 10.1094/pdis-10-20-2307-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A novel virus of the genus Mastrevirus, family Geminivirdae, has been reported in sugarcane germplasm collections in Florida, Guadeloupe, and Réunion, and was named sugarcane striate virus (SStrV). Although the full-length sequence of an SStrV isolate from China was obtained in 2015, the incidence, geographical distribution, and genetic diversity of this virus remained unclear. A single leaf sample from 2,368 sugarcane plants from main sugarcane-producing regions of China and germplasm collections were tested for SStrV by PCR. Average virus incidence was 25.1% for field-collected samples, and SStrV was detected in most Saccharum species and two sugarcane-related species, with the highest incidence in Saccharum officinarum (44.1%) followed by Saccharum spp. local varieties (33.3%) grown for chewing cane for a long time. The virus incidence was much lower (6.8%) in modern commercial cultivars (Saccharum spp. hybrids). Phylogenetic trees based on full-length genomes of 157 SStrV isolates revealed that Chinese isolates comprised strains A and B, but not C and D, that were reported in Florida, U.S.A. SStrV strain A was the most prominent (98.7%) and widespread strain in China and was further divided into eight subgroups. Almost half (45.6%) of the SStrV-positive samples from S. officinarum and Saccharum spp. local varieties were coinfected with sugarcane mosaic disease viruses or sugarcane yellow leaf virus. Interestingly, most of the plants infected by strain A of SStrV were asymptomatic. SStrV appears to be widespread in China, and its influence on chewing cane deserves further investigation.
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Affiliation(s)
- Yinfu Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bio-Resources and Guangxi Key Laboratory for Sugarcane Biology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Niyaz Ali
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bio-Resources and Guangxi Key Laboratory for Sugarcane Biology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - M R Hajimorad
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, U.S.A
| | - Lijuan Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bio-Resources and Guangxi Key Laboratory for Sugarcane Biology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Xiaohang Qi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bio-Resources and Guangxi Key Laboratory for Sugarcane Biology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Longwu Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bio-Resources and Guangxi Key Laboratory for Sugarcane Biology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Ronghui Wen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bio-Resources and Guangxi Key Laboratory for Sugarcane Biology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bio-Resources and Guangxi Key Laboratory for Sugarcane Biology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
- College of Agriculture, Guangxi University, Nanning 530004, China
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3
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Ortega-Del Campo S, Grigoras I, Timchenko T, Gronenborn B, Grande-Pérez A. Twenty years of evolution and diversification of digitaria streak virus in Digitaria setigera. Virus Evol 2021; 7:veab083. [PMID: 34659796 PMCID: PMC8516820 DOI: 10.1093/ve/veab083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 09/09/2021] [Accepted: 09/20/2021] [Indexed: 11/21/2022] Open
Abstract
Within the family Geminiviridae, the emergence of new species results from their high mutation and recombination rates. In this study, we report the variability and evolution of digitaria streak virus (DSV), a mastrevirus isolated in 1986 from the grass Digitaria setigera in an island of the Vanuatu archipelago. Viral DNA of DSV samples was amplified from D. setigera specimens, derived from the naturally infected original plant, which were propagated in different laboratories in France and Italy for more than 20 years. From the consensus sequences, the nucleotide substitution rate was estimated for the period between a sample and the original sequence published in 1987, as well as for the period between samples. In addition, the intra-host genetic complexity and diversity of 8 DSV populations with a total of 165 sequenced haplotypes was characterized. The evolutionary rate of DSV was estimated to be between 1.13 × 10−4 and 9.87 × 10−4 substitutions/site/year, within the ranges observed in other single-stranded DNA viruses and RNA viruses. Bioinformatic analyses revealed high variability and heterogeneity in DSV populations, which confirmed that mutant spectra are continuously generated and are organized as quasispecies. The analysis of polymorphisms revealed nucleotide substitution biases in viral genomes towards deamination and oxidation of single-stranded DNA. The differences in variability in each of the genomic regions reflected a dynamic and modular evolution in the mutant spectra that was not reflected in the consensus sequences. Strikingly, the most variable region of the DSV genome, encoding the movement protein, showed rapid fixation of the mutations in the consensus sequence and a concomitant dN/dS ratio of 6.130, which suggests strong positive selection in this region. Phylogenetic analyses revealed a possible divergence in three genetic lineages from the original Vanuatu DSV isolate.
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Affiliation(s)
| | - Ioana Grigoras
- CNRS, Institut des Sciences du Végétal, Gif-sur-Yvette 91198, France
| | - Tatiana Timchenko
- CNRS, Institut des Sciences du Végétal, Gif-sur-Yvette 91198, France
| | - Bruno Gronenborn
- CNRS, Institut des Sciences du Végétal, Gif-sur-Yvette 91198, France
| | - Ana Grande-Pérez
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora' (IHSM-UMA-CSIC), Área de Genética, Facultad de Ciencias, Campus de Teatinos, Málaga 29071, Spain
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4
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How virulent are emerging maize-infecting mastreviruses? Arch Virol 2021; 166:955-959. [PMID: 33502595 DOI: 10.1007/s00705-020-04906-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/15/2020] [Indexed: 10/22/2022]
Abstract
Maize streak disease (MSD) is one of the most significant biotic constraints on the production of Africa's most important cereal crop. Until recently, the only virus known to cause severe MSD was the A-strain of maize streak virus (MSV/A), a member of the genus Mastrevirus, family Geminiviridae. However, over the past decade, two other mastreviruses, MSV/C and maize streak Réunion virus (MSRV), have been repeatedly found in the absence of MSV/A in maize plants displaying severe MSD symptoms. Here, we report on infectious clones of MSV/C and MSRV and test their ability to cause severe MSD symptoms. Although cloned MSV/C and MSRV genomes could cause systemic symptomatic infections in MSD-sensitive maize genotypes, these infections yielded substantially milder symptoms than those observed in the field. The MSV/C and MSRV isolates that we have examined are therefore unlikely to cause severe MSD on their own. Furthermore, mixed infections of MSRV and MSV/C with other mild MSV strains also consistently yielded mild MSD symptoms. It is noteworthy that MSRV produces distinctive striate symptoms in maize that are similar in pattern, albeit not in severity, to those seen in the field, showing that this virus may contribute to the severe MSD symptoms seen in the field. Therefore, despite not fulfilling Koch's postulates for MSV/C and MSRV as causal agents of severe MSD, we cannot exclude the possibility that these viruses could be contributing to currently emerging maize diseases.
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5
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Tembo M, Adediji AO, Bouvaine S, Chikoti PC, Seal SE, Silva G. A quick and sensitive diagnostic tool for detection of Maize streak virus. Sci Rep 2020; 10:19633. [PMID: 33184360 PMCID: PMC7661706 DOI: 10.1038/s41598-020-76612-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/29/2020] [Indexed: 11/09/2022] Open
Abstract
Maize streak virus disease (MSVD), caused by Maize streak virus (MSV; genus Mastrevirus), is one of the most severe and widespread viral diseases that adversely reduces maize yield and threatens food security in Africa. An effective control and management of MSVD requires robust and sensitive diagnostic tests capable of rapid detection of MSV. In this study, a loop-mediated isothermal amplification (LAMP) assay was designed for the specific detection of MSV. This test has shown to be highly specific and reproducible and able to detect MSV in as little as 10 fg/µl of purified genomic DNA obtained from a MSV-infected maize plant, a sensitivity 105 times higher to that obtained with polymerase chain reaction (PCR) in current general use. The high degree of sequence identity between Zambian and other African MSV isolates indicate that this LAMP assay can be used for detecting MSV in maize samples from any region in Africa. Furthermore, this assay can be adopted in minimally equipped laboratories and with potential use in plant clinic laboratories across Africa strengthening diagnostic capacity in countries dealing with MSD.
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Affiliation(s)
- Mathias Tembo
- Zambia Agriculture Research Institute, Mount Makulu Research Station, P/Bag 7, Lusaka, Zambia.
| | - Adedapo O Adediji
- Department of Crop Protection and Environmental Biology, Faculty of Agriculture, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Sophie Bouvaine
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, ME4 4TB, Kent, UK
| | - Patrick C Chikoti
- Zambia Agriculture Research Institute, Mount Makulu Research Station, P/Bag 7, Lusaka, Zambia
| | - Susan E Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, ME4 4TB, Kent, UK
| | - Gonҫalo Silva
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, ME4 4TB, Kent, UK
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6
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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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7
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Claverie S, Ouattara A, Hoareau M, Filloux D, Varsani A, Roumagnac P, Martin DP, Lett JM, Lefeuvre P. Exploring the diversity of Poaceae-infecting mastreviruses on Reunion Island using a viral metagenomics-based approach. Sci Rep 2019; 9:12716. [PMID: 31481704 PMCID: PMC6722101 DOI: 10.1038/s41598-019-49134-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 08/20/2019] [Indexed: 01/22/2023] Open
Abstract
Mostly found in Africa and its surrounding islands, African streak viruses (AfSV) represent the largest group of known mastreviruses. Of the thirteen AfSV species that are known to infect either cultivated or wild Poaceae plant species, six have been identified on Reunion Island. To better characterize AfSV diversity on this island, we undertook a survey of a small agroecosystem using a new metagenomics-based approach involving rolling circle amplification with random PCR amplification tagging (RCA-RA-PCR), high-throughput sequencing (Illumina HiSeq) and the mastrevirus reads classification using phylogenetic placement. Mastreviruses that likely belong to three new species were discovered and full genome sequences of these were determined by Sanger sequencing. The geminivirus-focused metagenomics approach we applied in this study was useful in both the detection of known and novel mastreviruses. The results confirm that Reunion Island is indeed a hotspot of AfSV diversity and that many of the mastrevirus species have likely been introduced multiple times. Applying a similar approach in other natural and agricultural environments should yield sufficient detail on the composition and diversity of geminivirus communities to precipitate major advances in our understanding of the ecology and the evolutionary history of this important group of viruses.
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Affiliation(s)
- Sohini Claverie
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France.,Université de La Réunion, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, Saint-Pierre, 97410, France
| | - Alassane Ouattara
- INERA, 01 BP 476, Ouagadougou 01, Burkina Faso.,Laboratoire Biosciences, Université Joseph KI-ZERBO, 03 BP 7021, Ouagadougou 03, Burkina Faso
| | | | - Denis Filloux
- CIRAD, UMR BGPI, F-34398, Montpellier, France.,BGPI, Université de Montpellier, INRA, CIRAD, Montpellier SupAgro, F-34398, Montpellier, France
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287-5001, USA.,Structural Biology Research Unit, Departement of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Philippe Roumagnac
- CIRAD, UMR BGPI, F-34398, Montpellier, France.,BGPI, Université de Montpellier, INRA, CIRAD, Montpellier SupAgro, F-34398, Montpellier, France
| | - Darren P Martin
- Computational Biology Division, Departement of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, South Africa
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8
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García-Arenal F, Zerbini FM. Life on the Edge: Geminiviruses at the Interface Between Crops and Wild Plant Hosts. Annu Rev Virol 2019; 6:411-433. [PMID: 31180812 DOI: 10.1146/annurev-virology-092818-015536] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viruses constitute the largest group of emerging pathogens, and geminiviruses (plant viruses with circular, single-stranded DNA genomes) are the major group of emerging plant viruses. With their high potential for genetic variation due to mutation and recombination, their efficient spread by vectors, and their wide host range as a group, including both wild and cultivated hosts, geminiviruses are attractive models for the study of the evolutionary and ecological factors driving virus emergence. Studies on the epidemiological features of geminivirus diseases have traditionally focused primarily on crop plants. Nevertheless, knowledge of geminivirus infection in wild plants, and especially at the interface between wild and cultivated plants, is necessary to provide a complete view of their ecology, evolution, and emergence. In this review, we address the most relevant aspects of geminivirus variability and evolution in wild and crop plants and geminiviruses' potential to emerge in crops.
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Affiliation(s)
- Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain;
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), and National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil;
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9
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Wainaina JM, Kubatko L, Harvey J, Ateka E, Makori T, Karanja D, Boykin LM, Kehoe MA. Evolutionary insights of Bean common mosaic necrosis virus and Cowpea aphid-borne mosaic virus. PeerJ 2019; 7:e6297. [PMID: 30783563 PMCID: PMC6377593 DOI: 10.7717/peerj.6297] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 12/18/2018] [Indexed: 11/20/2022] Open
Abstract
Plant viral diseases are one of the major limitations in legume production within sub-Saharan Africa (SSA), as they account for up to 100% in production losses within smallholder farms. In this study, field surveys were conducted in the western highlands of Kenya with viral symptomatic leaf samples collected. Subsequently, next-generation sequencing was carried out to gain insights into the molecular evolution and evolutionary relationships of Bean common mosaic necrosis virus (BCMNV) and Cowpea aphid-borne mosaic virus (CABMV) present within symptomatic common bean and cowpea. Eleven near-complete genomes of BCMNV and two for CABMV were obtained from western Kenya. Bayesian phylogenomic analysis and tests for differential selection pressure within sites and across tree branches of the viral genomes were carried out. Three well-supported clades in BCMNV and one supported clade for CABMNV were resolved and in agreement with individual gene trees. Selection pressure analysis within sites and across phylogenetic branches suggested both viruses were evolving independently, but under strong purifying selection, with a slow evolutionary rate. These findings provide valuable insights on the evolution of BCMNV and CABMV genomes and their relationship to other viral genomes globally. The results will contribute greatly to the knowledge gap involving the phylogenomic relationship of these viruses, particularly for CABMV, for which there are few genome sequences available, and inform the current breeding efforts towards resistance for BCMNV and CABMV.
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Affiliation(s)
- James M Wainaina
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, Australia
| | - Laura Kubatko
- Ohio State University, Columbus, OH, United States of America
| | - Jagger Harvey
- Feed the Future Innovation Lab for the Reduction of Post-Harvest Loss, Kansas State University, Manhattan, KS, United States of America
| | - Elijah Ateka
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Timothy Makori
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - David Karanja
- Kenya Agricultural and Livestock Research Organization (KARLO), Machakos, Kenya
| | - Laura M Boykin
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, Australia
| | - Monica A Kehoe
- Plant Pathology, Department of Primary Industries and Regional Development Diagnostic Laboratory Service, South Perth, Australia
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10
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From Spatial Metagenomics to Molecular Characterization of Plant Viruses: A Geminivirus Case Study. Adv Virus Res 2018; 101:55-83. [PMID: 29908594 DOI: 10.1016/bs.aivir.2018.02.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The number of plant viruses that are known likely remains only a vanishingly small fraction of all extant plant virus species. Consequently, the distribution and population dynamics of plant viruses within even the best-studied ecosystems have only ever been studied for small groups of virus species. Even for the best studied of these groups very little is known about virus diversity at spatial scales ranging from an individual host, through individual local host populations to global host populations. To date, metagenomics studies that have assessed the collective or metagenomes of viruses at the ecosystem scale have revealed many previously unrecognized viral species. More recently, novel georeferenced metagenomics approaches have been devised that can precisely link individual sequence reads to both the plant hosts from which they were obtained, and the spatial arrangements of these hosts. Besides illuminating the diversity and the distribution of plant viruses at the ecosystem scale, application of these "geometagenomics" approaches has enabled the direct testing of hypotheses relating to the impacts of host diversity, host spatial variations, and environmental conditions on plant virus diversity and prevalence. To exemplify how such top-down approaches can provide a far deeper understanding of host-virus associations, we provide a case-study focusing on geminiviruses within two complex ecosystems containing both cultivated and uncultivated areas. Geminiviruses are a highly relevant model for studying the evolutionary and ecological aspects of viral emergence because the family Geminiviridae includes many of the most important crop pathogens that have emerged over the past century. In addition to revealing unprecedented degrees of geminivirus diversity within the analyzed ecosystems, the geometagenomics-based approach enabled the focused in-depth analysis of the complex evolutionary dynamics of some of the highly divergent geminivirus species that were discovered.
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