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Guevara-Rivera EA, Rodríguez-Negrete EA, Lozano-Durán R, Bejarano ER, Torres-Calderón AM, Arce-Leal ÁP, Leyva-López NE, Méndez-Lozano J. From Metagenomics to Ecogenomics: NGS-Based Approaches for Discovery of New Circular DNA Single-Stranded Viral Species. Methods Mol Biol 2024; 2732:103-117. [PMID: 38060120 DOI: 10.1007/978-1-0716-3515-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Viruses comprise the most abundant genetic material in the biosphere; however, global viral genomic population (virome) has been largely underestimated. Recently, high-throughput sequencing (HTS) has provided a powerful tool for the detection of known viruses and the discovery of novel viral species from environmental and individual samples using metagenomics and ecogenomics approaches, respectively. Viruses with circular DNA single-stranded (ssDNA) genomes belonging to the begomovirus genera (family Geminiviridae) constitute the largest group of emerging plant viruses worldwide. The knowledge of begomoviruses viromes is mostly restricted to crop plant systems; nevertheless, it has been described that noncultivated plants specifically at the interface between wild and cultivated plants are important reservoirs leading to viral evolution and the emergence of new diseases. Here we present a protocol that allows the identification and isolation of known and novel begomoviruses species infecting cultivated and noncultivated plant species. The method consists of circular viral molecules enrichment by rolling circle amplification (RCA) from begomovirus-positive total plant DNA, followed by NGS-based metagenomic sequencing. Subsequently, metagenomic reads are processed for taxonomic classification using Viromescan software and a customized Geminiviridae family database, and begomovirus-related reads are used for contigs assembly and annotation using Spades software and Blastn algorithm, respectively. Then, the obtained begomovirus-related signatures are used as templates for specific primers design and implemented for PCR-based ecogenomic identification of individual samples harboring the corresponding viral species. Lastly, full-length begomovirus genomes are obtained by RCA-based amplification from total plant DNA of selected individual samples, cloning, and viral molecular identity corroborated by Sanger sequencing. Conclusively, the identification and isolation of a novel monopartite begomovirus species native to the New World (NW) named Gallium leaf deformation virus (GLDV) is shown.
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Affiliation(s)
- Enrique A Guevara-Rivera
- Departamento de Biotecnología Agrícola, Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, Guasave, Sinaloa, Mexico
| | - Edgar A Rodríguez-Negrete
- Departamento de Biotecnología Agrícola, Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, Guasave, Sinaloa, Mexico
| | - Rosa Lozano-Durán
- Department of Plant Biochemistry, Center for Plant Molecular Biology (ZMBP), Eberhard Karls University, Tübingen, Germany
| | - Eduardo R Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
| | | | - Ángela P Arce-Leal
- Departamento de Biotecnología Agrícola, Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, Guasave, Sinaloa, Mexico
| | - Norma E Leyva-López
- Departamento de Biotecnología Agrícola, Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, Guasave, Sinaloa, Mexico
| | - Jesús Méndez-Lozano
- Departamento de Biotecnología Agrícola, Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, Guasave, Sinaloa, Mexico.
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Diaz-Lara A, Stevens K, Aguilar-Molina VH, Fernández-Cortés JM, Chabacano León VM, De Donato M, Sharma A, Erickson TM, Al Rwahnih M. High-Throughput Sequencing of Grapevine in Mexico Reveals a High Incidence of Viruses including a New Member of the Genus Enamovirus. Viruses 2023; 15:1561. [PMID: 37515247 PMCID: PMC10386000 DOI: 10.3390/v15071561] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/08/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
This is the first viral metagenomic analysis of grapevine conducted in Mexico. During the summer of 2021, 48 plants displaying virus-like symptoms were sampled in Queretaro, an important grapevine-producing area of Mexico, and analyzed for the presence of viruses via high-throughput sequencing (HTS). The results of HTS were verified by real-time RT-PCR following a standardized testing scheme (Protocol 2010). Fourteen different viruses were identified, including grapevine asteroid mosaic-associated virus (GAMaV), grapevine Cabernet Sauvignon reovirus (GCSV), grapevine fanleaf virus (GFLV), grapevine fleck virus (GFkV), grapevine Pinot gris virus (GPGV), grapevine red globe virus (GRGV), grapevine rupestris stem pitting-associated virus (GRSPaV), grapevine rupestris vein feathering virus (GRVFV), grapevine Syrah virus 1 (GSyV-1), grapevine virus B (GVB), and grapevine leafroll-associated viruses 1, 2, 3, 4 (GLRaV1, 2, 3, 4). Additionally, divergent variants of GLRaV4 and GFkV, and a novel Enamovirus-like virus were discovered. This is the first report of GAMaV, GCSV, GLRaV4, GPGV, GRGV, GRVFV, and GSyV-1 infecting grapevines in Mexico; the impact of these pathogens on production is unknown.
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Affiliation(s)
- Alfredo Diaz-Lara
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico
| | - Kristian Stevens
- Departments of Computer Science and Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA
| | | | | | | | - Marcos De Donato
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico
| | - Ashutosh Sharma
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico
| | - Teresa M Erickson
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA
| | - Maher Al Rwahnih
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA
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Fiallo-Olivé E, Navas-Castillo J. Begomoviruses: what is the secret(s) of their success? TRENDS IN PLANT SCIENCE 2023; 28:715-727. [PMID: 36805143 DOI: 10.1016/j.tplants.2023.01.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/16/2023] [Accepted: 01/26/2023] [Indexed: 05/13/2023]
Abstract
Begomoviruses constitute an extremely successful group of emerging plant viruses transmitted by whiteflies of the Bemisia tabaci complex. Hosts include important vegetable, root, and fiber crops grown in the tropics and subtropics. Factors contributing to the ever-increasing diversity and success of begomoviruses include their predisposition to recombine their genomes, interaction with DNA satellites recruited throughout their evolution, presence of wild plants as a virus reservoir and a source of speciation, and extreme polyphagia and continuous movement of the insect vectors to temperate regions. These features as well as some controversial issues (replication in the insect vector, putative seed transmission, transmission by insects other than B. tabaci, and expansion of the host range to monocotyledonous plants) will be analyzed in this review.
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Affiliation(s)
- Elvira Fiallo-Olivé
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora' (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, 29750 Algarrobo-Costa, Málaga, Spain.
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora' (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, 29750 Algarrobo-Costa, Málaga, Spain
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Quadros AFF, Ferro CG, de Rezende RR, Godinho MT, Xavier CAD, Nogueira AM, Alfenas-Zerbini P, Zerbini FM. Begomovirus populations in single plants are complex and may include both well-adapted and poorly-adapted viruses. Virus Res 2023; 323:198969. [PMID: 36257487 PMCID: PMC10194161 DOI: 10.1016/j.virusres.2022.198969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/10/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022]
Abstract
Begomoviruses (single-stranded DNA plant viruses transmitted by whiteflies) are economically important pathogens causing epidemics worldwide. Tomato-infecting begomoviruses emerged in Brazil in the 1990's following the introduction of Bemisia tabaci Middle East-Asia Minor 1. It is believed that these viruses evolved from indigenous viruses infecting non-cultivated hosts. However, tomato-infecting viruses are rarely found in non-cultivated hosts, and vice-versa. It is possible that viral populations in a given host are composed primarily of viruses which are well adapted to this host, but also include a small proportion of poorly adapted viruses. Following transfer to a new host, the composition of the viral population would shift rapidly, with the viruses which are better adapted to the new host becoming predominant. To test this hypothesis, we collected tomato and Sida plants growing next to each other at two locations in 2014 and 2018. Total DNA was extracted from tomato and Sida samples from each location and year and used as a template for high-throughput sequencing. Reads were mapped following a highly stringent set of criteria. For the 2014 samples, >98% of the Sida reads mapped to Sida micrantha mosaic virus (SiMMV), but 0.1% of the reads mapped to tomato severe rugose virus (ToSRV). Conversely, >99% of the tomato reads mapped to ToSRV, with 0.18% mapping to SiMMV. For the 2018 samples, 41% of the Sida reads mapped to three Sida-adapted viruses and 0.1% of the reads mapped to ToSRV, while 99.9% of the tomato reads mapped to ToSRV. These results are consistent with the hypothesis that viral populations in a single plant are composed primarily of the virus that is better adapted to the host but also include a small proportion of viruses that are poorly adapted.
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Affiliation(s)
- Ayane F F Quadros
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Camila G Ferro
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Rafael R de Rezende
- Dep. de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Márcio T Godinho
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - César A D Xavier
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Angélica M Nogueira
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - P Alfenas-Zerbini
- Dep. de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - F Murilo Zerbini
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
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García-Rodríguez DA, Partida-Palacios BL, Regla-Márquez CF, Centeno-Leija S, Serrano-Posada H, Bañuelos-Hernández B, Cárdenas-Conejo Y. Sida chlorotic leaf virus: a new recombinant begomovirus found in non-cultivated plants and Cucumis sativus L. PeerJ 2023; 11:e15047. [PMID: 36974135 PMCID: PMC10039651 DOI: 10.7717/peerj.15047] [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: 09/21/2022] [Accepted: 02/21/2023] [Indexed: 03/29/2023] Open
Abstract
Background Begomoviruses are circular single-stranded DNA plant viruses that cause economic losses worldwide. Weeds have been pointed out as reservoirs for many begomoviruses species, especially from members of the Sida and Malvastrum genera. These weeds have the ability to host multiple begomoviruses species simultaneously, which can lead to the emergence of new viral species that can spread to commercial crops. Additionally, begomoviruses have a natural tendency to recombine, resulting in the emergence of new variants and species. Methods To explore the begomoviruses biodiversity in weeds from genera Sida and Malvastrum in Colima, México, we collected symptomatic plants from these genera throughout the state. To identify BGVs infecting weeds, we performed circular DNA genomics (circomics) using the Illumina platform. Contig annotation was conducted with the BLASTn tool using the GenBank nucleotide "nr" database. We corroborated by PCR the presence of begomoviruses in weeds samples and isolated and sequenced the complete genome of a probable new species of begomovirus using the Sanger method. The demarcation process for new species determination followed the International Committee on Taxonomy of Viruses criteria. Phylogenetic and recombination analyses were implemented to infer the evolutionary relationship of the new virus. Results We identified a new begomovirus species from sida and malvastrum plants that has the ability to infect Cucumis sativus L. According to our findings, the novel species Sida chlorotic leaf virus is the result of a recombination event between one member of the group known as the Squash leaf curl virus (SLCV) clade and another from the Abutilon mosaic virus (AbMV) clade. Additionally, we isolated three previously identified begomoviruses species, two of which infected commercial crops: okra (Okra yellow mosaic Mexico virus) and cucumber (Cucumber chlorotic leaf virus). Conclusion These findings support the idea that weeds act as begomovirus reservoirs and play essential roles in begomovirus biodiversity. Therefore, controlling their populations near commercial crops must be considered in order to avoid the harmful effects of these phytopathogens and thus increase agricultural efficiency, ensuring food and nutritional security.
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Affiliation(s)
| | | | | | - Sara Centeno-Leija
- Universidad de Colima, Consejo Nacional de Ciencia y Tecnología-Laboratorio de Biología Sintética, Estructural y Molecular, Colima, México
| | - Hugo Serrano-Posada
- Universidad de Colima, Consejo Nacional de Ciencia y Tecnología-Laboratorio de Biología Sintética, Estructural y Molecular, Colima, México
| | | | - Yair Cárdenas-Conejo
- Universidad de Colima, Consejo Nacional de Ciencia y Tecnología-Laboratorio de Biología Sintética, Estructural y Molecular, Colima, México
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Muhammad K, Herath V, Ahmed K, Tahir M, Verchot J. Genetic diversity and molecular evolution of sugarcane mosaic virus, comparing whole genome and coat protein sequence phylogenies. Arch Virol 2022; 167:2239-2247. [PMID: 35999328 PMCID: PMC9556425 DOI: 10.1007/s00705-022-05572-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/13/2022] [Indexed: 11/29/2022]
Abstract
Sugarcane mosaic virus (SCMV) is a widely distributed potyvirus that causes mosaic disease in sugarcane, maize, sorghum, canna, and other monocot species worldwide. This study used 139 SCMV full-length genome sequences to analyze the phylogenetic relatedness of geographically distinct isolates. The phylogenetic analysis revealed four major groups of SCMV isolates that relate to their primary host. The geographic locations for some isolates appear to be mismatched within the tree, suggesting either that convergent molecular evolution has occurred or that the tree reconstruction produces statistically significant incongruences that create uncertainty in the true evolutionary relationships of these virus isolates. Recombination analysis showed hot spots across most of the genome except in the coat protein (CP) coding region. We examined 161 SCMV CP sequences from the GenBank database, including sequences from samples collected in Pakistan, a region that has not been included in prior phylogenetic studies. These data suggest that the SCMV isolates from sugarcane (Saccharum officinarum) predate isolates from all other hosts, regardless of their geographic origins.
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Affiliation(s)
- Khalid Muhammad
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Venura Herath
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA.,Department of Agriculture Biology, Faculty of Agriculture, University of Peradeniya, 20400, Peradeniya, Sri Lanka
| | - Khadija Ahmed
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Muhammad Tahir
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Jeanmarie Verchot
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA.
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Guevara-Rivera EA, Rodríguez-Negrete EA, Aréchiga-Carvajal ET, Leyva-López NE, Méndez-Lozano J. From Metagenomics to Discovery of New Viral Species: Galium Leaf Distortion Virus, a Monopartite Begomovirus Endemic in Mexico. Front Microbiol 2022; 13:843035. [PMID: 35547137 PMCID: PMC9083202 DOI: 10.3389/fmicb.2022.843035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/28/2022] [Indexed: 12/02/2022] Open
Abstract
Begomoviruses (Family Geminiviridae) are a major group of emerging plant viruses worldwide. The knowledge of begomoviruses is mostly restricted to crop plant systems. Nevertheless, it has been described that non-cultivated plants are important reservoirs and vessels of viral evolution that leads to the emergence of new diseases. High-throughput sequencing (HTS) has provided a powerful tool for speeding up the understanding of molecular ecology and epidemiology of plant virome and for discovery of new viral species. In this study, by performing earlier metagenomics library data mining, followed by geminivirus-related signature single plant searching and RCA-based full-length viral genome cloning, and based on phylogenetic analysis, genomes of two isolates of a novel monopartite begomovirus species tentatively named Galium leaf distortion virus (GLDV), which infects non-cultivated endemic plant Galium mexicanum, were identified in Colima, Mexico. Analysis of the genetic structure of both isolates (GLDV-1 and GLDV-2) revealed that the GLDV genome displays a DNA-A-like structure shared with the new world (NW) bipartite begomoviruses. Nonetheless, phylogenetic analysis using representative members of the main begomovirus American clades for tree construction grouped both GLDV isolates in a clade of the monopartite NW begomovirus, Tomato leaf deformation virus (ToLDeV). A comparative analysis of viral replication regulatory elements showed that the GLDV-1 isolate possesses an array and sequence conservation of iterons typical of NW begomovirus infecting the Solanaceae and Fabaceae families. Interestingly, GLDV-2 showed iteron sequences described only in monopartite begomovirus from OW belonging to a sweepovirus clade that infects plants of the Convolvulaceae family. In addition, the rep iteron related-domain (IRD) of both isolates display FRVQ or FRIS amino acid sequences corresponding to NW and sweepobegomovirus clades for GMV-1 and GMV-2, respectively. Finally, the lack of the GLDV DNA-B segment (tested by molecular detection and biological assays using GLDV-1/2 infectious clones) confirmed the monopartite nature of GLDV. This is the first time that a monopartite begomovirus is described in Mexican ecosystems, and “in silico” geometagenomics analysis indicates that it is restricted to a specific region. These data revealed additional complexity in monopartite begomovirus genetics and geographic distribution and highlighted the importance of metagenomic approaches in understanding global virome ecology and evolution.
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Affiliation(s)
- Enrique A Guevara-Rivera
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Mexico
| | - Edgar A Rodríguez-Negrete
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Mexico
| | - Elva T Aréchiga-Carvajal
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Departamento de Microbiología e Inmunología-Unidad de Manipulación Genética, San Nicolás de los Garza, Mexico
| | - Norma E Leyva-López
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Mexico
| | - Jesús Méndez-Lozano
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Mexico
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Lopez-Lopez K, Corredor-Rodríguez A, Correa-Forero AM, Álvarez-Rubiano LP, Suarez- Rodríguez A, Vaca-Vaca JC. DETECCIÓN MOLECULAR DE BEGOMOVIRUS AISLADOS DE ARVENSES ASOCIADAS AL CULTIVO DE AJÍ (Capsicum spp.) EN EL VALLE DEL CAUCA, COLOMBIA. ACTA BIOLÓGICA COLOMBIANA 2022. [DOI: 10.15446/abc.v27n3.89802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Los virus Potato yellow mosaic virus (PYMV/Co), Passionfruit leaf distortion virus (PLDV), Pepper rugose mosaic virus (PRMV) y Rhynchosia golden mosaic Colombia virus (RhGMCV) son begomovirus de interés agrícola, aislados y caracterizados molecularmente en el Valle del Cauca. Sin embargo, en la actualidad no hay suficiente información sobre sus hospederos alternos. Dado que las arvenses cumplen un papel importante en la ecología y epidemiología viral, este estudio tuvo como objetivo detectar la presencia de estos begomovirus en arvenses asociadas al cultivo de ají en el Valle del Cauca, Colombia. Se recolectaron 121 plantas arvenses en zonas productoras de ají, localizadas en 7 municipios del Valle del Cauca, las cuales fueron identificadas a nivel taxonómico. A partir del ADN genómico purificado de estas plantas se evaluó la presencia de virus por PCR, usando cebadores universales para el género Begomovirus y específicos para PYMV/Co, PLDV, PRMV y RhGMCV. Se detectaron begomovirus en 15 de las especies de arvenses evaluadas. Esta es la primera vez que las especies Ipomoea tiliacea, Melothria pendula, Caperonia palustris, Desmodium tortuosum, Desmodium intortum, Ammannia coccinea, Panicum polygonatum, Capsicum rhomboideum, Eclipta prostrata y Synedrella nodiflora se reportan como hospederas de begomovirus en Colombia. Se detectaron los begomovirus RhGMCV, PYMV/Co, PRMV y PLDV en infecciones simples y mixtas. Estos resultados aportan nuevos datos sobre los hospederos alternos de begomovirus. Esta información servirá para implementar un plan de manejo integrado de enfermedades virales con el potencial para afectar negativamente el rendimiento del cultivo de ají, y otros cultivos en Colombia.
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Lal A, Kim YH, Vo TTB, Wira Sanjaya IGNP, Ho PT, Byun HS, Choi HS, Kil EJ, Lee S. Identification of a Novel Geminivirus in Fraxinus rhynchophylla in Korea. Viruses 2021; 13:2385. [PMID: 34960653 PMCID: PMC8705360 DOI: 10.3390/v13122385] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/20/2021] [Accepted: 11/22/2021] [Indexed: 02/07/2023] Open
Abstract
Fraxinus rhynchophylla, common name ash, belongs to the family Oleaceae and is found in China, Korea, North America, the Indian subcontinent, and eastern Russia. It has been used as a traditional herbal medicine in Korea and various parts of the world due to its chemical constituents. During a field survey in March 2019, mild vein thickening (almost negligible) was observed in a few ash trees. High-throughput sequencing of libraries of total DNA from ash trees, rolling-circle amplification (RCA), and polymerase chain reaction (PCR) allowed the identification of a Fraxinus symptomless virus. This virus has five confirmed open reading frames along with a possible sixth open reading frame that encodes the movement protein and is almost 2.7 kb in size, with a nonanucleotide and stem loop structure identical to begomoviruses. In terms of its size and structure, this virus strongly resembles begomoviruses, but does not show any significant sequence identity with them. To confirm movement of the virus within the trees, different parts of infected trees were examined, and viral movement was successfully observed. No satellite molecules or DNA B were identified. Two-step PCR confirmed the virion and complementary strands during replication in both freshly collected infected samples of ash tree and Nicotiana benthamiana samples agro-inoculated with infectious clones. This taxon is so distantly grouped from other known geminiviruses that it likely represents a new geminivirus genus.
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Affiliation(s)
- Aamir Lal
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea; (A.L.); (T.T.B.V.); (I.G.N.P.W.S.); (P.T.H.)
| | - Yong-Ho Kim
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 55365, Korea; (Y.-H.K.); (H.-S.B.)
| | - Thuy Thi Bich Vo
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea; (A.L.); (T.T.B.V.); (I.G.N.P.W.S.); (P.T.H.)
| | | | - Phuong Thi Ho
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea; (A.L.); (T.T.B.V.); (I.G.N.P.W.S.); (P.T.H.)
| | - Hee-Seong Byun
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 55365, Korea; (Y.-H.K.); (H.-S.B.)
| | - Hong-Soo Choi
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 55365, Korea; (Y.-H.K.); (H.-S.B.)
| | - Eui-Joon Kil
- Department of Plant Medicals, Andong National University, Andong 36729, Korea
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea; (A.L.); (T.T.B.V.); (I.G.N.P.W.S.); (P.T.H.)
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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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11
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Xavier CAD, Nogueira AM, Bello VH, Watanabe LFM, Barbosa TMC, Alves Júnior M, Barbosa L, Beserra-Júnior JEA, Boari A, Calegario R, Gorayeb ES, Honorato Júnior J, Koch G, Lima GSDA, Lopes C, de Mello RN, Pantoja K, Silva FN, Ramos Sobrinho R, Santana EN, da Silva JWP, Krause-Sakate R, Zerbini FM. Assessing the diversity of whiteflies infesting cassava in Brazil. PeerJ 2021; 9:e11741. [PMID: 34316398 PMCID: PMC8286705 DOI: 10.7717/peerj.11741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/17/2021] [Indexed: 11/20/2022] Open
Abstract
Background The necessity of a competent vector for transmission is a primary ecological factor driving the host range expansion of plant arthropod-borne viruses, with vectors playing an essential role in disease emergence. Cassava begomoviruses severely constrain cassava production in Africa. Curiously, begomoviruses have never been reported in cassava in South America, the center of origin for this crop. It has been hypothesized that the absence of a competent vector in cassava is the reason why begomoviruses have not emerged in South America. Methods We performed a country-wide whitefly diversity study in cassava in Brazil. Adults and/or nymphs of whiteflies were collected from sixty-six cassava fields in the main agroecological zones of the country. A total of 1,385 individuals were genotyped based on mitochondrial cytochrome oxidase I sequences. Results A high species richness was observed, with five previously described species and two putative new ones. The prevalent species were Tetraleurodes acaciae and Bemisia tuberculata, representing over 75% of the analyzed individuals. Although we detected, for the first time, the presence of Bemisia tabaci Middle East-Asia Minor 1 (BtMEAM1) colonizing cassava in Brazil, it was not prevalent. The species composition varied across regions, with fields in the Northeast region showing a higher diversity. These results expand our knowledge of whitefly diversity in cassava and support the hypothesis that begomovirus epidemics have not occurred in cassava in Brazil due to the absence of competent vector populations. However, they indicate an ongoing adaptation process of BtMEAM1 to cassava, increasing the likelihood of begomovirus emergence in this crop.
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Affiliation(s)
- Cesar A D Xavier
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | | | | | | | | | - Miguel Alves Júnior
- Faculdade de Engenharia Agronômica, Universidade Federal do Pará, Altamira, PA, Brazil
| | - Leonardo Barbosa
- Instituto Federal do Sudeste de Minas Gerais, Rio Pomba, MG, Brazil
| | | | | | - Renata Calegario
- Dep. de Fitotecnia e Fitossanidade, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Eduardo Silva Gorayeb
- Centro de Ciências Agroveterinárias, Universidade do Estado de Santa Catarina, Lages, SC, Brazil
| | - Jaime Honorato Júnior
- Centro Multidisciplinar do Campus de Barra, Universidade Federal do Oeste da Bahia, Barra, BA, Brazil
| | - Gabriel Koch
- Dep. de Fitotecnia e Fitossanidade, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | | | - Cristian Lopes
- Instituto Federal do Sudeste de Minas Gerais, Rio Pomba, MG, Brazil
| | | | | | - Fábio Nascimento Silva
- Centro de Ciências Agroveterinárias, Universidade do Estado de Santa Catarina, Lages, SC, Brazil
| | - Roberto Ramos Sobrinho
- Centro de Ciências Agrárias/Fitossanidade, Universidade Federal de Alagoas, Rio Largo, AL, Brazil
| | | | | | | | - Francisco M Zerbini
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
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12
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Avalos-Calleros JA, Pastor-Palacios G, Bolaños-Martínez OC, Mauricio-Castillo A, Gregorio-Jorge J, Martínez-Marrero N, Bañuelos-Hernández B, Méndez-Lozano J, Arguello-Astorga GR. Two strains of a novel begomovirus encoding Rep proteins with identical β1 strands but different β5 strands are not compatible in replication. Arch Virol 2021; 166:1691-1709. [PMID: 33852083 DOI: 10.1007/s00705-021-05066-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 02/20/2021] [Indexed: 10/21/2022]
Abstract
Geminiviruses have genomes composed of single-stranded DNA molecules and encode a rolling-circle replication (RCR) initiation protein ("Rep"), which has multiple functions. Rep binds to specific repeated DNA motifs ("iterons"), which are major determinants of virus-specific replication. The particular amino acid (aa) residues that determine the preference of a geminivirus Rep for specific iterons (i.e., the trans-acting replication "specificity determinants", or SPDs) are largely unknown, but diverse lines of evidence indicate that most of them are closely associated with the so-called RCR motif I (FLTYP), located in the first 12-19 aa residues of the protein. In this work, we characterized two strains of a novel begomovirus, rhynchosia golden mosaic Sinaloa virus (RhGMSV), that were incompatible in replication in pseudorecombination experiments. Systematic comparisons of the Rep proteins of both RhGMSV strains in the DNA-binding domain allowed the aa residues at positions 71 and 74 to be identified as the residues most likely to be responsible for differences in replication specificity. Residue 71 is part of the β-5 strand structural element, which was predicted in previous studies to contain Rep SPDs. Since the Rep proteins encoded by both RhGMSV strains are identical in their first 24 aa residues, where other studies have mapped potential SPDs, this is the first study lending direct support to the notion that geminivirus Rep proteins contain separate SPDs in their N-terminal domain.
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Affiliation(s)
- Jesús Aarón Avalos-Calleros
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C. Camino a la Presa de San José 2055, Lomas 4a Sección, C.P. 78216, San Luis Potosí, S.L.P., Mexico
| | - Guillermo Pastor-Palacios
- CONACYT-Consorcio de Investigación Innovación y Desarrollo para las Zonas Áridas, Instituto Potosino de Investigación Científica y Tecnológica, A.C. Camino a La Presa de San José 2055, Lomas 4a Sección, C.P. 78216, San Luis Potosí, S.L.P., Mexico
| | - Omayra C Bolaños-Martínez
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C. Camino a la Presa de San José 2055, Lomas 4a Sección, C.P. 78216, San Luis Potosí, S.L.P., Mexico
| | | | - Josefat Gregorio-Jorge
- Consejo Nacional de Ciencia y Tecnología, Universidad Politécnica de Tlaxcala (UPTx)., Av. Insurgentes Sur 1582, Col. Crédito Constructor, Del. Benito Juárez, 03940, Mexico City, Mexico
| | - Nadia Martínez-Marrero
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C. Camino a la Presa de San José 2055, Lomas 4a Sección, C.P. 78216, San Luis Potosí, S.L.P., Mexico
| | - Bernardo Bañuelos-Hernández
- Facultad de Agronomia y Veterinaria, Universidad De La Salle Bajio, Avenida Universidad 602, Lomas del Campestre, 37150, León Guanajuato, Mexico
| | - Jesús Méndez-Lozano
- Departamento de Biotecnología Agrícola, Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, 81101, Guasave, Sinaloa, Mexico
| | - Gerardo Rafael Arguello-Astorga
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C. Camino a la Presa de San José 2055, Lomas 4a Sección, C.P. 78216, San Luis Potosí, S.L.P., Mexico.
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13
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New World Cactaceae Plants Harbor Diverse Geminiviruses. Viruses 2021; 13:v13040694. [PMID: 33923787 PMCID: PMC8073023 DOI: 10.3390/v13040694] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/11/2021] [Accepted: 04/13/2021] [Indexed: 12/15/2022] Open
Abstract
The family Cactaceae comprises a diverse group of typically succulent plants that are native to the American continent but have been introduced to nearly all other continents, predominantly for ornamental purposes. Despite their economic, cultural, and ecological importance, very little research has been conducted on the viral community that infects them. We previously identified a highly divergent geminivirus that is the first known to infect cacti. Recent research efforts in non-cultivated and asymptomatic plants have shown that the diversity of this viral family has been under-sampled. As a consequence, little is known about the effects and interactions of geminiviruses in many plants, such as cacti. With the objective to expand knowledge on the diversity of geminiviruses infecting cacti, we used previously acquired high-throughput sequencing results to search for viral sequences using BLASTx against a viral RefSeq protein database. We identified two additional sequences with similarity to geminiviruses, for which we designed abutting primers and recovered full-length genomes. From 42 cacti and five scale insects, we derived 42 complete genome sequences of a novel geminivirus species that we have tentatively named Opuntia virus 2 (OpV2) and 32 genomes of an Opuntia-infecting becurtovirus (which is a new strain of the spinach curly top Arizona virus species). Interspecies recombination analysis of the OpV2 group revealed several recombinant regions, in some cases spanning half of the genome. Phylogenetic analysis demonstrated that OpV2 is a novel geminivirus more closely related to viruses of the genus Curtovirus, which was further supported by the detection of three recombination events between curtoviruses and OpV2. Both OpV2 and Opuntia becurtoviruses were identified in mixed infections, which also included the previously characterized Opuntia virus 1. Viral quantification of the co-infected cactus plants compared with single infections did not show any clear trend in viral dynamics that might be associated with the mixed infections. Using experimental Rhizobium-mediated inoculations, we found that the initial accumulation of OpV2 is facilitated by co-infection with OpV1. This study shows that the diversity of geminiviruses that infect cacti is under-sampled and that cacti harbor diverse geminiviruses. The detection of the Opuntia becurtoviruses suggests spill-over events between viruses of cultivated species and native vegetation. The threat this poses to cacti needs to be further investigated.
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14
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Mishra M, Verma RK, Marwal A, Sharma P, Gaur RK. Biology and Interaction of the Natural Occurrence of Distinct Monopartite Begomoviruses Associated With Satellites in Capsicum annum From India. Front Microbiol 2020; 11:512957. [PMID: 33117300 PMCID: PMC7575687 DOI: 10.3389/fmicb.2020.512957] [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: 11/18/2019] [Accepted: 09/03/2020] [Indexed: 01/29/2023] Open
Abstract
Chili (Capsicum annuum L.) is an important vegetable and spice crop of tropical and sub-tropical regions. Chili plants showing upward leaf curling, leaf crinkling, and leaf yellowing symptoms, collected from Sikar district of Rajasthan, India, were found to be associated with begomovirus and satellite molecules. The presence of virus was confirmed by PCR using virus-specific primer. The full-length genomic DNA-A of three begomovirus (MM-1, CS-1 and RV-1) and two satellites (MM-2 and MM-3) were cloned which was identified from single symptomatic chili plant. The genome organization of isolated three viruses is similar to those of other Old World monopartite begomoviruses. The comparison of the sequences and closest phylogenetic relationships for the begomoviruses, betasatellite and alphasatellite DNAs revealed that MM-1 was designated as DNA-A of Chili leaf curl virus (ChiLCV), CS-1 is considered to be a new distinct species of Tomato leaf curl Gujrat virus (ToLCGV) whereas RV-1 as a new strain of Cotton leaf curl Multan virus (CLCuMuV). The DNA-A component of ChiLCV showed 8.6%, ToLCGV of 16.6% and CLCuMuV of 7.7% average evolutionary divergence, concomitantly, the betasatellite and alphasatellite molecule had 9.9% and 5.9% overall sequence divergence, respectively. Interestingly, most of the begomoviruses were found to be intra-species recombinants. The dN/dS ratio and Tajima D value of all viral DNA-A component and their associated betasatellite showed their selective control on evolutionary relationships. The nucleotide substitution rates were determined for the DNA-A genomes of ChiLCV (7.22 × 10–4 substitutions site–1 year–1), CLCuMuV (1.49 × 10–4 substitutions site–1 year–1), ToLCGV (7.47 × 10–4 substitutions site–1 year–1), the genome of associated ChiLCB (4.20 × 10–4 substitutions site–1 year–1) and CLCuMuA (1.49 × 10–4 substitutions site–1 year–1). Agro-inoculation studies indicate that the presence of DNA betasatellite induce severe symptoms in N. benthamiana and chili, suggesting prerequisite association for typical disease development.
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Affiliation(s)
- Megha Mishra
- Department of Biosciences, School of Liberal Arts and Sciences, Mody University of Science and Technology, Sikar, India
| | - Rakesh Kumar Verma
- Department of Biosciences, School of Liberal Arts and Sciences, Mody University of Science and Technology, Sikar, India
| | - Avinash Marwal
- Department of Biotechnology, Mohanlal Sukhadia University, Udaipur, India
| | - Pradeep Sharma
- Biotechnology Unit, ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - R K Gaur
- Department of Biotechnology, D.D.U Gorakhpur University, Gorakhpur, India
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15
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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. FRONTIERS IN PLANT SCIENCE 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] [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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16
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Sanchez-Chavez S, Regla-Marquez CF, Cardenas-Conejo ZE, Garcia-Rodriguez DA, Centeno-Leija S, Serrano-Posada H, Liñan-Rico A, Partida-Palacios BL, Cardenas-Conejo Y. First report of begomoviruses infecting Cucumis sativus L. in North America and identification of a proposed new begomovirus species. PeerJ 2020; 8:e9245. [PMID: 32728488 PMCID: PMC7357562 DOI: 10.7717/peerj.9245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/06/2020] [Indexed: 12/02/2022] Open
Abstract
Background Members of the Begomovirus genus are phytopathogens that infect dicotyledonous plants, producing economic losses in tropical and subtropical regions. To date, only seven species of begomoviruses (BGVs) infecting cucumber have been described. Most cucumber infections were reported in South Asia. In the Americas, begomoviral infections affecting cucumber are scarce; just one report of begomovirus has been described in South America. The presence of whitefly and typical symptoms of viral infections observed in a cucumber field in Colima, Mexico, suggested that plants in this field were affected by BGVs. Methods To identify the BGVs infecting cucumber, we performed a high-throughput sequencing and compared the assembled contigs against the GenBank nucleic acid sequence database. To confirm the presence of viruses in cucumber samples, we performed a PCR detection using specific oligonucleotides. We cloned and sequenced by Sanger method the complete genome of a potential new begomovirus. Begomovirus species demarcation was performed according to the International Committee on Taxonomy of Viruses. The evolutionary relationship of the new virus was inferred using phylogenetic and recombination analyses. Results We identified five species of begomovirus infecting plants in a field. None of these have been previously reported infecting cucumber. One of the five species of viruses here reported is a new begomovirus species. Cucumber chlorotic leaf virus, the new species, is a bipartite begomovirus that has distinctive features of viruses belonging to the squash leaf curl virus clade. Conclusions The findings here described represent the first report of begomoviral infection affecting cucumber plants in North America. Previous to this report, only seven begomovirus species have been reported in the world, here we found five species infecting cucumber plants in a small sample suggesting that cucumber is vulnerable to BGVs. One of these viruses is a new species of begomovirus which is the first begomovirus originally isolated from the cucumber. The findings of this report could help to develop strategies to fight the begomoviral infections that affect cucumber crops.
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Affiliation(s)
| | | | | | | | - Sara Centeno-Leija
- Laboratorio de Agrobiotecnologia, Consejo Nacional de Ciencia y Tecnologia-Universidad de Colima, Colima, Mexico
| | - Hugo Serrano-Posada
- Laboratorio de Agrobiotecnologia, Consejo Nacional de Ciencia y Tecnologia-Universidad de Colima, Colima, Mexico
| | - Andromeda Liñan-Rico
- Centro Universitario de Investigaciones Biomedicas, Consejo Nacional de Ciencia y Tecnologia-Universidad de Colima, Colima, Mexico
| | | | - Yair Cardenas-Conejo
- Laboratorio de Agrobiotecnologia, Consejo Nacional de Ciencia y Tecnologia-Universidad de Colima, Colima, Mexico
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17
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Metagenomics of Neotropical Single-Stranded DNA Viruses in Tomato Cultivars with and without the Ty-1 Gene. Viruses 2020; 12:v12080819. [PMID: 32731641 PMCID: PMC7472167 DOI: 10.3390/v12080819] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 12/17/2022] Open
Abstract
A complex of begomoviruses (Geminiviridae) can cause severe tomato yield losses in the neotropics. Here, next-generation sequencing was employed for large-scale assessment of single-stranded (ss)DNA virus diversity in tomatoes either harboring or lacking the large-spectrum begomovirus tolerance Ty-1 gene. Individual leaf samples exhibiting begomovirus-like symptoms (n = 107) were field-collected, circular DNA-enriched, subdivided into pools (with and without Ty-1), and Illumina-sequenced. Virus-specific PCR and Sanger dideoxy sequencing validations confirmed 15 distinct ssDNA virus/subviral agents (occurring mainly in mixed infections), which highlight the potential drawbacks of employing virus-specific resistance in tomato breeding. More viruses (14 versus 6 species) were observed in tomatoes without the Ty-1 gene. A gemycircularvirus (Genomoviridae), a new alpha-satellite, and two novel Begomovirus species were identified exclusively in samples without the Ty-1 gene. A novel begomovirus was found only in the Ty-1 pool, being the only species associated with severe symptoms in Ty-1 plants in our survey. Our work is the first step towards the elucidation of the potential begomovirus adaptation to Ty-1 and its specific filtering effects on a subset of ssDNA viral/subviral agents.
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18
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Martínez-Marrero N, Avalos-Calleros JA, Chiquito-Almanza E, Acosta-Gallegos JA, Ambriz-Granados S, Anaya-López JL, Argüello-Astorga GR. A new begomovirus isolated from a potyvirus-infected bean plant causes asymptomatic infections in bean and N. benthamiana. Arch Virol 2020; 165:1659-1665. [PMID: 32405827 DOI: 10.1007/s00705-020-04646-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/08/2020] [Indexed: 10/25/2022]
Abstract
In this work, a begomovirus isolated from a bean plant coinfected with the potyviruses bean common mosaic virus and bean common mosaic necrosis virus was characterized. The three viruses were detected by high-throughput sequencing and assembly of total small RNAs, but the begomovirus-related contigs did not allow precise identification. Molecular analysis based on standard DNA amplification techniques revealed the presence of a single bipartite virus, which is a novel begomovirus according to the current taxonomic criteria. Infectious clones were generated and agroinoculated into Phaseolus vulgaris and Nicotiana benthamiana plants. In all cases, viral DNA-A and DNA-B were detected in new growths, but no symptoms were observed, thus indicating that this virus produces asymptomatic infections in both host species.
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Affiliation(s)
- Nadia Martínez-Marrero
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, C.P. 78216, San Luis Potosí, San Luis Potosí, México
| | - Jesús Aarón Avalos-Calleros
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, C.P. 78216, San Luis Potosí, San Luis Potosí, México
| | - Elizabeth Chiquito-Almanza
- Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Camino a la Presa San Jose 2055, C.P. 38110, San Luis Potosi, San Luis Potosi, México
| | - Jorge Alberto Acosta-Gallegos
- Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Camino a la Presa San Jose 2055, C.P. 38110, San Luis Potosi, San Luis Potosi, México
| | - Salvador Ambriz-Granados
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, C.P. 78216, San Luis Potosí, San Luis Potosí, México
| | - José Luis Anaya-López
- Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Camino a la Presa San Jose 2055, C.P. 38110, San Luis Potosi, San Luis Potosi, México
| | - Gerardo Rafael Argüello-Astorga
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, C.P. 78216, San Luis Potosí, San Luis Potosí, México.
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19
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Fontenele RS, Salywon AM, Majure LC, Cobb IN, Bhaskara A, Avalos-Calleros JA, Argüello-Astorga GR, Schmidlin K, Khalifeh A, Smith K, Schreck J, Lund MC, Köhler M, Wojciechowski MF, Hodgson WC, Puente-Martinez R, Van Doorslaer K, Kumari S, Vernière C, Filloux D, Roumagnac P, Lefeuvre P, Ribeiro SG, Kraberger S, Martin DP, Varsani A. A Novel Divergent Geminivirus Identified in Asymptomatic New World Cactaceae Plants. Viruses 2020; 12:E398. [PMID: 32260283 PMCID: PMC7232249 DOI: 10.3390/v12040398] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/29/2020] [Accepted: 03/31/2020] [Indexed: 12/17/2022] Open
Abstract
Cactaceae comprise a diverse and iconic group of flowering plants which are almost exclusively indigenous to the New World. The wide variety of growth forms found amongst the cacti have led to the trafficking of many species throughout the world as ornamentals. Despite the evolution and physiological properties of these plants having been extensively studied, little research has focused on cactus-associated viral communities. While only single-stranded RNA viruses had ever been reported in cacti, here we report the discovery of cactus-infecting single-stranded DNA viruses. These viruses all apparently belong to a single divergent species of the family Geminiviridae and have been tentatively named Opuntia virus 1 (OpV1). A total of 79 apparently complete OpV1 genomes were recovered from 31 different cactus plants (belonging to 20 different cactus species from both the Cactoideae and Opuntioideae clades) and from nine cactus-feeding cochineal insects (Dactylopius sp.) sampled in the USA and Mexico. These 79 OpV1 genomes all share > 78.4% nucleotide identity with one another and < 64.9% identity with previously characterized geminiviruses. Collectively, the OpV1 genomes display evidence of frequent recombination, with some genomes displaying up to five recombinant regions. In one case, recombinant regions span ~40% of the genome. We demonstrate that an infectious clone of an OpV1 genome can replicate in Nicotiana benthamiana and Opuntia microdasys. In addition to expanding the inventory of viruses that are known to infect cacti, the OpV1 group is so distantly related to other known geminiviruses that it likely represents a new geminivirus genus. It remains to be determined whether, like its cactus hosts, its geographical distribution spans the globe.
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Affiliation(s)
- Rafaela S. Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Andrew M. Salywon
- Desert Botanical Garden, Phoenix, AZ 85008, USA; (A.M.S.); (L.C.M.); (W.C.H.); (R.P.-M.)
| | - Lucas C. Majure
- Desert Botanical Garden, Phoenix, AZ 85008, USA; (A.M.S.); (L.C.M.); (W.C.H.); (R.P.-M.)
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Ilaria N. Cobb
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Amulya Bhaskara
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- Center for Research in Engineering, Science and Technology, Paradise Valley High School, 3950 E Bell Rd, Phoenix, AZ 85032, USA
| | - Jesús A. Avalos-Calleros
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., Camino a la Presa de San José 2055, Lomas 4ta Secc, San Luis Potosi 78216, S.L.P., Mexico; (J.A.A.-C.); (G.R.A.-A.)
| | - Gerardo R. Argüello-Astorga
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., Camino a la Presa de San José 2055, Lomas 4ta Secc, San Luis Potosi 78216, S.L.P., Mexico; (J.A.A.-C.); (G.R.A.-A.)
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Anthony Khalifeh
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Kendal Smith
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Joshua Schreck
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Michael C. Lund
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Matias Köhler
- Departamento de BotânicaPrograma de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501970, Brazil;
| | | | - Wendy C. Hodgson
- Desert Botanical Garden, Phoenix, AZ 85008, USA; (A.M.S.); (L.C.M.); (W.C.H.); (R.P.-M.)
| | - Raul Puente-Martinez
- Desert Botanical Garden, Phoenix, AZ 85008, USA; (A.M.S.); (L.C.M.); (W.C.H.); (R.P.-M.)
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, Department of Immunobiology, BIO5 Institute, and UA Cancer Center, University of Arizona, Tucson, AZ 85721, USA;
| | - Safaa Kumari
- International Center for Agricultural Research in the Dry Areas (ICARDA), Terbol Station, Beqa’a, Zahle, Lebanon;
| | - Christian Vernière
- CIRAD, BGPI, 34398 Montpellier, France; (C.V.); (D.F.); (P.R.)
- BGPI, INRAE, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France
| | - Denis Filloux
- CIRAD, BGPI, 34398 Montpellier, France; (C.V.); (D.F.); (P.R.)
- BGPI, INRAE, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France
| | - Philippe Roumagnac
- CIRAD, BGPI, 34398 Montpellier, France; (C.V.); (D.F.); (P.R.)
- BGPI, INRAE, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France
| | | | - Simone G. Ribeiro
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, CEP 70770-917, Brazil;
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
| | - 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 7925, South Africa;
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town 7925, South Africa
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