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Torralba B, Blanc S, Michalakis Y. Reassortments in single-stranded DNA multipartite viruses: Confronting expectations based on molecular constraints with field observations. Virus Evol 2024; 10:veae010. [PMID: 38384786 PMCID: PMC10880892 DOI: 10.1093/ve/veae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/23/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024] Open
Abstract
Single-stranded DNA multipartite viruses, which mostly consist of members of the genus Begomovirus, family Geminiviridae, and all members of the family Nanoviridae, partly resolve the cost of genomic integrity maintenance through two remarkable capacities. They are able to systemically infect a host even when their genomic segments are not together in the same host cell, and these segments can be separately transmitted by insect vectors from host to host. These capacities potentially allow such viruses to reassort at a much larger spatial scale, since reassortants could arise from parental genotypes that do not co-infect the same cell or even the same host. To assess the limitations affecting reassortment and their implications in genome integrity maintenance, the objective of this review is to identify putative molecular constraints influencing reassorted segments throughout the infection cycle and to confront expectations based on these constraints with empirical observations. Trans-replication of the reassorted segments emerges as the major constraint, while encapsidation, viral movement, and transmission compatibilities appear more permissive. Confronting the available molecular data and the resulting predictions on reassortments to field population surveys reveals notable discrepancies, particularly a surprising rarity of interspecific natural reassortments within the Nanoviridae family. These apparent discrepancies unveil important knowledge gaps in the biology of ssDNA multipartite viruses and call for further investigation on the role of reassortment in their biology.
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Affiliation(s)
- Babil Torralba
- PHIM, Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Avenue du Campus d’Agropolis - ZAC de Baillarguet, Montpellier 34980, France
| | - Stéphane Blanc
- PHIM, Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Avenue du Campus d’Agropolis - ZAC de Baillarguet, Montpellier 34980, France
| | - Yannis Michalakis
- MIVEGEC, Université Montpellier, CNRS, IRD, 911, Avenue Agropolis, Montpellier 34394, France
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2
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Moubset O, François S, Maclot F, Palanga E, Julian C, Claude L, Fernandez E, Rott P, Daugrois JH, Antoine-Lorquin A, Bernardo P, Blouin AG, Temple C, Kraberger S, Fontenele RS, Harkins GW, Ma Y, Marais A, Candresse T, Chéhida SB, Lefeuvre P, Lett JM, Varsani A, Massart S, Ogliastro M, Martin DP, Filloux D, Roumagnac P. Virion-Associated Nucleic Acid-Based Metagenomics: A Decade of Advances in Molecular Characterization of Plant Viruses. PHYTOPATHOLOGY 2022; 112:2253-2272. [PMID: 35722889 DOI: 10.1094/phyto-03-22-0096-rvw] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Over the last decade, viral metagenomic studies have resulted in the discovery of thousands of previously unknown viruses. These studies are likely to play a pivotal role in obtaining an accurate and robust understanding of how viruses affect the stability and productivity of ecosystems. Among the metagenomics-based approaches that have been developed since the beginning of the 21st century, shotgun metagenomics applied specifically to virion-associated nucleic acids (VANA) has been used to disentangle the diversity of the viral world. We summarize herein the results of 24 VANA-based studies, focusing on plant and insect samples conducted over the last decade (2010 to 2020). Collectively, viruses from 85 different families were reliably detected in these studies, including capsidless RNA viruses that replicate in fungi, oomycetes, and plants. Finally, strengths and weaknesses of the VANA approach are summarized and perspectives of applications in detection, epidemiological surveillance, environmental monitoring, and ecology of plant viruses are provided. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Oumaima Moubset
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | - François Maclot
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Essowè Palanga
- Institut Togolais de Recherche Agronomique (ITRA-CRASS), B.P. 129, Kara, Togo
| | - Charlotte Julian
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Lisa Claude
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Emmanuel Fernandez
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Philippe Rott
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Jean-Heinrich Daugrois
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | | | - Arnaud G Blouin
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
- Plant Protection Department, Agroscope, 1260, Nyon, Switzerland
| | - Coline Temple
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
| | - Gordon W Harkins
- South African Medical Research Council Capacity Development Unit, South African National Bioinformatics, Institute, University of the Western Cape, South Africa
| | - Yuxin Ma
- Univ. Bordeaux, INRAE, UMR BFP, 33140 Villenave d'Ornon, France
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR BFP, 33140 Villenave d'Ornon, France
| | | | | | | | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Sébastien Massart
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | | | - Darren P Martin
- Division of Computational Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Denis Filloux
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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3
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Guo Y, Ma J, Li J. The complete chloroplast genome of Vicia cracca L. Mitochondrial DNA B Resour 2021; 6:1793-1795. [PMID: 34179462 PMCID: PMC8205000 DOI: 10.1080/23802359.2021.1926355] [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] [Indexed: 11/11/2022] Open
Abstract
Vicia cracca L. is a widespread perennial herb in the Northern Hemisphere. It has purple flowers and leave tendrils for climbing on neighboring vegetation. For knowing the chloroplast genome, a sample’s genomic was extracted, sequenced, assembled and annotated. The chloroplast genome of this plant is a circular form of 126,272bp in length with IR loss. After annotation, a total of 108 genes were predicted, of which, 75 encode proteins, 3 rRNA, 30 tRNA. The evolutionary history, inferred using Maximum Likelihood method, indicates that V. cracca was grouped within Vicia in Fabaceae. The complete cp genome will be helpful for further studies on molecular biology, evolution, population genetics, taxonomy or resources protection.
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Affiliation(s)
- Yupeng Guo
- Qinghai Provincial Key Laboratory of High value Utilization of Characteristic Economic Plants, College of Ecological Environment and Resources, Qinghai Nationalities University, Xining, P. R. China
| | - Jiali Ma
- Qinghai Provincial Key Laboratory of High value Utilization of Characteristic Economic Plants, College of Ecological Environment and Resources, Qinghai Nationalities University, Xining, P. R. China
| | - Junqiao Li
- Qinghai Provincial Key Laboratory of High value Utilization of Characteristic Economic Plants, College of Ecological Environment and Resources, Qinghai Nationalities University, Xining, P. R. China
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4
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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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5
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Hasanvand V, Heydanejad J, Massumi H, Kleinow T, Jeske H, Fontenele RS, Kraberger S, Varsani A. Genome characterization of parsley severe stunt-associated virus in Iran. Virus Genes 2021; 57:293-301. [PMID: 33881682 DOI: 10.1007/s11262-021-01835-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 04/08/2021] [Indexed: 11/28/2022]
Abstract
Parsley severe stunt-associated virus (PSSaV) is a recently identified nanovirus first reported in Germany. During a survey for identification of nanoviruses infecting apiaceous plants in south-eastern Iran, PSSaV was identified and characterized using a combination of rolling circle amplification (RCA) and high-throughput sequencing. Parsley plant samples were collected from vegetable production farms in Kerman province. From two symptomatic samples (39Ba and 40Ba), seven PSSaV components (DNA-C, -S, -M, -R, -N, -U1 and -U2) with two phylogenetically distinct variants of DNA-R (R1 and R2) were identified. In common with the German isolate of PSSaV, no DNA-U4 component was identified. In addition, associated alphasatellite molecules were identified in samples 39Ba [n = 6] and 40Ba [n = 5]. Sequence analyses showed that concatenated component sequences of the two Iranian PSSaVs share 97.2% nucleotide identity with each other and 82% to the German isolate. The coat proteins (CPs) of the PSSaV Iranian sequences share 97.2% amino acid identity and ~ 84% identity with that of the German isolate. Sequence and phylogenetic analyses of a total of 11 recovered alphasatellites from the two samples can be classified into the genera Fabenesatellite [n = 2], Milvetsatellite [n = 1], Mivedwarsatellite [n = 2], Subclovsatellite [n = 2], Sophoyesatellite [n = 4] in the family Alphasatellitidae. Identification of PSSaV and other nanoviruses in wild and cultivated plants in Iran reveals that nanoviruses could be causing yield reduction in crops plants in this country.
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Affiliation(s)
- Vahid Hasanvand
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, 7616914111, Kerman, Iran
| | - Jahangir Heydanejad
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, 7616914111, Kerman, Iran. .,Research and Technology Institute of Plant Production (RTIPP), Shahid Bahonar University of Kerman, 7616914111, Kerman, Iran.
| | - Hossain Massumi
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, 7616914111, Kerman, Iran
| | - Tatjana Kleinow
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Holger Jeske
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Rafaela S Fontenele
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287-5001, USA
| | - Simona Kraberger
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287-5001, USA
| | - Arvind Varsani
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287-5001, USA.,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, Cape Town, 7701, South Africa
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6
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Gaafar YZA, Herz K, Hartrick J, Fletcher J, Blouin AG, MacDiarmid R, Ziebell H. Investigating the Pea Virome in Germany-Old Friends and New Players in the Field(s). Front Microbiol 2020; 11:583242. [PMID: 33281777 PMCID: PMC7691430 DOI: 10.3389/fmicb.2020.583242] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/28/2020] [Indexed: 12/21/2022] Open
Abstract
Peas are an important legume for human and animal consumption and are also being used as green manure or intermediate crops to sustain and improve soil condition. Pea production faces constraints from fungal, bacterial, and viral diseases. We investigated the virome of German pea crops over the course of three successive seasons in different regions of pea production to gain an overview of the existing viruses. Pools from 540 plants, randomly selected from symptomatic and asymptomatic peas, and non-crop plants surrounding the pea fields were used for ribosomal RNA-depleted total RNA extraction followed by high-throughput sequencing (HTS) and RT-PCR confirmation. Thirty-five different viruses were detected in addition to nine associated nucleic acids. From these viruses, 25 are classified as either new viruses, novel strains or viruses that have not been reported previously from Germany. Pea enation mosaic virus 1 and 2 were the most prevalent viruses detected in the pea crops, followed by pea necrotic yellow dwarf virus (PNYDV) and turnip yellows virus which was also found also in the surrounding non-legume weeds. Moreover, a new emaravirus was detected in symptomatic peas in one region for two successive seasons. Most of the identified viruses are known to be aphid transmissible. The results revealed a high virodiversity in the German pea fields that poses new challenges to diagnosticians, researchers, risk assessors and policy makers, as the impact of the new findings are currently unknown.
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Affiliation(s)
- Yahya Z A Gaafar
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Kerstin Herz
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Jonas Hartrick
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - John Fletcher
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Arnaud G Blouin
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand.,School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Robin MacDiarmid
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand.,School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Heiko Ziebell
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
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7
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Gaafar YZA, Ziebell H. Aphid transmission of nanoviruses. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2020; 104:e21668. [PMID: 32212397 DOI: 10.1002/arch.21668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 02/28/2020] [Accepted: 03/03/2020] [Indexed: 06/10/2023]
Abstract
The genus Nanovirus consists of plant viruses that predominantly infect legumes leading to devastating crop losses. Nanoviruses are transmitted by various aphid species. The transmission occurs in a circulative nonpropagative manner. It was long suspected that a virus-encoded helper factor would be needed for successful transmission by aphids. Recently, a helper factor was identified as the nanovirus-encoded nuclear shuttle protein (NSP). The mode of action of NSP is currently unknown in contrast to helper factors from other plant viruses that, for example, facilitate binding of virus particles to receptors within the aphids' stylets. In this review, we are summarizing the current knowledge about nanovirus-aphid vector interactions.
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Affiliation(s)
- Yahya Z A Gaafar
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kuehn Institute, Braunschweig, Lower Saxony, Germany
| | - Heiko Ziebell
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kuehn Institute, Braunschweig, Lower Saxony, Germany
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8
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Hassan-Sheikhi P, Heydarnejad J, Massumi H, Kraberger S, Varsani A. Novel nanovirus and associated alphasatellites identified in milk vetch plants with chlorotic dwarf disease in Iran. Virus Res 2019; 276:197830. [PMID: 31790775 DOI: 10.1016/j.virusres.2019.197830] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 02/03/2023]
Abstract
Members of the family Nanoviridae are multi-component single-stranded DNA viruses that infect a variety of plant species. Using a combination of conventional PCR and high throughput sequencing-based approach, we identified a novel nanovirus infecting two symptomatic milk vetch plants (Astragalus myriacanthus Boiss.; family Fabaceae) showing marginal leaf chlorosis, little leaves and dwarfing in Iran. All eight segments (DNA-C, DNA-M, DNA-N, DNA-R, DNA-S, DNA-U1, DNA-U2 and DNAU4) were recovered and Sanger sequenced. The genome of this new nanovirus, hereby referred to as milk vetch chlorotic dwarf virus (MVCDV), shares 62.2-74.7 % nucleotide pairwise identity with the genomes of other nanoviruses. DNA-C, DNA-M, DNA-N, DNA-S components are most closely related to those of black medic leaf roll virus (BMLRV), sharing between 67.8-81.2 % identity. We also identified three nanoalphasatellites (family Alphasatellitidae) associated with the nanovirus which belong to species Faba bean necrotic yellows alphasatellite 1 (genus Subclovsatellite), Faba bean necrotic yellows alphasatellite 2 (genus Fabenesatellite) and Sophora yellow stunt alphasatellite 5 (genus Clostunsatellite). Given the significant diversity of Astragalus spp. in Iran, it is likely that there could be more nanoviruses circulating in these plants and that these may play a role in the spread of these nanovirus to cultivated fabaceous hosts.
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Affiliation(s)
- Parisa Hassan-Sheikhi
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman 7616914111, Iran
| | - Jahangir Heydarnejad
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman 7616914111, Iran; Research and Technology Institute of Plant Production (RTIPP), Shahid Bahonar University of Kerman, 7616914111, Iran.
| | - Hossain Massumi
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman 7616914111, Iran
| | - Simona Kraberger
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287-5001, USA
| | - Arvind Varsani
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287-5001, USA; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, South Africa
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9
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Vetten HJ, Knierim D, Rakoski MS, Menzel W, Maiss E, Gronenborn B, Winter S, Krenz B. Identification of a novel nanovirus in parsley. Arch Virol 2019; 164:1883-1887. [PMID: 31079213 DOI: 10.1007/s00705-019-04280-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/09/2019] [Indexed: 11/30/2022]
Abstract
Using next-generation sequencing to characterize agents associated with a severe stunting disease of parsley from Germany, we identified a hitherto undescribed virus. We sequenced total RNA and rolling-circle-amplified DNA from diseased plants. The genome sequence of the virus shows that it is a member of the genus Nanovirus, but it lacks DNA-U4. In addition to the seven genomic DNAs of the virus, we identified a second DNA-R and seven distinct alphasatellites associated with the disease. We propose the name "parsley severe stunt associated virus" (PSSaV) for this novel nanovirus.
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Affiliation(s)
| | - Dennis Knierim
- Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ), Messeweg 11/12, 38104, Brunswick, Germany
| | - Mirko Sebastian Rakoski
- Department of Phytomedicine, Plant Virology, Institute of Horticultural Production Systems, Leibniz University, 30419, Hannover, Germany
| | - Wulf Menzel
- Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ), Messeweg 11/12, 38104, Brunswick, Germany
| | - Edgar Maiss
- Department of Phytomedicine, Plant Virology, Institute of Horticultural Production Systems, Leibniz University, 30419, Hannover, Germany
| | - Bruno Gronenborn
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Avenue de la Terrasse, 91198, Gif sur Yvette, France
| | - Stephan Winter
- Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ), Messeweg 11/12, 38104, Brunswick, Germany
| | - Björn Krenz
- Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ), Messeweg 11/12, 38104, Brunswick, Germany.
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10
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Knierim D, Barrière Q, Grigoras I, Winter S, Vetten HJ, Schwinghamer M, Thomas J, Chu P, Gronenborn B, Timchenko T. Subterranean Clover Stunt Virus Revisited: Detection of Two Missing Genome Components. Viruses 2019; 11:v11020138. [PMID: 30720711 PMCID: PMC6410307 DOI: 10.3390/v11020138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 01/28/2019] [Accepted: 02/01/2019] [Indexed: 01/15/2023] Open
Abstract
Subterranean clover stunt virus (SCSV) is a type species of the genus Nanovirus in the family Nanoviridae. It was the first single-stranded DNA plant virus with a multipartite genome, of which genomic DNA sequences had been determined. All nanoviruses have eight genome components except SCSV, for which homologs of two genome components present in all other nanovirus genomes, DNA-U2 and DNA-U4, were lacking. We analysed archived and more recent samples from SCSV-infected legume plants to verify its genome composition and found the missing genome components. These results indicated that SCSV also has eight genome components and is a typical member of the genus Nanovirus.
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Affiliation(s)
- Dennis Knierim
- Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ), Inhoffenstraße 7B, 38124 Braunschweig, Germany.
| | - Quentin Barrière
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, 91198 Gif-sur-Yvette, France.
| | - Ioana Grigoras
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, 91198 Gif-sur-Yvette, France.
| | - Stephan Winter
- Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ), Inhoffenstraße 7B, 38124 Braunschweig, Germany.
| | | | - Mark Schwinghamer
- NSW Department of Primary Industries, Tamworth Agricultural Institute, 4 Marsden Park Road, Calala, NSW 2340, Australia
| | - John Thomas
- The University of Queensland, QAAFI, Ecosciences Precinct, GPO Box 267, Brisbane, QLD 4001, Australia.
| | - Paul Chu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
- Megalong Crescent, Harrison, ACT 2914, Australia.
| | - Bruno Gronenborn
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, 91198 Gif-sur-Yvette, France.
| | - Tatiana Timchenko
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, 91198 Gif-sur-Yvette, France.
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Novel circular DNA viruses associated with Apiaceae and Poaceae from South Africa and New Zealand. Arch Virol 2018; 164:237-242. [PMID: 30220037 DOI: 10.1007/s00705-018-4031-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 07/21/2018] [Indexed: 10/28/2022]
Abstract
Advances in molecular techniques used in viral metagenomics coupled with high throughput sequencing is rapidly expanding our knowledge of plant-associated virus diversity. Applying such approaches, we have identified five novel circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses from Poaceae and Apiaceae plant from South Africa and New Zealand. These viruses have a simple genomic organization, including two open reading frames that likely encode a Rep and a capsid protein (CP), a conserved nonanucleotide motif on the apex of a putative stem loop structure, and conserved rolling-circle replication and helicase motifs within their likely Rep: all suggesting that they replicate through rolling-circle replication. The Reps and the CPs putatively encoded by these five novel viruses share low to moderate degrees of similarity (22.1 - 44.6%) with other CRESS DNA viruses.
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Grigoras I, Vetten HJ, Commandeur U, Ziebell H, Gronenborn B, Timchenko T. Nanovirus DNA-N encodes a protein mandatory for aphid transmission. Virology 2018; 522:281-291. [PMID: 30071404 DOI: 10.1016/j.virol.2018.07.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/04/2018] [Accepted: 07/04/2018] [Indexed: 12/15/2022]
Abstract
Nanoviruses possess a multipartite single-stranded DNA genome and are naturally transmitted to plants by various aphid species in a circulative non-propagative manner. Using the cloned genomic DNAs of faba bean necrotic stunt virus (FBNSV) for reconstituting nanovirus infections we analyzed the necessity of different virus components for infection and transmission by aphids. We found that in the absence of DNA-U1 and DNA-U2 symptom severity decreased, and in the absence of DNA-U1 the transmission efficiency decreased. Most significantly, we demonstrated that the protein encoded by DNA-N (NSP) is mandatory for aphid transmission. Moreover, we showed that the NSP of FBNSV could substitute for that of a distantly related nanovirus, pea necrotic yellow dwarf virus. Altering the FBNSV NSP by adding 13 amino acids to its carboxy-terminus resulted in an infectious but non-transmissible virus. We demonstrate that the NSP acts as a nanovirus transmission factor, the existence of which had been hypothesized earlier.
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Affiliation(s)
- Ioana Grigoras
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France
| | | | - Ulrich Commandeur
- Institute for Molecular Biotechnology (Biology VII), RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Heiko Ziebell
- Julius Kühn Institute (JKI), Bundesforschungsinstitut für Kulturpflanzen, Institut für Epidemiologie und Pathogendiagnostik, 38104 Braunschweig, Germany
| | - Bruno Gronenborn
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France; Institute for Integrative Biology of the Cell, UMR 9198, CNRS, Université Paris-Sud, CEA, Avenue de la Terrasse, 91198 Gif sur Yvette, France
| | - Tatiana Timchenko
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France; Institute for Integrative Biology of the Cell, UMR 9198, CNRS, Université Paris-Sud, CEA, Avenue de la Terrasse, 91198 Gif sur Yvette, France.
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Alphasatellitidae: a new family with two subfamilies for the classification of geminivirus- and nanovirus-associated alphasatellites. Arch Virol 2018; 163:2587-2600. [PMID: 29740680 DOI: 10.1007/s00705-018-3854-2] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 04/25/2018] [Indexed: 10/16/2022]
Abstract
Nanoviruses and geminiviruses are circular, single stranded DNA viruses that infect many plant species around the world. Nanoviruses and certain geminiviruses that belong to the Begomovirus and Mastrevirus genera are associated with additional circular, single stranded DNA molecules (~ 1-1.4 kb) that encode a replication-associated protein (Rep). These Rep-encoding satellite molecules are commonly referred to as alphasatellites and here we communicate the establishment of the family Alphasatellitidae to which these have been assigned. Within the Alphasatellitidae family two subfamilies, Geminialphasatellitinae and Nanoalphasatellitinae, have been established to respectively accommodate the geminivirus- and nanovirus-associated alphasatellites. Whereas the pairwise nucleotide sequence identity distribution of all the known geminialphasatellites (n = 628) displayed a troughs at ~ 70% and 88% pairwise identity, that of the known nanoalphasatellites (n = 54) had a troughs at ~ 67% and ~ 80% pairwise identity. We use these pairwise identity values as thresholds together with phylogenetic analyses to establish four genera and 43 species of geminialphasatellites and seven genera and 19 species of nanoalphasatellites. Furthermore, a divergent alphasatellite associated with coconut foliar decay disease is assigned to a species but not a subfamily as it likely represents a new alphasatellite subfamily that could be established once other closely related molecules are discovered.
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Analysis of DNAs associated with coconut foliar decay disease implicates a unique single-stranded DNA virus representing a new taxon. Sci Rep 2018; 8:5698. [PMID: 29632309 PMCID: PMC5890292 DOI: 10.1038/s41598-018-23739-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/16/2018] [Indexed: 12/11/2022] Open
Abstract
The unique ecology, pathology and undefined taxonomy of coconut foliar decay virus (CFDV), found associated with coconut foliar decay disease (CFD) in 1986, prompted analyses of old virus samples by modern methods. Rolling circle amplification and deep sequencing applied to nucleic acid extracts from virion preparations and CFD-affected palms identified twelve distinct circular DNAs, eleven of which had a size of about 1.3 kb and one of 641 nt. Mass spectrometry-based protein identification proved that a 24 kDa protein encoded by two 1.3 kb DNAs is the virus capsid protein with highest sequence similarity to that of grabloviruses (family Geminiviridae), even though CFDV particles are not geminate. The nine other 1.3 kb DNAs represent alphasatellites coding for replication initiator proteins that differ clearly from those encoded by nanovirid DNA-R. The 641 nt DNA-gamma is unique and may encode a movement protein. Three DNAs, alphasatellite CFDAR, capsid protein encoding CFDV DNA-S.1 and DNA-gamma share sequence motifs near their replication origins and were consistently present in all samples analysed. These DNAs appear to be integral components of a possibly tripartite CFDV genome, different from those of any Geminiviridae or Nanoviridae family member, implicating CFDV as representative of a new genus and family.
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Molecular characterization of faba bean necrotic yellows viruses in Tunisia. Arch Virol 2017; 163:687-694. [PMID: 29147784 DOI: 10.1007/s00705-017-3651-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/06/2017] [Indexed: 10/18/2022]
Abstract
Faba bean necrotic yellows virus (FBNYV) (genus Nanovirus; family Nanoviridae) has a genome comprising eight individually encapsidated circular single-stranded DNA components. It has frequently been found infecting faba bean (Vicia faba L.) and chickpea (Cicer arietinum L.) in association with satellite molecules (alphasatellites). Genome sequences of FBNYV from Azerbaijan, Egypt, Iran, Morocco, Spain and Syria have been determined previously and we now report the first five genome sequences of FBNYV and associated alphasatellites from faba bean sampled in Tunisia. In addition, we have determined the genome sequences of two additional FBNYV isolates from chickpea plants sampled in Syria and Iran. All individual FBNYV genome component sequences that were determined here share > 84% nucleotide sequence identity with FBNYV sequences available in public databases, with the DNA-M component displaying the highest degree of diversity. As with other studied nanoviruses, recombination and genome component reassortment occurs frequently both between FBNYV genomes and between genomes of nanoviruses belonging to other species.
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