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Wu X, Chen S, Zhang Z, Zhang Y, Li P, Chen X, Liu M, Lu Q, Li Z, Wei Z, Xu P. Development of Recombinase Polymerase Amplification Combined with Lateral Flow Strips for Rapid Detection of Cowpea Mild Mottle Virus. THE PLANT PATHOLOGY JOURNAL 2023; 39:486-493. [PMID: 37817494 PMCID: PMC10580057 DOI: 10.5423/ppj.oa.02.2023.0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/31/2023] [Accepted: 09/10/2023] [Indexed: 10/12/2023]
Abstract
Cowpea mild mottle virus (CPMMV) is a global plant virus that poses a threat to the production and quality of legume crops. Early and accurate diagnosis is essential for effective managing CPMMV outbreaks. With the advancement in isothermal recombinase polymerase amplification and lateral flow strips technologies, more rapid and sensitive methods have become available for detecting this pathogen. In this study, we have developed a reverse transcription recombinase polymerase amplification combined with lateral flow strips (RT-RPA-LFS) method for the detection of CPMMV, specifically targeting the CPMMV coat protein (CP) gene. The RT-RPA-LFS assay only requires 20 min at 40°C and demonstrates high specificity. Its detection limit was 10 copies/μl, which is approximately up to 100 times more sensitive than RT-PCR on agarose gel electrophoresis. The developed RT-RPA-LFS method offers a rapid, convenient, and sensitive approach for field detection of CPMMV, which contribute to controlling the spread of the virus.
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Affiliation(s)
- Xinyang Wu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang, Hangzhou 310018, China
| | - Shuting Chen
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Zixin Zhang
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Yihan Zhang
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Pingmei Li
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Xinyi Chen
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Miaomiao Liu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Qian Lu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Zhongyi Li
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Zhongyan Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Pei Xu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang, Hangzhou 310018, China
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Silva JMF, Melo FL, Elena SF, Candresse T, Sabanadzovic S, Tzanetakis IE, Blouin AG, Villamor DEV, Mollov D, Constable F, Cao M, Saldarelli P, Cho WK, Nagata T. Virus classification based on in-depth sequence analyses and development of demarcation criteria using the Betaflexiviridae as a case study. J Gen Virol 2022; 103. [DOI: 10.1099/jgv.0.001806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Currently, many viruses are classified based on their genome organization and nucleotide/amino acid sequence identities of their capsid and replication-associated proteins. Although biological traits such as vector specificities and host range are also considered, this later information is scarce for the majority of recently identified viruses, characterized only from genomic sequences. Accordingly, genomic sequences and derived information are being frequently used as the major, if not only, criteria for virus classification and this calls for a full review of the process. Herein, we critically addressed current issues concerning classification of viruses in the family Betaflexiviridae in the era of high-throughput sequencing and propose an updated set of demarcation criteria based on a process involving pairwise identity analyses and phylogenetics. The proposed framework has been designed to solve the majority of current conundrums in taxonomy and to facilitate future virus classification. Finally, the analyses performed herein, alongside the proposed approaches, could be used as a blueprint for virus classification at-large.
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Affiliation(s)
- João Marcos Fagundes Silva
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, University of Brasília, Brasília 70910-900, Brazil
| | - Fernando Lucas Melo
- Departamento de Fitopatologia, Instituto de Biología Integrativa de Sistemas, University of Brasília, Brasília 70910-900, Brazil
| | - Santiago F. Elena
- The Santa Fe Institute, Santa Fe, NM 87501, USA
- Instituto de Biología Integrativa de Sistemas (I2 13 SysBio), CSIC-Universitat de València, Paterna 14 46980 València, Spain
| | - Thierry Candresse
- Univ. Bordeaux, INRAE, UMR 1332 BFP, 33140 Villenave d’Ornon, France
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | | | - Arnaud G. Blouin
- Virology-Phytoplasmology Laboratory, Agroscope, 1260 Nyon, Switzerland
| | | | - Dimitre Mollov
- USDA-ARS Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR, 97330, USA
| | - Fiona Constable
- Department of Jobs Precincts and Regions, Agriculture Victoria Research, Agribio, Bundoora, VIC 3083, Australia
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, PR China
| | - Pasquale Saldarelli
- National Research Council of Italy (CNR), Institute for Sustainable Plant Protection (IPSP), Via Amendola 122/D, 70126 Bari, Italy
| | - Won Kyong Cho
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Seoburo 2066, Suwon 16419, Gyeonggi, Republic of Korea
| | - Tatsuya Nagata
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, University of Brasília, Brasília 70910-900, Brazil
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3
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Jiang C, Shan S, Huang Y, Mao C, Zhang H, Li Y, Chen J, Wei Z, Sun Z. The C-Terminal Transmembrane Domain of Cowpea Mild Mottle Virus TGBp2 Is Critical for Plasmodesmata Localization and for Its Interaction With TGBp1 and TGBp3. Front Microbiol 2022; 13:860695. [PMID: 35495691 PMCID: PMC9051516 DOI: 10.3389/fmicb.2022.860695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
The movement of some plant RNA viruses is mediated by triple gene block (TGB) proteins, which cooperate to transfer the viral genome from cell to cell through plasmodesmata. Here, we investigated the function of the TGB proteins of cowpea mild mottle virus (CPMMV; genus Carlavirus, family Betaflexiviridae), which causes severe damage to soybean production. Subcellular localization experiments demonstrated that TGBp1 and TGBp3 were localized to the endoplasmic reticulum (ER), plasmodesmata (PD) and nucleus in Nicotiana benthamiana leaves. TGBp2 was unusually localized to PD. In protein interaction assays TGBp2 significantly enhanced the interaction between TGBp3 and TGBp1. Interaction assays using deletion mutants showed that the C-terminal transmembrane (TM) domain of TGBp2 is critical for its localization to PD and for its interaction with TGBp1 and TGBp3.
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Synonymous Codon Pattern of Cowpea Mild Mottle Virus Sheds Light on Its Host Adaptation and Genome Evolution. Pathogens 2022; 11:pathogens11040419. [PMID: 35456094 PMCID: PMC9026141 DOI: 10.3390/pathogens11040419] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/22/2022] [Accepted: 03/28/2022] [Indexed: 02/07/2023] Open
Abstract
Cowpea mild mottle virus (CpMMV) is an economically significant virus that causes severe disease on several legume crops. Aside from recombination, other factors driving its rapid evolution are elusive. In this study, the synonymous codon pattern of CpMMV and factors shaping it were analyzed. Phylogeny and nucleotide composition analyses showed that isolates of different geography or hosts had very similar nucleotide compositions. Relative synonymous codon usage (RSCU) and neutrality analyses suggest that CpMMV prefers A/U-ending codons and natural selection is the dominative factor that affects its codon bias. Dinucleotide composition and codon adaptation analyses indicate that the codon pattern of CpMMV is mainly shaped by the requirement of escaping of host dinucleotide-associated antiviral responses and translational efficiency.
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Wei Z, Mao C, Jiang C, Zhang H, Chen J, Sun Z. Identification of a New Genetic Clade of Cowpea Mild Mottle Virus and Characterization of Its Interaction With Soybean Mosaic Virus in Co-infected Soybean. Front Microbiol 2021; 12:650773. [PMID: 33897664 PMCID: PMC8060446 DOI: 10.3389/fmicb.2021.650773] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/15/2021] [Indexed: 11/16/2022] Open
Abstract
Cowpea mild mottle virus (CPMMV; genus Carlavirus) can be a destructive pathogen of soybean but there is little information about its distribution on soybean in China. Here, we collected soybean plants with virus-like symptoms from 11 fields widely scattered within China, and used high-throughput sequencing to determine their virome. Most samples (8/11) were co-infected by the well-studied potyvirus soybean mosaic virus (SMV) and CPMMV, and the remaining three samples were singly infected with CPMMV. The near-complete genome sequences of the 11 CPMMV isolates were determined and phylogenetic analysis showed that they constituted a new genetic clade. One recombination event was detected among the CPMMV sequences, and the isolate CPMMV_JL_CC was identified as recombinant. In mechanical inoculation assays, co-infection by CPMMV and SMV resulted in an enhancement of disease symptoms, but decreased the expression level of the genomic RNAs and CP of CPMMV, without significantly affecting SMV accumulation. The interaction between these viruses needs further investigation.
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Affiliation(s)
| | | | | | | | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Zongtao Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
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Zanardo LG, Trindade TA, Mar TB, Barbosa TMC, Milanesi DF, Alves MS, Lima RRPN, Zerbini FM, Janssen A, Mizubuti ESG, Elliot SL, Carvalho CM. Experimental evolution of cowpea mild mottle virus reveals recombination-driven reduction in virulence accompanied by increases in diversity and viral fitness. Virus Res 2021; 303:198389. [PMID: 33716182 DOI: 10.1016/j.virusres.2021.198389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 12/22/2022]
Abstract
Major themes in pathogen evolution are emergence, evolution of virulence, host adaptation and the processes that underlie them. RNA viruses are of particular interest due to their rapid evolution. The in vivo molecular evolution of an RNA plant virus was demonstrated here using a necrotic isolate of cowpea mild mottle virus (CPMMV) and a susceptible soybean genotype submitted to serial inoculations. We show that the virus lost the capacity to cause necrosis after six passages through the host plant. When a severe bottleneck was imposed, virulence reduction occurred in the second passage. The change to milder symptoms had fitness benefits for the virus (higher RNA accumulation) and for its vector, the whitefly Bemisia tabaci. Genetic polymorphisms were highest in ORF1 (viral replicase) and were independent of the symptom pattern. Recombination was a major contributor to this diversity - even with the strong genetic bottleneck, recombination events and hot spots were detected within ORF1. Virulence reduction was associated with different sites in ORF1 associated to recombination events in both experiments. Overall, the results demonstrate that the reduction in virulence was a consequence of the emergence of new variants, driven by recombination. Besides providing details of the evolutionary mechanisms behind a reduction in virulence and its effect under viral and vector fitness, we propose that this recombination-driven switch in virulence allows the pathogen to rapidly adapt to a new host and, potentially, switch back.
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Affiliation(s)
- Larissa G Zanardo
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Tiago A Trindade
- Departamento de Entomologia, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Talita B Mar
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Tarsiane M C Barbosa
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Diogo F Milanesi
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Murilo S Alves
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | - Roberta R P N Lima
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - F Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Arne Janssen
- Departamento de Entomologia, Universidade Federal de Viçosa, Viçosa, MG, Brazil; IBED, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Eduardo S G Mizubuti
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Simon L Elliot
- Departamento de Entomologia, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Claudine M Carvalho
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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Krause-Sakate R, Watanabe LFM, Gorayeb ES, da Silva FB, Alvarez DDL, Bello VH, Nogueira AM, de Marchi BR, Vicentin E, Ribeiro-Junior MR, Marubayashi JM, Rojas-Bertini CA, Muller C, Bueno RCODF, Rosales M, Ghanim M, Pavan MA. Population Dynamics of Whiteflies and Associated Viruses in South America: Research Progress and Perspectives. INSECTS 2020; 11:insects11120847. [PMID: 33260578 PMCID: PMC7760982 DOI: 10.3390/insects11120847] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/30/2020] [Accepted: 11/26/2020] [Indexed: 11/16/2022]
Abstract
Simple Summary Whiteflies are one of the most important and widespread pests in the world. In South America, the currently most important species occurring are Bemisia afer,Trialeurodes vaporariorum, and the cryptic species Middle East-Asia Minor 1, Mediterranean, and New World, from Bemisia tabaci complex. The present review compiles information from several studies conducted in South America regarding these insects, providing data related to the dynamics and distribution of whiteflies, the associated viruses, and the management strategies to keep whiteflies under the economic damage threshold. Abstract By having an extensive territory and suitable climate conditions, South America is one of the most important agricultural regions in the world, providing different kinds of vegetable products to different regions of the world. However, such favorable conditions for plant production also allow the development of several pests, increasing production costs. Among them, whiteflies (Hemiptera: Aleyrodidae) stand out for their potential for infesting several crops and for being resistant to insecticides, having high rates of reproduction and dispersal, besides their efficient activity as virus vectors. Currently, the most important species occurring in South America are Bemisia afer, Trialeurodes vaporariorum, and the cryptic species Middle East-Asia Minor 1, Mediterranean, and New World, from Bemisia tabaci complex. In this review, a series of studies performed in South America were compiled in an attempt to unify the advances that have been developed in whitefly management in this continent. At first, a background of the current whitefly distribution in South American countries as well as factors affecting them are shown, followed by a background of the whitefly transmitted viruses in South America, addressing their location and association with whiteflies in each country. Afterwards, a series of management strategies are proposed to be implemented in South American fields, including cultural practices and biological and chemical control, finalizing with a section containing future perspectives and directions for further research.
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Affiliation(s)
- Renate Krause-Sakate
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
- Correspondence: ; Tel.: +55-14-3880-7487
| | - Luís Fernando Maranho Watanabe
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | - Eduardo Silva Gorayeb
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
- Facultad de Agronomía e Ingeniería, Pontificia Universidad Católica de Chile, Forestal, Vicuña Mackena, 4860, Macul, Santiago 7820436, Chile; (C.A.R.-B.); (M.R.)
| | - Felipe Barreto da Silva
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | - Daniel de Lima Alvarez
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | - Vinicius Henrique Bello
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | - Angélica Maria Nogueira
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | | | - Eduardo Vicentin
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | - Marcos Roberto Ribeiro-Junior
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | - Julio Massaharu Marubayashi
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | - Claudia Andrea Rojas-Bertini
- Facultad de Agronomía e Ingeniería, Pontificia Universidad Católica de Chile, Forestal, Vicuña Mackena, 4860, Macul, Santiago 7820436, Chile; (C.A.R.-B.); (M.R.)
| | | | - Regiane Cristina Oliveira de Freitas Bueno
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | - Marlene Rosales
- Facultad de Agronomía e Ingeniería, Pontificia Universidad Católica de Chile, Forestal, Vicuña Mackena, 4860, Macul, Santiago 7820436, Chile; (C.A.R.-B.); (M.R.)
| | - Murad Ghanim
- Department of Entomology, Institute of Plant Protection, The Volcani Center, Rishon LeZion 7505101, Israel;
| | - Marcelo Agenor Pavan
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
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8
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Barreto da Silva F, Muller C, Bello VH, Watanabe LFM, Rossitto De Marchi B, Fusco LM, Ribeiro-Junior MR, Minozzi GB, Vivan LM, Tamai MA, Farias JR, Nogueira AM, Sartori MMP, Krause-Sakate R. Effects of cowpea mild mottle virus on soybean cultivars in Brazil. PeerJ 2020; 8:e9828. [PMID: 32944424 PMCID: PMC7469931 DOI: 10.7717/peerj.9828] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/05/2020] [Indexed: 11/25/2022] Open
Abstract
Soybean stem necrosis is caused by cowpea mild mottle virus (CPMMV), transmitted by the whitefly Bemisia tabaci. CPMMV has already been recorded in all major soybean-producing areas of Brazil. The impacts caused by CPMMV to the current Brazilian soybean production are unknown, thus the main objective of this study was to evaluate the effects of CPMMV infection on the main important soybean cultivars grown in the Southern and Midwestern regions of Brazil. Although asymptomatic in some of the tested cultivars, CPMMV infection significantly reduced the plant height, the number of pods per plant and the 1,000-grain weight. In addition, estimated yield losses ranged from 174 to 638 kg ha−1, depending on the cultivar. Evidence of seed transmission of CPMMV was observed in the BMX POTÊNCIA RR cultivar. These results suggest that CPMMV could have an important role in the reduction of soybean productivity in Brazil, but symptomless infections might be hiding the actual impact of this pathogen in commercial fields and infected seeds could be the primary inoculum source of the virus in the field.
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Affiliation(s)
- Felipe Barreto da Silva
- Department of Plant Protection, Universidade Estadual Paulista "Julio de Mesquita Filho" (UNESP), Botucatu, São Paulo, Brazil
| | | | - Vinicius Henrique Bello
- Department of Plant Protection, Universidade Estadual Paulista "Julio de Mesquita Filho" (UNESP), Botucatu, São Paulo, Brazil
| | - Luís Fernando Maranho Watanabe
- Department of Plant Protection, Universidade Estadual Paulista "Julio de Mesquita Filho" (UNESP), Botucatu, São Paulo, Brazil
| | - Bruno Rossitto De Marchi
- Department of Plant Protection, Universidade Estadual Paulista "Julio de Mesquita Filho" (UNESP), Botucatu, São Paulo, Brazil
| | - Lucas Machado Fusco
- Department of Plant Protection, Universidade Estadual Paulista "Julio de Mesquita Filho" (UNESP), Botucatu, São Paulo, Brazil
| | - Marcos Roberto Ribeiro-Junior
- Department of Plant Protection, Universidade Estadual Paulista "Julio de Mesquita Filho" (UNESP), Botucatu, São Paulo, Brazil
| | | | - Lucia Madalena Vivan
- Fundação de Apoio a Pesquisa à Pesquisa Agropecuária de Mato Grosso/Fundação MT, Rondonópolis, Mato Grosso, Brazil
| | - Marco Antonio Tamai
- Department of Human Sciences, Universidade do Estado da Bahia/UNEB, Campus IX, Barreiras, Bahia, Brazil
| | | | - Angélica Maria Nogueira
- Department of Plant Protection, Universidade Estadual Paulista "Julio de Mesquita Filho" (UNESP), Botucatu, São Paulo, Brazil
| | - Maria Márcia Pereira Sartori
- Department of Plant Protection, Universidade Estadual Paulista "Julio de Mesquita Filho" (UNESP), Botucatu, São Paulo, Brazil
| | - Renate Krause-Sakate
- Department of Plant Protection, Universidade Estadual Paulista "Julio de Mesquita Filho" (UNESP), Botucatu, São Paulo, Brazil
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Figueira ADR, Geraldino-Duarte PS, Pinzón Nuñez AM, Lent JV, Galvino-Costa SBF, Farman M, Goodin MM. Characterization of Soybean yellow shoot virus, a New Member of the Family Potyviridae Infecting Soybean Plants in Brazil. PLANT DISEASE 2019; 103:1172-1180. [PMID: 30907693 DOI: 10.1094/pdis-06-18-1067-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A new virus species, belonging to the family Potyviridae and capable of infecting most of the soybean cultivars grown in Brazil, was collected in Lavras, Minas Gerais, Brazil, and named Soybean yellow shoot virus (SoyYSV). In this study, the complete 9,052-nucleotide genome of SoyYSV was determined and the structural, biological, and molecular properties of the virus were investigated. The SoyYSV genome encoded a single polyprotein that could be subsequently cleaved, generating 11 proteins. The SoyYSV genome shared 49% nucleotide and 36% amino acid sequence identity with Blackberry virus Y. However, the P1 protein of SoyYSV was much smaller and lacked the ALK1 domain characteristic of the genus Brambyvirus. Electron microscopy revealed flexuous filamentous virus particles, 760 to 780 nm in length, and cytoplasmic inclusions typical of those found in plant cells infected with Potyviridae species. In addition to soybean, SoyYSV infected species in the Amaranthaceae, Caricaceae, Fabaceae, and Solanaceae families. Among the most common potyviruses present in Brazil, only SoyYSV induced local necrotic lesions in Carica papaya L. SoyYSV was transmissible by Myzus persicae and Aphis gossypii but lacked the HC-Pro domain required for aphid transmission in other potyviruses. No seed transmission in soybean was observed.
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Affiliation(s)
- Antonia Dos Reis Figueira
- 1 Department of Fitopatologia, Universidade Federal de Lavras, Lavras, Minas Gerais 37200-000, Brazil
| | | | | | - Jan van Lent
- 2 Department of Plant Science, Wageningen University and Research, 6708 PB Wageningen, The Netherlands; and
| | - Suellen B F Galvino-Costa
- 1 Department of Fitopatologia, Universidade Federal de Lavras, Lavras, Minas Gerais 37200-000, Brazil
| | - M Farman
- 3 Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, U.S.A
| | - Michael M Goodin
- 3 Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, U.S.A
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Alves-Freitas DMT, Pinheiro-Lima B, Faria JC, Lacorte C, Ribeiro SG, Melo FL. Double-Stranded RNA High-Throughput Sequencing Reveals a New Cytorhabdovirus in a Bean Golden Mosaic Virus-Resistant Common Bean Transgenic Line. Viruses 2019; 11:E90. [PMID: 30669683 PMCID: PMC6357046 DOI: 10.3390/v11010090] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 12/13/2022] Open
Abstract
Using double-strand RNA (dsRNA) high-throughput sequencing, we identified five RNA viruses in a bean golden mosaic virus (BGMV)-resistant common bean transgenic line with symptoms of viral infection. Four of the identified viruses had already been described as infecting common bean (cowpea mild mottle virus, bean rugose mosaic virus, Phaseolus vulgaris alphaendornavirus 1, and Phaseolus vulgaris alphaendornavirus 2) and one is a putative new plant rhabdovirus (genus Cytorhabdovirus), tentatively named bean-associated cytorhabdovirus (BaCV). The BaCV genome presented all five open reading frames (ORFs) found in most rhabdoviruses: nucleoprotein (N) (ORF1) (451 amino acids, aa), phosphoprotein (P) (ORF2) (445 aa), matrix (M) (ORF4) (287 aa), glycoprotein (G) (ORF5) (520 aa), and an RNA-dependent RNA polymerase (L) (ORF6) (114 aa), as well as a putative movement protein (P3) (ORF3) (189 aa) and the hypothetical small protein P4. The predicted BaCV proteins were compared to homologous proteins from the closest cytorhabdoviruses, and a low level of sequence identity (15⁻39%) was observed. The phylogenetic analysis shows that BaCV clustered with yerba mate chlorosis-associated virus (YmCaV) and rice stripe mosaic virus (RSMV). Overall, our results provide strong evidence that BaCV is indeed a new virus species in the genus Cytorhabdovirus (family Rhabdoviridae), the first rhabdovirus to be identified infecting common bean.
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Affiliation(s)
| | - Bruna Pinheiro-Lima
- Embrapa Recursos Genéticos e Biotecnologia, 70.770-917 Brasília, Brazil.
- Departamento de Biologia Celular, Universidade de Brasília, 70910-900 Brasília, Brazil.
| | | | - Cristiano Lacorte
- Embrapa Recursos Genéticos e Biotecnologia, 70.770-917 Brasília, Brazil.
| | - Simone G Ribeiro
- Embrapa Recursos Genéticos e Biotecnologia, 70.770-917 Brasília, Brazil.
| | - Fernando L Melo
- Departamento de Biologia Celular, Universidade de Brasília, 70910-900 Brasília, Brazil.
- Departamento de Fitopatologia, Universidade de Brasília, 70910-900 Brasília, Brazil.
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11
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Thekke-Veetil T, Ho T, Postman JD, Martin RR, Tzanetakis IE. A Virus in American Blackcurrant ( Ribes americanum) with Distinct Genome Features Reshapes Classification in the Tymovirales. Viruses 2018; 10:v10080406. [PMID: 30081487 PMCID: PMC6115964 DOI: 10.3390/v10080406] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 07/16/2018] [Accepted: 07/26/2018] [Indexed: 12/15/2022] Open
Abstract
A novel virus with distinct genome features was discovered by high throughput sequencing in a symptomatic blackcurrant plant. The virus, tentatively named Ribes americanum virus A (RAVA), has distinct genome organization and molecular features bridging genera in the order Tymovirales. The genome consists of 7106 nucleotides excluding the poly(A) tail. Five open reading frames were identified, with the first encoding a putative viral replicase with methyl transferase (MTR), AlkB, helicase, and RNA dependent RNA polymerase (RdRp) domains. The genome organization downstream of the replicase resembles that of members of the order Tymovirales with an unconventional triple gene block (TGB) movement protein arrangement with none of the other four putative proteins exhibiting significant homology to viral proteins. Phylogenetic analysis using replicase conserved motifs loosely placed RAVA within the Betaflexiviridae. Data strongly suggest that RAVA is a novel virus that should be classified as a species in a new genus in the Betaflexiviridae or a new family within the order Tymovirales.
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Affiliation(s)
- Thanuja Thekke-Veetil
- Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA.
| | - Thien Ho
- Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA.
| | - Joseph D Postman
- National Clonal Germplasm Repository, United States Department of Agriculture, Corvallis, OR 97333, USA.
| | - Robert R Martin
- Horticultural Crops Research Unit, United States Department of Agriculture, Corvallis, OR 97331, USA.
| | - Ioannis E Tzanetakis
- Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA.
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New Insights into Asian Prunus Viruses in the Light of NGS-Based Full Genome Sequencing. PLoS One 2016; 11:e0146420. [PMID: 26741704 PMCID: PMC4704818 DOI: 10.1371/journal.pone.0146420] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 12/16/2015] [Indexed: 11/20/2022] Open
Abstract
Double stranded RNAs were purified from five Prunus sources of Asian origin and submitted to 454 pyrosequencing after a random, whole genome amplification. Four complete genomes of Asian prunus virus 1 (APV1), APV2 and APV3 were reconstructed from the sequencing reads, as well as four additional, near-complete genome sequences. Phylogenetic analyses confirmed the close relationships of these three viruses and the taxonomical position previously proposed for APV1, the only APV so far completely sequenced. The genetic distances in the respective polymerase and coat protein genes as well as their gene products suggest that APV2 should be considered as a distinct viral species in the genus Foveavirus, even if the amino acid identity levels in the polymerase are very close to the species demarcation criteria for the family Betaflexiviridae. However, the situation is more complex for APV1 and APV3, for which opposite conclusions are obtained depending on the gene (polymerase or coat protein) analyzed. Phylogenetic and recombination analyses suggest that recombination events may have been involved in the evolution of APV. Moreover, genome comparisons show that the unusually long 3’ non-coding region (3' NCR) is highly variable and a hot spot for indel polymorphisms. In particular, two APV3 variants differing only in their 3’ NCR were identified in a single Prunus source, with 3' NCRs of 214–312 nt, a size similar to that observed in other foveaviruses, but 567–850 nt smaller than in other APV3 isolates. Overall, this study provides critical genome information of these viruses, frequently associated with Prunus materials, even though their precise role as pathogens remains to be elucidated.
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Marais A, Faure C, Mustafayev E, Candresse T. Characterization of New Isolates of Apricot vein clearing-associated virus and of a New Prunus-Infecting Virus: Evidence for Recombination as a Driving Force in Betaflexiviridae Evolution. PLoS One 2015; 10:e0129469. [PMID: 26086395 PMCID: PMC4472227 DOI: 10.1371/journal.pone.0129469] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 05/08/2015] [Indexed: 11/26/2022] Open
Abstract
Double stranded RNAs from Prunus samples gathered from various surveys were analyzed by a deep-sequencing approach. Contig annotations revealed the presence of a potential new viral species in an Azerbaijani almond tree (Prunus amygdalus) and its genome sequence was completed. Its genomic organization is similar to that of the recently described Apricot vein clearing associated virus (AVCaV) for which two new isolates were also characterized, in a similar fashion, from two Japanese plums (Prunus salicina) from a French germplasm collection. The amino acid identity values between the four proteins encoded by the genome of the new virus have identity levels with those of AVCaV which fall clearly outside the species demarcation criteria. The new virus should therefore be considered as a new species for which the name of Caucasus prunus virus (CPrV) has been proposed. Phylogenetic relationships and nucleotide comparisons suggested that together with AVCaV, CPrV could define a new genus (proposed name: Prunevirus) in the family Betaflexiviridae. A molecular test targeting both members of the new genus was developed, allowing the detection of additional AVCaV isolates, and therefore extending the known geographical distribution and the host range of AVCaV. Moreover, the phylogenetic trees reconstructed with the amino acid sequences of replicase, movement and coat proteins of representative Betaflexiviridae members suggest that Citrus leaf blotch virus (CLBV, type member of the genus Citrivirus) may have evolved from a recombination event involving a Prunevirus, further highlighting the importance of recombination as a driving force in Betaflexiviridae evolution. The sequences reported in the present manuscript have been deposited in the GenBank database under accession numbers KM507061-KM504070.
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Affiliation(s)
- Armelle Marais
- INRA, UMR 1332 BFP, Villenave d’Ornon, France
- Université de Bordeaux, UMR 1332 BFP, Villenave d’Ornon, France
- * E-mail:
| | - Chantal Faure
- INRA, UMR 1332 BFP, Villenave d’Ornon, France
- Université de Bordeaux, UMR 1332 BFP, Villenave d’Ornon, France
| | - Eldar Mustafayev
- Genetic Resource Institute of the Azerbaijan National Academy of Sciences, Baku, Azerbaijan
| | - Thierry Candresse
- INRA, UMR 1332 BFP, Villenave d’Ornon, France
- Université de Bordeaux, UMR 1332 BFP, Villenave d’Ornon, France
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Kalinowska E, Marsella-Herrick P, Fuchs M. Genetic variability of blueberry scorch virus isolates from highbush blueberry in New York State. Arch Virol 2015; 160:1537-42. [PMID: 25809019 DOI: 10.1007/s00705-015-2402-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 03/15/2015] [Indexed: 11/28/2022]
Abstract
The genetic variability of blueberry scorch virus (BlScV) isolates from New York was determined within a portion of the RNA-dependent RNA polymerase gene and the triple gene block and coat protein (CP) genes. Phylogenetic analysis of 19 New York isolates and other isolates for which sequence information is available in GenBank revealed two distinct clades, regardless of the coding region analyzed, and limited variability within (0.029 ± 0.007) and between (0.183 ± 0.032) phylogroups. Recombination events were identified in the CP gene of three New York isolates, and codons of the five BlScV genes characterized were found to be under neutral or negative selective pressure.
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Affiliation(s)
- Elżbieta Kalinowska
- Department of Plath Pathology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, 159 Nowoursynowska Street, 02-776, Warsaw, Poland,
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