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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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2
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Chaves LFG, Ferro MMM, de Lima MO, Assunção IP, Lima GSA, da Silva SJC. Cnidoscolus mild mosaic virus: a new bipartite begomovirus isolated from Cnidoscolus urens in Brazil. Arch Virol 2022; 167:1003-1005. [PMID: 35147804 DOI: 10.1007/s00705-022-05367-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/08/2021] [Indexed: 11/27/2022]
Abstract
A novel bipartite begomovirus infecting Cnidoscolus urens (Euphorbiaceae) from Pernambuco State, Brazil, has been characterized. The complete DNA-A (2657 nt) and DNA-B (2622 nt) components of the viral isolates show the typical genome organization of New World bipartite begomoviruses. DNA-A of the isolates had the highest percentage of nucleotide sequence identity (88.6-88.9%) to cnidoscolus mosaic leaf deformation virus. Based on the current classification criteria for the genus Begomovirus, the virus infecting C. urens should be considered a new member of the genus, and the name "cnidoscolus mild mosaic virus" is proposed for the virus, and the name "Begomovirus caboniensis" is proposed for its species.
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Affiliation(s)
- Lívia F G Chaves
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil.
| | - Mayra M M Ferro
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Mayara O de Lima
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Iraildes P Assunção
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Gaus S A Lima
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Sarah J C da Silva
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
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3
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Fiallo-Olivé E, Bastidas L, Chirinos DT, Navas-Castillo J. Insights into Emerging Begomovirus-Deltasatellite Complex Diversity: The First Deltasatellite Infecting Legumes. BIOLOGY 2021; 10:1125. [PMID: 34827118 PMCID: PMC8615175 DOI: 10.3390/biology10111125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 11/30/2022]
Abstract
Begomoviruses and associated DNA satellites are involved in pathosystems that include many cultivated and wild dicot plants and the whitefly vector Bemisia tabaci. A survey of leguminous plants, both crops and wild species, was conducted in Venezuela, an understudied country, to determine the presence of begomoviruses. Molecular analysis identified the presence of bipartite begomoviruses in 37% of the collected plants. Four of the six begomoviruses identified constituted novel species, and two others had not been previously reported in Venezuela. In addition, a novel deltasatellite (cabbage leaf curl deltasatellite, CabLCD) was found to be associated with cabbage leaf curl virus (CabLCV) in several plant species. CabLCD was the first deltasatellite found to infect legumes and the first found in the New World to infect a crop plant. Agroinoculation experiments using Nicotiana benthamiana plants and infectious viral clones confirmed that CabLCV acts as a helper virus for CabLCD. The begomovirus-deltasatellite complex described here is also present in wild legume plants, suggesting the possible role of these plants in the emergence and establishment of begomoviral diseases in the main legume crops in the region. Pathological knowledge of these begomovirus-deltasatellite complexes is fundamental to develop control methods to protect leguminous crops from the diseases they cause.
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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, Avenida Dr. Wienberg s/n, 29750 Algarrobo-Costa, Málaga, Spain;
| | - Liseth Bastidas
- Departamento Fitosanitario, Facultad de Agronomía, Universidad del Zulia, Maracaibo 4005, Zulia, Venezuela;
| | - Dorys T. Chirinos
- Facultad de Ingeniería Agronómica, Universidad Técnica de Manabí, Portoviejo 130105, Manabí, Ecuador;
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Avenida Dr. Wienberg s/n, 29750 Algarrobo-Costa, Málaga, Spain;
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4
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Mendes ALSF, Melo AM, Ramos-Sobrinho R, Silva SJC, Ferro CG, Ferro MMM, Murilo Zerbini F, Lima GSA, Assunção IP. High molecular diversity and divergent subpopulations of the begomovirus cnidoscolus mosaic leaf deformation virus associated with Cnidoscolus urens. Arch Virol 2021; 166:3289-3299. [PMID: 34554304 DOI: 10.1007/s00705-021-05245-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/07/2021] [Indexed: 11/26/2022]
Abstract
Begomoviruses have circular, single-stranded DNA genomes encapsidated into twinned quasi-icosahedral particles and are transmitted by whiteflies of the Bemisia tabaci sibling group. Begomoviruses infect cultivated and non-cultivated plants, causing great losses in economically important crops worldwide. To better understand the genetic diversity of begomoviruses infecting the non-cultivated host Cnidoscolus urens, leaf samples exhibiting virus-like symptoms were collected in different localities in the state of Alagoas, Brazil, during 2015 and 2016. Forty-two complete DNA-A sequences were cloned and sequenced by the Sanger method. Based on nucleotide sequence comparisons, the 42 new isolates were identified as the bipartite begomovirus cnidoscolus mosaic leaf deformation virus (CnMLDV). The CnMLDV isolates were clustered in two phylogenetic groups (clusters I and II) corresponding to their sampling areas, and the high value of Wright's F fixation index observed for the DNA-A sequences suggests population structuring. At least seven independent intraspecies recombination events were predicted among CnMLDV isolates, with recombination breakpoints located in the common region (CR) and in the CP and Rep genes. Also, a high per site nucleotide diversity (π) was observed for CnMLDV isolates, with CP being significantly more variable than Rep. Despite the high genetic variability, strong negative or purifying selection was identified as the main selective force acting upon CP and Rep.
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Affiliation(s)
- Adso L S F Mendes
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Aline M Melo
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | | | - Sarah J C Silva
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Camila G Ferro
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
- Departamento de Fitopatologia e Nematologia, Universidade de São Paulo, Piracicaba, 13418-900, Brazil
| | - Mayra M M Ferro
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - F Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
| | - Gaus S A Lima
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Iraildes P Assunção
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil.
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Fiallo-Olivé E, Navas-Castillo J. Molecular and Biological Characterization of a New World Mono-/Bipartite Begomovirus/Deltasatellite Complex Infecting Corchorus siliquosus. Front Microbiol 2020; 11:1755. [PMID: 32793176 PMCID: PMC7390960 DOI: 10.3389/fmicb.2020.01755] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/06/2020] [Indexed: 12/02/2022] Open
Abstract
The genus Begomovirus (family Geminiviridae) is the largest genus in the entire virosphere, with more than 400 species recognized. Begomoviruses are single-stranded DNA plant viruses transmitted by whiteflies of the Bemisia tabaci complex and are considered one of the most important groups of emerging plant viruses in tropical and subtropical regions. Several types of DNA satellites have been described to be associated with begomoviruses: betasatellites, alphasatellites, and deltasatellites. Recently, a family of single-stranded DNA satellites associated with begomoviruses has been created, Tolecusatellitidae, including the genera Betasatellite and Deltasatellite. In this work, we analyzed the population of begomoviruses and associated DNA satellites present in Corchorus siliquosus, a malvaceous plant growing wild in Central America, southeastern North America and the Caribbean, collected in Cuba. The genomes of isolates of two New World begomoviruses [(Desmodium leaf distortion virus (DesLDV) and Corchorus yellow vein Cuba virus (CoYVCUV)] and two deltasatellites [tomato yellow leaf distortion deltasatellite 2 (TYLDD2) and Desmodium leaf distortion deltasatellite (DesLDD)] have been cloned and sequenced from plants showing yellow vein symptoms. Isolates of one of the begomoviruses, CoYVCUV, and one of the deltasatellites, DesLDD, represent novel species. Experiments with infectious clones showed the monopartite nature of CoYVCUV and that DesLDD utilizes the bipartite DesLDV as helper virus, but not the monopartite CoYVCUV. Also, CoYVCUV was shown to infect common bean in addition to Nicotiana benthamiana. This is the first time that (i) a monopartite New World begomovirus is found in a host other than tomato and (ii) deltasatellites have been found in C. siliquosus, thus extending the host and helper virus ranges of this recently recognized class of DNA satellites.
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Affiliation(s)
- Elvira Fiallo-Olivé
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Consejo Superior de Investigaciones Cient ficas - Universidad de Málaga (IHSM-CSIC-UMA), Málaga, Spain
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Consejo Superior de Investigaciones Cient ficas - Universidad de Málaga (IHSM-CSIC-UMA), Málaga, Spain
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6
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Croton golden mosaic virus: a new bipartite begomovirus isolated from Croton hirtus in Colombia. Arch Virol 2018; 163:3199-3202. [PMID: 30097742 DOI: 10.1007/s00705-018-3989-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 06/27/2018] [Indexed: 10/28/2022]
Abstract
A new begomovirus infecting Croton hirtus (Euphorbiaceae) from Colombia has been characterized. The complete DNA-A and DNA-B components were determined to be 2613 and 2551 nt in length, respectively, showing the typical genome organization of bipartite New World begomoviruses. DNA-A showed the highest nucleotide sequence identity (81.2%) to sida yellow mottle virus (JN411687), a begomovirus isolated from Sida rhombifolia in Cuba. Based on the current ICTV species demarcation criterion for the genus Begomovirus, we report a new member of this genus infecting C. hirtus. We propose that it be named Croton golden mosaic virus (CroGMV), based on the symptoms observed in the weed. Phylogenetic analysis revealed that CroGMV segregates into a single clade and has some relationship with viruses from Central America and the Caribbean. CroGMV is the first Croton-infecting bipartite begomovirus reported in the world.
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7
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Fiallo-Olivé E, Chirinos DT, Geraud-Pouey F, Navas-Castillo J. Complete genome sequence of jacquemontia yellow vein virus, a novel begomovirus infecting Jacquemontia tamnifolia in Venezuela. Arch Virol 2017; 162:2463-2466. [PMID: 28434100 DOI: 10.1007/s00705-017-3372-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/03/2017] [Indexed: 10/19/2022]
Abstract
Wild plants of the family Convolvulaceae are hosts for a few New World begomoviruses (genus Begomovirus, family Geminiviridae). In this work, we report the complete genome sequence of a new begomovirus infecting the wild convolvulaceous plant Jacquemontia tamnifolia in Venezuela. The cloned bipartite genome showed the organization of typical New World begomoviruses and was found to be phylogenetically related to those of begomoviruses from Venezuela and other Caribbean countries. Several recombination events have been shown to have occurred involving genome fragment exchange with related begomoviruses infecting crops such as tomato and cucurbits and wild plants, including Jacquemontia sp. We propose the name jacquemontia yellow vein virus (JacYVV) for this new begomovirus.
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Affiliation(s)
- Elvira Fiallo-Olivé
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental "La Mayora", 29750, Algarrobo-Costa, Málaga, Spain.
| | - Dorys T Chirinos
- Unidad Técnica Fitosanitaria, Facultad de Agronomía, Universidad del Zulia, Maracaibo, 4005, Zulia, Venezuela.,Laboratorio de Entomología, Facultad de Ciencias Agrarias, Universidad Agraria del Ecuador, Guayaquil, Ecuador
| | - Francis Geraud-Pouey
- Unidad Técnica Fitosanitaria, Facultad de Agronomía, Universidad del Zulia, Maracaibo, 4005, Zulia, Venezuela
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental "La Mayora", 29750, Algarrobo-Costa, Málaga, Spain
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8
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Melo AM, Silva SJC, Ramos-Sobrinho R, Ferro MMM, Assunção IP, Lima GSA. Cnidoscolus mosaic leaf deformation virus: a novel begomovirus infecting euphorbiaceous plants in Brazil. Arch Virol 2016; 161:2605-8. [PMID: 27278930 DOI: 10.1007/s00705-016-2919-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 05/31/2016] [Indexed: 10/21/2022]
Abstract
Begomoviruses have been detected infecting the weed Cnidoscolus urens (family Euphorbiaceae) since 2004, but the viral species to which these viruses belonged was not known. Here, we report for the first time the complete genome sequence of a bipartite begomovirus obtained from C. urens collected in the state of Alagoas, Brazil. This isolate met the criteria to be classified as a member of a new begomovirus species, and the tentative name cnidoscolus mosaic leaf deformation virus (CnMLDV) is proposed. Pairwise sequence comparisons and phylogenetic analysis showed that the DNA-A genomic component of CnMLDV is most closely related to that of passionfruit severe leaf distortion virus, with 86.3 % nucleotide sequence identity.
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Affiliation(s)
- Aline M Melo
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Sarah J C Silva
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Roberto Ramos-Sobrinho
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Mayra M M Ferro
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Iraildes P Assunção
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Gaus S A Lima
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil.
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Fiallo-Olivé E, Márquez-Martín B, Hassan I, Chirinos DT, Geraud-Pouey F, Navas-Castillo J, Moriones E. Complete genome sequences of two novel begomoviruses infecting common bean in Venezuela. Arch Virol 2012. [PMID: 23178970 DOI: 10.1007/s00705-012-1545-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The complete genome sequences of isolates of two new bipartite begomoviruses (genus Begomovirus, family Geminiviridae) found infecting common bean in Venezuela are provided. The names proposed for each of these viruses are "bean yellow chlorosis virus" (BYCV) and "bean white chlorosis mosaic virus" (BWCMV). Phylogenetic analysis showed that they segregated in two distinct clades of New World begomoviruses. This is the first report of begomoviruses infecting common bean in Venezuela.
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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, Estación Experimental "La Mayora", Algarrobo-Costa, 29750 Málaga, Spain
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