1
|
Jaybhaye SG, Chavhan RL, Hinge VR, Deshmukh AS, Kadam US. CRISPR-Cas assisted diagnostics of plant viruses and challenges. Virology 2024; 597:110160. [PMID: 38955083 DOI: 10.1016/j.virol.2024.110160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/04/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024]
Abstract
Plant viruses threaten global food security by infecting commercial crops, highlighting the critical need for efficient virus detection to enable timely preventive measures. Current techniques rely on polymerase chain reaction (PCR) for viral genome amplification and require laboratory conditions. This review explores the applications of CRISPR-Cas assisted diagnostic tools, specifically CRISPR-Cas12a and CRISPR-Cas13a/d systems for plant virus detection and analysis. The CRISPR-Cas12a system can detect viral DNA/RNA amplicons and can be coupled with PCR or isothermal amplification, allowing multiplexed detection in plants with mixed infections. Recent studies have eliminated the need for expensive RNA purification, streamlining the process by providing a visible readout through lateral flow strips. The CRISPR-Cas13a/d system can directly detect viral RNA with minimal preamplification, offering a proportional readout to the viral load. These approaches enable rapid viral diagnostics within 30 min of leaf harvest, making them valuable for onsite field applications. Timely identification of diseases associated with pathogens is crucial for effective treatment; yet developing rapid, specific, sensitive, and cost-effective diagnostic technologies remains challenging. The current gold standard, PCR technology, has drawbacks such as lengthy operational cycles, high costs, and demanding requirements. Here we update the technical advancements of CRISPR-Cas in viral detection, providing insights into future developments, versatile applications, and potential clinical translation. There is a need for approaches enabling field plant viral nucleic acid detection with high sensitivity, specificity, affordability, and portability. Despite challenges, CRISPR-Cas-mediated pathogen diagnostic solutions hold robust capabilities, paving the way for ideal diagnostic tools. Alternative applications in virus research are also explored, acknowledging the technology's limitations and challenges.
Collapse
Affiliation(s)
- Siddhant G Jaybhaye
- Vilasrao Deshmukh College of Agricultural Biotechnology, Nanded Road, Latur, Vasantrao Naik Marathwada Krishi Vidyapeeth, Maharashtra, India
| | - Rahul L Chavhan
- Vilasrao Deshmukh College of Agricultural Biotechnology, Nanded Road, Latur, Vasantrao Naik Marathwada Krishi Vidyapeeth, Maharashtra, India
| | - Vidya R Hinge
- Vilasrao Deshmukh College of Agricultural Biotechnology, Nanded Road, Latur, Vasantrao Naik Marathwada Krishi Vidyapeeth, Maharashtra, India
| | - Abhijit S Deshmukh
- Vilasrao Deshmukh College of Agricultural Biotechnology, Nanded Road, Latur, Vasantrao Naik Marathwada Krishi Vidyapeeth, Maharashtra, India
| | - Ulhas S Kadam
- Plant Molecular Biology and Biotechnology Research Centre (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Gyeongsangnam-do, South Korea.
| |
Collapse
|
2
|
Mahillon M, Brodard J, Schoen R, Botermans M, Dubuis N, Groux R, Pannell JR, Blouin AG, Schumpp O. Revisiting a pollen-transmitted ilarvirus previously associated with angular mosaic of grapevine. Virus Res 2024; 344:199362. [PMID: 38508402 PMCID: PMC10979282 DOI: 10.1016/j.virusres.2024.199362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 03/22/2024]
Abstract
We report the characterization of a novel tri-segmented RNA virus infecting Mercurialis annua, a common crop weed and model species in plant science. The virus, named "Mercurialis latent virus" (MeLaV) was first identified in a mixed infection with the recently described Mercurialis orthotospovirus 1 (MerV1) on symptomatic plants grown in glasshouses in Lausanne (Switzerland). Both viruses were found to be transmitted by Thrips tabaci, which presumably help the inoculation of infected pollen in the case of MeLaV. Complete genome sequencing of the latter revealed a typical ilarviral architecture and close phylogenetic relationship with members of the Ilarvirus subgroup 1. Surprisingly, a short portion of MeLaV replicase was found to be identical to the partial sequence of grapevine angular mosaic virus (GAMV) reported in Greece in the early 1990s. However, we have compiled data that challenge the involvement of GAMV in angular mosaic of grapevine, and we propose alternative causal agents for this disorder. In parallel, three highly-conserved MeLaV isolates were identified in symptomatic leaf samples in The Netherlands, including a herbarium sample collected in 1991. The virus was also traced in diverse RNA sequencing datasets from 2013 to 2020, corresponding to transcriptomic analyses of M. annua and other plant species from five European countries, as well as metaviromics analyses of bees in Belgium. Additional hosts are thus expected for MeLaV, yet we argue that infected pollen grains have likely contaminated several sequencing datasets and may have caused the initial characterization of MeLaV as GAMV.
Collapse
Affiliation(s)
- Mathieu Mahillon
- Research group Virology, Bacteriology and Phytoplasmology, Department of Plant protection, Agroscope, Nyon, Switzerland
| | - Justine Brodard
- Research group Virology, Bacteriology and Phytoplasmology, Department of Plant protection, Agroscope, Nyon, Switzerland
| | - Ruben Schoen
- Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), Netherlands Food and Consumer Product Safety Authority, Wageningen, The Netherlands
| | - Marleen Botermans
- Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), Netherlands Food and Consumer Product Safety Authority, Wageningen, The Netherlands
| | - Nathalie Dubuis
- Research group Virology, Bacteriology and Phytoplasmology, Department of Plant protection, Agroscope, Nyon, Switzerland
| | - Raphaël Groux
- Research group Virology, Bacteriology and Phytoplasmology, Department of Plant protection, Agroscope, Nyon, Switzerland
| | - John R Pannell
- Department of Ecology and Evolution, University of Lausanne (UNIL), Switzerland
| | - Arnaud G Blouin
- Research group Virology, Bacteriology and Phytoplasmology, Department of Plant protection, Agroscope, Nyon, Switzerland
| | - Olivier Schumpp
- Research group Virology, Bacteriology and Phytoplasmology, Department of Plant protection, Agroscope, Nyon, Switzerland.
| |
Collapse
|
3
|
Qureshi MA, Lal A, Nawaz-ul-Rehman MS, Vo TTB, Sanjaya GNPW, Ho PT, Nattanong B, Kil EJ, Jahan SMH, Lee KY, Tsai CW, Dao HT, Hoat TX, Aye TT, Win NK, Lee J, Kim SM, Lee S. Emergence of Asian endemic begomoviruses as a pandemic threat. FRONTIERS IN PLANT SCIENCE 2022; 13:970941. [PMID: 36247535 PMCID: PMC9554542 DOI: 10.3389/fpls.2022.970941] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/05/2022] [Indexed: 06/16/2023]
Abstract
Plant viruses are responsible for the most devastating and commercially significant plant diseases, especially in tropical and subtropical regions. The genus begomovirus is the largest one in the family Geminiviridae, with a single-stranded DNA genome, either monopartite or bipartite. Begomoviruses are transmitted by insect vectors, such as Bemisia tabaci. Begomoviruses are the major causative agents of diseases in agriculture globally. Because of their diversity and mode of evolution, they are thought to be geographic specific. The emerging begomoviruses are of serious concern due to their increasing host range and geographical expansion. Several begomoviruses of Asiatic origin have been reported in Europe, causing massive economic losses; insect-borne transmission of viruses is a critical factor in virus outbreaks in new geographical regions. This review highlights crucial information regarding Asia's four emerging and highly destructive begomoviruses. We also provided information regarding several less common but still potentially important pathogens of different crops. This information will aid possible direction of future studies in adopting preventive measures to combat these emerging viruses.
Collapse
Affiliation(s)
- Muhammad Amir Qureshi
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Aamir Lal
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | | | - Thuy Thi Bich Vo
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | | | - Phuong Thi Ho
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Bupi Nattanong
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Eui-Joon Kil
- Department of Plant Medicals, Andong National University, Andong, South Korea
| | | | - Kyeong-Yeoll Lee
- Division of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Chi-Wei Tsai
- Department of Entomology, National Taiwan University, Taipei, Taiwan
| | - Hang Thi Dao
- Plant Protection Research Institute, Hanoi, Vietnam
| | | | - Tin-Tin Aye
- Department of Entomology, Yezin Agricultural University, Yezin, Myanmar
| | - Nang Kyu Win
- Department of Plant Pathology, Yezin Agricultural University, Yezin, Myanmar
| | - Jangha Lee
- Crop Breeding Research Center, NongWoo Bio, Yeoju, South Korea
| | - Sang-Mok Kim
- Plant Quarantine Technology Center, Animal and Plant Quarantine Agency, Gimcheon, South Korea
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| |
Collapse
|
4
|
The invasion biology of tomato begomoviruses in Costa Rica reveals neutral synergism that may lead to increased disease pressure and economic loss. Virus Res 2022; 317:198793. [DOI: 10.1016/j.virusres.2022.198793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/25/2022] [Accepted: 04/29/2022] [Indexed: 11/22/2022]
|
5
|
Maliano MR, Melgarejo TA, Rojas MR, Barboza N, Gilbertson RL. The Begomovirus Species Melon Chlorotic Leaf Curl Virus is Composed of Two Highly Divergent Strains that Differ in Their Genetic and Biological Properties. PLANT DISEASE 2021; 105:3162-3170. [PMID: 33591835 DOI: 10.1094/pdis-08-20-1759-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Since the early 1990s, squash production in Costa Rica has been affected by a whitefly-transmitted disease characterized by stunting and yellow mottling of leaves. The squash yellow mottle disease (SYMoD) was shown to be associated with a bipartite begomovirus, originally named squash yellow mild mottle virus (SYMMoV). It was subsequently established that SYMMoV is a strain of melon chlorotic leaf curl virus (MCLCuV), a bipartite begomovirus that causes a chlorotic leaf curl disease of melons in Guatemala. In the present study, the complete sequences of the DNA-A and DNA-B components of a new isolate of the strain MCLCuV-Costa Rica (MCLCuV-CR) were determined. Comparisons of full-length DNA-A sequences revealed 97% identity with a previously characterized isolate of MCLCuV-CR and identities of 90 to 91% with those of isolates of the strain MCLCuV-Guatemala (MCLCuV-GT), which is below or at the current begomovirus species demarcation threshold of 91%. A more extensive analysis of the MCLCuV-CR and -GT sequences revealed substantial divergence in both components and different histories of recombination for the DNA-A components. The cloned full-length DNA-A and DNA-B components of this new MCLCuV-CR isolate were infectious and induced SYMoD in a range of squashes and in pumpkin, thereby fulfilling Koch's postulates for this disease. However, in contrast to MCLCuV-GT, MCLCuV-CR induced mild symptoms in watermelon and no symptoms in melon and cucumber. Taken together, our results indicate that MCLCuV-CR and -GT have substantially diverged, genetically and biologically, and have evolved to cause distinct diseases of different cucurbit crops. Taxonomically, these viruses are at the strain/species boundary, but retain the designation as strains of Melon chlorotic leaf curl virus under current International Committee on Taxonomy guidelines.
Collapse
Affiliation(s)
- Minor R Maliano
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | - Tomas A Melgarejo
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | - Maria R Rojas
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | - Natalia Barboza
- Centro de Investigación en Biología Celular y Molecular, Escuela de Tecnología de Alimentos, Centro Nacional en Ciencia y Tecnología de Alimentos, Universidad de Costa Rica, 2060 San José, Costa Rica
| | - Robert L Gilbertson
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| |
Collapse
|
6
|
Maliano MR, Macedo MA, Rojas MR, Gilbertson RL. Weed-infecting viruses in a tropical agroecosystem present different threats to crops and evolutionary histories. PLoS One 2021; 16:e0250066. [PMID: 33909644 PMCID: PMC8081230 DOI: 10.1371/journal.pone.0250066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/30/2021] [Indexed: 01/21/2023] Open
Abstract
In the Caribbean Basin, malvaceous weeds commonly show striking golden/yellow mosaic symptoms. Leaf samples from Malachra sp. and Abutilon sp. plants with these symptoms were collected in Hispaniola from 2014 to 2020. PCR tests with degenerate primers revealed that all samples were infected with a bipartite begomovirus, and sequence analyses showed that Malachra sp. plants were infected with tobacco leaf curl Cuba virus (TbLCuCV), whereas the Abutilon sp. plants were infected with a new bipartite begomovirus, tentatively named Abutilon golden yellow mosaic virus (AbGYMV). Phylogenetic analyses showed that TbLCuCV and AbGYMV are distinct but closely related species, which are most closely related to bipartite begomoviruses infecting weeds in the Caribbean Basin. Infectious cloned DNA-A and DNA-B components were used to fulfilled Koch's postulates for these diseases of Malachra sp. and Abutilon sp. In host range studies, TbLCuCV also induced severe symptoms in Nicotiana benthamiana, tobacco and common bean plants; whereas AbGYMV induced few or no symptoms in plants of these species. Pseudorecombinants generated with the infectious clones of these viruses were highly infectious and induced severe symptoms in N. benthamiana and Malachra sp., and both viruses coinfected Malachra sp., and possibly facilitating virus evolution via recombination and pseudorecombination. Together, our results suggest that TbLCuCV primarily infects Malachra sp. in the Caribbean Basin, and occasionally spills over to infect and cause disease in crops; whereas AbGYMV is well-adapted to an Abutilon sp. in the Dominican Republic and has not been reported infecting crops.
Collapse
Affiliation(s)
- Minor R. Maliano
- Department of Plant Pathology, University of California, Davis, California, United States of America
| | - Mônica A. Macedo
- Department of Plant Pathology, University of California, Davis, California, United States of America
- Federal Institute of Education, Science and Technology Goiano, Campus Urutaí, Goias, Brazil
| | - Maria R. Rojas
- Department of Plant Pathology, University of California, Davis, California, United States of America
| | - Robert L. Gilbertson
- Department of Plant Pathology, University of California, Davis, California, United States of America
| |
Collapse
|
7
|
Alcaide C, Sardanyés J, Elena SF, Gómez P. Increasing temperature alters the within-host competition of viral strains and influences virus genetic variability. Virus Evol 2021; 7:veab017. [PMID: 33815829 PMCID: PMC8007957 DOI: 10.1093/ve/veab017] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Environmental conditions can affect viral accumulation, virulence and adaptation, which have implications in the disease outcomes and efficiency of control measures. Concurrently, mixed viral infections are relevant in plants, being their epidemiology shaped by within-host virus–virus interactions. However, the extent in which the combined effect of variations in abiotic components of the plant ecological niche and the prevalence of mixed infections affect the evolutionary dynamics of viral populations is not well understood. Here, we explore the interplay between ecological and evolutionary factors during viral infections and show that isolates of two strains of Pepino mosaic potexvirus coexisted in tomato plants in a temperature-dependent continuum between neutral and antagonistic interactions. After a long-term infection, the mutational analysis of the evolved viral genomes revealed strain-specific single-nucleotide polymorphisms that were modulated by the interaction between the type of infection and temperature. These results suggest that the temperature is an ecological driver of virus-virus interactions, with an effect on the genetic diversity of individual viruses that are co-infecting an individual host. This research provides insights into the effect that changes in host growth temperatures might have on the evolutionary dynamics of viral populations in mixed infections.
Collapse
Affiliation(s)
- Cristina Alcaide
- Departamento de Biología del Estrés y Patología Vegetal, Centro de Edafología y Biología Aplicada del Segura (CEBAS), CSIC, PO Box 164, 30100 Murcia, Spain
| | - Josep Sardanyés
- Centre de Recerca Matemàtica (CRM), Edifici C, Campus de Bellaterra, Cerdanyola del Vallès, Barcelona 08193, Spain
- Dynamical Systems and Computational Virology Associated Unit Instituto de Biología Integrativa de Sistemas (I2SysBio) - CRM, Edifici C, Campus de Bellaterra, Cerdanyola del Vallès, Barcelona 08193, Spain
| | - Santiago F Elena
- I2SysBio, CSIC-Universitat de València, Paterna, 46980 València, Spain
- The Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Pedro Gómez
- Departamento de Biología del Estrés y Patología Vegetal, Centro de Edafología y Biología Aplicada del Segura (CEBAS), CSIC, PO Box 164, 30100 Murcia, Spain
- Corresponding author: E-mail:
| |
Collapse
|
8
|
More P, Agarwal P, Anand A, Sanan-Mishra N, Agarwal PK. Artificial miRNA mediated resistance in tobacco against Jatropha leaf curl Gujarat virus by targeting RNA silencing suppressors. Sci Rep 2021; 11:890. [PMID: 33441589 PMCID: PMC7806619 DOI: 10.1038/s41598-020-79134-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/03/2020] [Indexed: 11/09/2022] Open
Abstract
The leaf curl disease of Jatropha caused by geminiviruses results in heavy economic losses. In the present study, we report the identification of a new strain of a Jatropha leaf curl Gujarat virus (JLCuGV), which encodes six ORFs with each one having RNA silencing suppressor activity. Therefore, three artificial microRNAs (amiRNAs; C1/C4, C2/C3 and V1/V2) were designed employing overlapping regions, each targeting two ORFs of JLCuGV genomic DNA and transformed in tobacco. The C1/C4 and C2/C3 amiRNA transgenics were resistant while V1/V2 amiRNA transgenics were tolerant against JLCuGV. The relative level of amiRNA inversely related to viral load indicating a correlation with disease resistance. The assessment of photosynthetic parameters suggests that the transgenics perform significantly better in response to JLCuGV infiltration as compared to wild type (WT). The metabolite contents were not altered remarkably in amiRNA transgenics, but sugar metabolism and tricarboxylic acid (TCA) cycle showed noticeable changes in WT on virus infiltration. The overall higher methylation and demethylation observed in amiRNA transgenics correlated with decreased JLCuGV accumulation. This study demonstrates that amiRNA transgenics showed enhanced resistance to JLCuGV while efficiently maintaining normalcy in their photosynthesis and metabolic pathways as well as homeostasis in the methylation patterns.
Collapse
Affiliation(s)
- Prashant More
- Plant Omics Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Gijubhai Badheka Marg, 364 002, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Parinita Agarwal
- Plant Omics Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Gijubhai Badheka Marg, 364 002, Bhavnagar, Gujarat, India.
| | - Abhishek Anand
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110 067, India
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110 067, India
| | - Pradeep K Agarwal
- Plant Omics Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Gijubhai Badheka Marg, 364 002, Bhavnagar, Gujarat, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| |
Collapse
|
9
|
Kumar M, Bharti R, Ranjan T. The Evolutionary Significance of Generalist Viruses with Special Emphasis on Plant Viruses and their Hosts. Open Virol J 2020. [DOI: 10.2174/1874357902014010022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The host range of a virus is defined as the number of species a virus potentially infects. The specialist virus infects one or few related species while the generalist virus infects several different species, possibly in different families. Origin of generalist viruses from their specialist nature and the expansion of the host range of the generalist virus occur with the host shift event in which the virus encounters and adapts to a new host. Host shift events have resulted in the majority of the newly emerging viral diseases. This review discusses the advantages and disadvantages of generalist over specialist viruses and the unique features of plant viruses and their hosts that result in a higher incidence of generalist viruses in plants.
Collapse
|
10
|
Hančinský R, Mihálik D, Mrkvová M, Candresse T, Glasa M. Plant Viruses Infecting Solanaceae Family Members in the Cultivated and Wild Environments: A Review. PLANTS 2020; 9:plants9050667. [PMID: 32466094 PMCID: PMC7284659 DOI: 10.3390/plants9050667] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/22/2020] [Accepted: 05/22/2020] [Indexed: 12/01/2022]
Abstract
Plant viruses infecting crop species are causing long-lasting economic losses and are endangering food security worldwide. Ongoing events, such as climate change, changes in agricultural practices, globalization of markets or changes in plant virus vector populations, are affecting plant virus life cycles. Because farmer’s fields are part of the larger environment, the role of wild plant species in plant virus life cycles can provide information about underlying processes during virus transmission and spread. This review focuses on the Solanaceae family, which contains thousands of species growing all around the world, including crop species, wild flora and model plants for genetic research. In a first part, we analyze various viruses infecting Solanaceae plants across the agro-ecological interface, emphasizing the important role of virus interactions between the cultivated and wild zones as global changes affect these environments on both local and global scales. To cope with these changes, it is necessary to adjust prophylactic protection measures and diagnostic methods. As illustrated in the second part, a complex virus research at the landscape level is necessary to obtain relevant data, which could be overwhelming. Based on evidence from previous studies we conclude that Solanaceae plant communities can be targeted to address complete life cycles of viruses with different life strategies within the agro-ecological interface. Data obtained from such research could then be used to improve plant protection methods by taking into consideration environmental factors that are impacting the life cycles of plant viruses.
Collapse
Affiliation(s)
- Richard Hančinský
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 91701 Trnava, Slovakia; (R.H.); (D.M.); (M.M.)
| | - Daniel Mihálik
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 91701 Trnava, Slovakia; (R.H.); (D.M.); (M.M.)
- Institute of High Mountain Biology, University of Žilina, Univerzitná 8215/1, 01026 Žilina, Slovakia
- National Agricultural and Food Centre, Research Institute of Plant Production, Bratislavská cesta 122, 92168 Piešťany, Slovakia
| | - Michaela Mrkvová
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 91701 Trnava, Slovakia; (R.H.); (D.M.); (M.M.)
| | - Thierry Candresse
- INRAE, University Bordeaux, UMR BFP, 33140 Villenave d’Ornon, France;
| | - Miroslav Glasa
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 91701 Trnava, Slovakia; (R.H.); (D.M.); (M.M.)
- Biomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 84505 Bratislava, Slovakia
- Correspondence: ; Tel.: +421-2-5930-2447
| |
Collapse
|
11
|
Chen K, Khatabi B, Fondong VN. The AC4 Protein of a Cassava Geminivirus Is Required for Virus Infection. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:865-875. [PMID: 30699305 DOI: 10.1094/mpmi-12-18-0354-r] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Geminiviruses (family Geminiviridae) are among the most devastating plant viruses worldwide, causing severe damage in crops of economic and subsistence importance. These viruses have very compact genomes and many of the encoded proteins are multifunctional. Here, we investigated the role of the East African cassava mosaic Cameroon virus (EACMCV) AC4 on virus infectivity in Nicotiana benthamiana. Results showed that plants inoculated with EACMCV containing a knockout mutation in an AC4 open reading frame displayed symptoms 2 to 3 days later than plants inoculated with wild-type virus, and these plants recovered from infection, whereas plants inoculated with the wild-type virus did not. Curiously, when an additional mutation was made in the knockout mutant, the resulting double mutant virus completely failed to cause any apparent symptoms. Interestingly, the role of AC4 on virus infectivity appeared to be dependent on an encoded N-myristoylation motif that mediates cell membrane binding. We previously showed that EACMCV containing the AC4T38I mutant produced virus progeny characterized by second-site mutations and reversion to wild-type virus. These results were confirmed in this study using additional mutations. Together, these results show involvement of EACMCV AC4 in virus infectivity; they also suggest a role for the combined action of mutation and selection, under prevailing environmental conditions, on begomovirus genetic variation and diversity.
Collapse
Affiliation(s)
- Kegui Chen
- 1 Delaware State University, Department of Biological Sciences, Dover, Delaware, U.S.A
- 2 Kegui Chen, Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, P.R. China
| | - Behnam Khatabi
- 1 Delaware State University, Department of Biological Sciences, Dover, Delaware, U.S.A
- 3 Department of Natural Sciences, Department of Agriculture, Food and Resource Sciences, Princess Anne, MD 21853, U.S.A
| | - Vincent N Fondong
- 1 Delaware State University, Department of Biological Sciences, Dover, Delaware, U.S.A
| |
Collapse
|
12
|
Miozzi L, Vaira AM, Catoni M, Fiorilli V, Accotto GP, Lanfranco L. Arbuscular Mycorrhizal Symbiosis: Plant Friend or Foe in the Fight Against Viruses? Front Microbiol 2019; 10:1238. [PMID: 31231333 PMCID: PMC6558290 DOI: 10.3389/fmicb.2019.01238] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/17/2019] [Indexed: 11/13/2022] Open
Abstract
Plant roots establish interactions with several beneficial soil microorganisms including arbuscular mycorrhizal fungi (AMF). In addition to promoting plant nutrition and growth, AMF colonization can prime systemic plant defense and enhance tolerance to a wide range of environmental stresses and below-ground pathogens. A protective effect of the AMF against above-ground pathogens has also been described in different plant species, but it seems to largely rely on the type of attacker. Viruses are obligate biotrophic pathogens able to infect a large number of plant species, causing massive losses in crop yield worldwide. Despite their economic importance, information on the effect of the AM symbiosis on viral infection is limited and not conclusive. However, several experimental evidences, obtained under controlled conditions, show that AMF colonization may enhance viral infection, affecting susceptibility, symptomatology and viral replication, possibly related to the improved nutritional status and to the delayed induction of pathogenesis-related proteins in the mycorrhizal plants. In this review, we give an overview of the impact of the AMF colonization on plant infection by pathogenic viruses and summarize the current knowledge of the underlying mechanisms. For the cases where AMF colonization increases the susceptibility of plants to viruses, the term "mycorrhiza-induced susceptibility" (MIS) is proposed.
Collapse
Affiliation(s)
- Laura Miozzi
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Turin, Italy
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Turin, Italy
| | - Marco Catoni
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Valentina Fiorilli
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Gian Paolo Accotto
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Turin, Italy
| | - Luisa Lanfranco
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| |
Collapse
|
13
|
Maio F, Arroyo-Mateos M, Bobay BG, Bejarano ER, Prins M, van den Burg HA. A Lysine Residue Essential for Geminivirus Replication Also Controls Nuclear Localization of the Tomato Yellow Leaf Curl Virus Rep Protein. J Virol 2019; 93:e01910-18. [PMID: 30842320 PMCID: PMC6498046 DOI: 10.1128/jvi.01910-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/20/2019] [Indexed: 02/07/2023] Open
Abstract
Geminiviruses are single-stranded DNA (ssDNA) viruses that infect a wide range of plants. To promote viral replication, geminiviruses manipulate the host cell cycle. The viral protein Rep is essential to reprogram the cell cycle and then initiate viral DNA replication by interacting with a plethora of nuclear host factors. Even though many protein domains of Rep have been characterized, little is known about its nuclear targeting. Here, we show that one conserved lysine in the N-terminal part of Rep is pivotal for nuclear localization of the Rep protein from Tomato yellow leaf curl virus (TYLCV), with two other lysines also contributing to its nuclear import. Previous work had identified that these residues are essential for Rep from Tomato golden mosaic virus (TGMV) to interact with the E2 SUMO-conjugating enzyme (SCE1). We here show that mutating these lysines leads to nuclear exclusion of TYLCV Rep without compromising its interaction with SCE1. Moreover, the ability of TYLCV Rep to promote viral DNA replication also depends on this highly conserved lysine independently of its role in nuclear import of Rep. Our data thus reveal that this lysine potentially has a broad role in geminivirus replication, but its role in nuclear import and SCE1 binding differs depending on the Rep protein examined.IMPORTANCE Nuclear activity of the replication initiator protein (Rep) of geminiviruses is essential for viral replication. We now define that one highly conserved lysine is important for nuclear import of Rep from three different begomoviruses. To our knowledge, this is the first time that nuclear localization has been mapped for any geminiviral Rep protein. Our data add another key function to this lysine residue, besides its roles in viral DNA replication and interaction with host factors, such as the SUMO E2-conjugating enzyme.
Collapse
Affiliation(s)
- Francesca Maio
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Manuel Arroyo-Mateos
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, Málaga, Spain
| | - Benjamin G Bobay
- Duke University NMR Center, Duke University Medical Center, Durham, North Carolina, USA
- Department of Biochemistry, Duke University, Durham, North Carolina, USA
- Department of Radiology, Duke University, Durham, North Carolina, USA
| | - Eduardo R Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, Málaga, Spain
| | - Marcel Prins
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
- Keygene N.V., Wageningen, the Netherlands
| | - Harrold A van den Burg
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| |
Collapse
|
14
|
Sánchez-Campos S, Domínguez-Huerta G, Díaz-Martínez L, Tomás DM, Navas-Castillo J, Moriones E, Grande-Pérez A. Differential Shape of Geminivirus Mutant Spectra Across Cultivated and Wild Hosts With Invariant Viral Consensus Sequences. FRONTIERS IN PLANT SCIENCE 2018; 9:932. [PMID: 30013589 PMCID: PMC6036239 DOI: 10.3389/fpls.2018.00932] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 06/11/2018] [Indexed: 05/12/2023]
Abstract
Geminiviruses (family Geminiviridae) possess single-stranded circular DNA genomes that are replicated by cellular polymerases in plant host cell nuclei. In their hosts, geminivirus populations behave as ensembles of mutant and recombinant genomes, known as viral quasispecies. This favors the emergence of new geminiviruses with altered host range, facilitating new or more severe diseases or overcoming resistance traits. In warm and temperate areas several whitefly-transmitted geminiviruses of the genus Begomovirus cause the tomato yellow leaf curl disease (TYLCD) with significant economic consequences. TYLCD is frequently controlled in commercial tomatoes by using the dominant Ty-1 resistance gene. Over a 45 day period we have studied the diversification of three begomoviruses causing TYLCD: tomato yellow leaf curl virus (TYLCV), tomato yellow leaf curl Sardinia virus (TYLCSV) and tomato yellow leaf curl Malaga virus (TYLCMaV, a natural recombinant between TYLCV and TYLCSV). Viral quasispecies resulting from inoculation of geminivirus infectious clones were examined in plants of susceptible tomato (ty-1/ty-1), heterozygous resistant tomato (Ty-1/ty-1), common bean, and the wild reservoir Solanum nigrum. Differences in virus fitness across hosts were observed while viral consensus sequences remained invariant. However, the complexity and heterogeneity of the quasispecies were high, especially in common bean and the wild host. Interestingly, the presence or absence of the Ty-1 allele in tomato did not lead to differences in begomovirus mutant spectra. However, the fitness decrease of TYLCSV and TYLCV in tomato at 45 dpi might be related to an increase in CP (Coat protein) mutation frequency. In Solanum nigrum the recombinant TYLCMaV, which showed lower fitness than TYLCSV, at 45 dpi actively explored Rep (Replication associated protein) ORF but not the overlapping C4. Our results underline the importance of begomovirus mutant spectra during infections. This is especially relevant in the wild reservoir of the viruses, which has the potential to maintain highly diverse mutant spectra without modifying their consensus sequences.
Collapse
Affiliation(s)
- Sonia Sánchez-Campos
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Estación Experimental “La Mayora,” Algarrobo-Costa, Málaga, Spain
| | - Guillermo Domínguez-Huerta
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Estación Experimental “La Mayora,” Algarrobo-Costa, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Área de Genética, Facultad de Ciencias, Campus de Teatinos, Málaga, Spain
| | - Luis Díaz-Martínez
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Área de Genética, Facultad de Ciencias, Campus de Teatinos, Málaga, Spain
| | - Diego M. Tomás
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Estación Experimental “La Mayora,” Algarrobo-Costa, Málaga, Spain
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Estación Experimental “La Mayora,” Algarrobo-Costa, Málaga, Spain
| | - Enrique Moriones
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Estación Experimental “La Mayora,” Algarrobo-Costa, Málaga, Spain
| | - Ana Grande-Pérez
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Área de Genética, Facultad de Ciencias, Campus de Teatinos, Málaga, Spain
| |
Collapse
|
15
|
Tamisier L, Rousseau E, Barraillé S, Nemouchi G, Szadkowski M, Mailleret L, Grognard F, Fabre F, Moury B, Palloix A. Quantitative trait loci in pepper control the effective population size of two RNA viruses at inoculation. J Gen Virol 2017; 98:1923-1931. [PMID: 28691663 DOI: 10.1099/jgv.0.000835] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Infection of plants by viruses is a complex process involving several steps: inoculation into plant cells, replication in inoculated cells and plant colonization. The success of the different steps depends, in part, on the viral effective population size (Ne), defined as the number of individuals passing their genes to the next generation. During infection, the virus population will undergo bottlenecks, leading to drastic reductions in Ne and, potentially, to the loss of the fittest variants. Therefore, it is crucial to better understand how plants affect Ne. We aimed to (i) identify the plant genetic factors controlling Ne during inoculation, (ii) understand the mechanisms used by the plant to control Ne and (iii) compare these genetic factors with the genes controlling plant resistance to viruses. Ne was measured in a doubled-haploid population of Capsicum annuum. Plants were inoculated with either a Potato virus Y (PVY) construct expressing the green fluorescent protein or a necrotic variant of Cucumber mosaic virus (CMV). Newas assessed by counting the number of primary infection foci on cotyledons for PVY or the number of necrotic local lesions on leaves for CMV. The number of foci and lesions was correlated (r=0.57) and showed a high heritability (h2=0.93 for PVY and h2=0.98 for CMV). The Ne of the two viruses was controlled by both common quantitative trait loci (QTLs) and virus-specific QTLs, indicating the contribution of general and specific mechanisms. The PVY-specific QTL colocalizes with a QTL that reduces PVY accumulation and the capacity to break down a major-effect resistance gene.
Collapse
Affiliation(s)
- Lucie Tamisier
- INRA, UR1052 GAFL, Unité de Génétique et Amélioration des Fruits et Légumes, Domaine St Maurice - 67 Allée des Chênes, CS 60094, F-84143 Montfavet Cedex, France.,INRA, UR407 PV, Unité de Pathologie Végétale, Domaine St Maurice - 67 Allée des Chênes, CS 60094, F-84143 Montfavet Cedex, France
| | - Elsa Rousseau
- INRIA, Biocore Team, F-06902 Sophia Antipolis, France.,INRA, Université Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, Sophia Antipolis, France.,INRA, UR407 PV, Unité de Pathologie Végétale, Domaine St Maurice - 67 Allée des Chênes, CS 60094, F-84143 Montfavet Cedex, France
| | - Sebastien Barraillé
- INRA, UR407 PV, Unité de Pathologie Végétale, Domaine St Maurice - 67 Allée des Chênes, CS 60094, F-84143 Montfavet Cedex, France
| | - Ghislaine Nemouchi
- INRA, UR1052 GAFL, Unité de Génétique et Amélioration des Fruits et Légumes, Domaine St Maurice - 67 Allée des Chênes, CS 60094, F-84143 Montfavet Cedex, France
| | - Marion Szadkowski
- INRA, UR1052 GAFL, Unité de Génétique et Amélioration des Fruits et Légumes, Domaine St Maurice - 67 Allée des Chênes, CS 60094, F-84143 Montfavet Cedex, France
| | - Ludovic Mailleret
- INRIA, Biocore Team, F-06902 Sophia Antipolis, France.,INRA, Université Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, Sophia Antipolis, France
| | | | - Frederic Fabre
- INRA, UMR 1065 Santé et Agroécologie du Vignoble, BP 81, 33883 Villenave d'Ornon cedex, France
| | - Benoit Moury
- INRA, UR407 PV, Unité de Pathologie Végétale, Domaine St Maurice - 67 Allée des Chênes, CS 60094, F-84143 Montfavet Cedex, France
| | - Alain Palloix
- INRA, UR1052 GAFL, Unité de Génétique et Amélioration des Fruits et Légumes, Domaine St Maurice - 67 Allée des Chênes, CS 60094, F-84143 Montfavet Cedex, France
| |
Collapse
|
16
|
Saeed ST, Samad A. Emerging threats of begomoviruses to the cultivation of medicinal and aromatic crops and their management strategies. Virusdisease 2017; 28:1-17. [PMID: 28466050 PMCID: PMC5377872 DOI: 10.1007/s13337-016-0358-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 12/30/2016] [Indexed: 12/01/2022] Open
Abstract
Begomoviruses (family Geminiviridae) are responsible for extreme yield reduction in a number of economically important crops including medicinal and aromatic plants (MAPs). Emergence of new variants of viruses due to recombination and mutations in the genomes, modern cropping systems, introduction of susceptible plant varieties, global trade in agricultural products, and changes in climatic conditions are responsible for aggravating the begomovirus problems during the last two decades. This review summaries the current research work on begomoviruses affecting MAPs and provides various traditional and advanced strategies for the management of begomoviruses and vector in MAPs.
Collapse
Affiliation(s)
- Sana Tabanda Saeed
- Department of Plant Pathology, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015 India
| | - Abdul Samad
- Department of Plant Pathology, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015 India
| |
Collapse
|
17
|
Gilbertson RL, Batuman O, Webster CG, Adkins S. Role of the Insect SupervectorsBemisia tabaciandFrankliniella occidentalisin the Emergence and Global Spread of Plant Viruses. Annu Rev Virol 2015; 2:67-93. [DOI: 10.1146/annurev-virology-031413-085410] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Robert L. Gilbertson
- Department of Plant Pathology, University of California, Davis, California 95616; ,
| | - Ozgur Batuman
- Department of Plant Pathology, University of California, Davis, California 95616; ,
| | - Craig G. Webster
- US Horticultural Research Laboratory, Agricultural Research Service, US Department of Agriculture, Fort Pierce, Florida 34945; ,
| | - Scott Adkins
- US Horticultural Research Laboratory, Agricultural Research Service, US Department of Agriculture, Fort Pierce, Florida 34945; ,
| |
Collapse
|
18
|
Melgarejo TA, Kon T, Rojas MR, Paz-Carrasco L, Zerbini FM, Gilbertson RL. Characterization of a new world monopartite begomovirus causing leaf curl disease of tomato in Ecuador and Peru reveals a new direction in geminivirus evolution. J Virol 2013; 87:5397-413. [PMID: 23468482 PMCID: PMC3648196 DOI: 10.1128/jvi.00234-13] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 02/25/2013] [Indexed: 01/17/2023] Open
Abstract
All characterized whitefly-transmitted geminiviruses (begomoviruses) with origins in the New World (NW) have bipartite genomes composed of a DNA-A and DNA-B component. Recently, an NW begomovirus lacking a DNA-B component was associated with tomato leaf curl disease (ToLCD) in Peru, and it was named Tomato leaf deformation virus (ToLDeV). Here, we show that isolates of ToLDeV associated with ToLCD in Ecuador and Peru have a single, genetically diverse genomic DNA that is most closely related to DNA-A components of NW bipartite begomoviruses. Agroinoculation of multimeric clones of the genomic DNA of three ToLDeV genotypes (two variants and a strain) resulted in the development of tomato leaf curl symptoms indistinguishable from those of ToLCD in Ecuador and Peru. Biological properties of these ToLDeV genotypes were similar to those of Old World (OW) monopartite tomato-infecting begomoviruses, including lack of sap transmissibility, phloem limitation, a resistance phenotype in tomato germplasm with the Ty-1 gene, and functional properties of the V1 (capsid protein) and C4 genes. Differences in symptom phenotypes induced by the ToLDeV genotypes in tomato and Nicotiana benthamiana plants were associated with a highly divergent left intergenic region and C4 gene. Together, these results establish that ToLDeV is an emergent NW monopartite begomovirus that is causing ToLCD in Ecuador and Peru. This is the first report of an indigenous NW monopartite begomovirus, and evidence is presented that it emerged from the DNA-A component of a NW bipartite progenitor via convergent evolution and recombination.
Collapse
Affiliation(s)
- Tomas A. Melgarejo
- Department of Plant Pathology, University of California, Davis, Davis, California, USA
- Departamento de Fitopatologia, Universidad Nacional Agraria La Molina, Lima, Peru
| | - Tatsuya Kon
- Department of Plant Pathology, University of California, Davis, Davis, California, USA
| | - Maria R. Rojas
- Department of Plant Pathology, University of California, Davis, Davis, California, USA
| | - Lenin Paz-Carrasco
- Departamento de Fitopatologia/Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
- INIAP, EELS Enrique Ampuero Pareja, Guayaquil, Ecuador
| | - F. Murilo Zerbini
- Departamento de Fitopatologia/Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Robert L. Gilbertson
- Department of Plant Pathology, University of California, Davis, Davis, California, USA
| |
Collapse
|
19
|
Abstract
Viral metagenomics is the study of viruses in environmental samples, using next generation sequencing that produces very large data sets. For plant viruses, these studies are still relatively new, but are already indicating that our current knowledge grossly underestimates the diversity of these viruses. Some plant virus studies are using thousands of individual plants so that each sequence can be traced back to its precise host. These studies should allow for deeper ecological and evolutionary analyses. The finding of so many new plant viruses that do not cause any obvious symptoms in wild plant hosts certainly changes our perception of viruses and how they interact with their hosts. The major difficulty in these (as in all) metagenomic studies continues to be the need for better bioinformatics tools to decipher the large data sets. The implications of this new information on plant viruses for international agriculture remain to be addressed.
Collapse
Affiliation(s)
- Marilyn J Roossinck
- Center for Infectious Disease Dynamics, Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
| |
Collapse
|
20
|
Min BE, Feldman TS, Ali A, Wiley G, Muthukumar V, Roe BA, Roossinck M, Melcher U, Palmer MW, Nelson RS. Molecular characterization, ecology, and epidemiology of a novel Tymovirus in Asclepias viridis from Oklahoma. PHYTOPATHOLOGY 2012; 102:166-76. [PMID: 22026416 DOI: 10.1094/phyto-05-11-0154] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Native virus-plant interactions require more understanding and their study will provide a basis from which to identify potential sources of emerging destructive viruses in crops. A novel tymovirus sequence was detected in Asclepias viridis (green milkweed), a perennial growing in a natural setting in the Tallgrass Prairie Preserve (TGPP) of Oklahoma. It was abundant within and frequent among A. viridis plants and, to varying extents, within other dicotyledonous and one grass (Panicum virgatum) species obtained from the TGPP. Extracts from A. viridis containing the sequence were infectious to a limited number of species. The virus genome was cloned and determined to be closely related to Kennedya yellow mosaic virus. The persistence of the virus within the Oklahoma A. viridis population was monitored for five successive years. Virus was present in a high percentage of plants within representative areas of the TGPP in all years and was spreading to additional plants. Virus was present in regions adjacent to the TGPP but not in plants sampled from central and south-central Oklahoma. Virus was present in the underground caudex of the plant during the winter, suggesting overwintering in this tissue. The RNA sequence encoding the virus coat protein varied considerably between individual plants (≈3%), likely due to drift rather than selection. An infectious clone was constructed and the virus was named Asclepias asymptomatic virus (AsAV) due to the absence of obvious symptoms on A. viridis.
Collapse
Affiliation(s)
- Byoung-Eun Min
- Plant Biology Division, Samuel Roberts Nobel Foundation, Inc., Ardmore, OK 73401, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Two genetically related begomoviruses causing tomato leaf curl disease in Togo and Nigeria differ in virulence and host range but do not require a betasatellite for induction of disease symptoms. Arch Virol 2011; 157:107-20. [DOI: 10.1007/s00705-011-1139-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 10/03/2011] [Indexed: 11/26/2022]
|
22
|
Acosta-Leal R, Duffy S, Xiong Z, Hammond RW, Elena SF. Advances in plant virus evolution: translating evolutionary insights into better disease management. PHYTOPATHOLOGY 2011; 101:1136-48. [PMID: 21554186 DOI: 10.1094/phyto-01-11-0017] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Recent studies in plant virus evolution are revealing that genetic structure and behavior of virus and viroid populations can explain important pathogenic properties of these agents, such as host resistance breakdown, disease severity, and host shifting, among others. Genetic variation is essential for the survival of organisms. The exploration of how these subcellular parasites generate and maintain a certain frequency of mutations at the intra- and inter-host levels is revealing novel molecular virus-plant interactions. They emphasize the role of host environment in the dynamic genetic composition of virus populations. Functional genomics has identified host factors that are transcriptionally altered after virus infections. The analyses of these data by means of systems biology approaches are uncovering critical plant genes specifically targeted by viruses during host adaptation. Also, a next-generation resequencing approach of a whole virus genome is opening new avenues to study virus recombination and the relationships between intra-host virus composition and pathogenesis. Altogether, the analyzed data indicate that systematic disruption of some specific parameters of evolving virus populations could lead to more efficient ways of disease prevention, eradication, or tolerable virus-plant coexistence.
Collapse
|
23
|
Navas-Castillo J, Fiallo-Olivé E, Sánchez-Campos S. Emerging virus diseases transmitted by whiteflies. ANNUAL REVIEW OF PHYTOPATHOLOGY 2011; 49:219-48. [PMID: 21568700 DOI: 10.1146/annurev-phyto-072910-095235] [Citation(s) in RCA: 444] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Virus diseases that have emerged in the past two decades limit the production of important vegetable crops in tropical, subtropical, and temperate regions worldwide, and many of the causal viruses are transmitted by whiteflies (order Hemiptera, family Aleyrodidae). Most of these whitefly-transmitted viruses are begomoviruses (family Geminiviridae), although whiteflies are also vectors of criniviruses, ipomoviruses, torradoviruses, and some carlaviruses. Factors driving the emergence and establishment of whitefly-transmitted diseases include genetic changes in the virus through mutation and recombination, changes in the vector populations coupled with polyphagy of the main vector, Bemisia tabaci, and long distance traffic of plant material or vector insects due to trade of vegetables and ornamental plants. The role of humans in increasing the emergence of virus diseases is obvious, and the effect that climate change may have in the future is unclear.
Collapse
Affiliation(s)
- Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, 29750 Algarrobo-Costa, Málaga, Spain.
| | | | | |
Collapse
|
24
|
Batuman O, Kuo YW, Palmieri M, Rojas MR, Gilbertson RL. Tomato chocolate spot virus, a member of a new torradovirus species that causes a necrosis-associated disease of tomato in Guatemala. Arch Virol 2010; 155:857-69. [PMID: 20376682 PMCID: PMC2880234 DOI: 10.1007/s00705-010-0653-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 02/28/2010] [Indexed: 11/25/2022]
Abstract
Tomatoes in Guatemala have been affected by a new disease, locally known as "mancha de chocolate" (chocolate spot). The disease is characterized by distinct necrotic spots on leaves, stems and petioles that eventually expand and cause a dieback of apical tissues. Samples from symptomatic plants tested negative for infection by tomato spotted wilt virus, tobacco streak virus, tobacco etch virus and other known tomato-infecting viruses. A virus-like agent was sap-transmitted from diseased tissue to Nicotiana benthamiana and, when graft-transmitted to tomato, this agent induced chocolate spot symptoms. This virus-like agent also was sap-transmitted to Datura stramonium and Nicotiana glutinosa, but not to a range of non-solanaceous indicator plants. Icosahedral virions approximately 28-30 nm in diameter were purified from symptomatic N. benthamiana plants. When rub-inoculated onto leaves of N. benthamiana plants, these virions induced symptoms indistinguishable from those in N. benthamiana plants infected with the sap-transmissible virus associated with chocolate spot disease. Tomatoes inoculated with sap or grafted with shoots from N. benthamiana plants infected with purified virions developed typical chocolate spot symptoms, consistent with this virus being the causal agent of the disease. Analysis of nucleic acids associated with purified virions of the chocolate-spot-associated virus, revealed a genome composed of two single-stranded RNAs of approximately 7.5 and approximately 5.1 kb. Sequence analysis of these RNAs revealed a genome organization similar to recently described torradoviruses, a new group of picorna-like viruses causing necrosis-associated diseases of tomatoes in Europe [tomato torrado virus (ToTV)] and Mexico [tomato apex necrosis virus (ToANV) and tomato marchitez virus (ToMarV)]. Thus, the approximately 7.5 kb and approximately 5.1 kb RNAs of the chocolate-spot-associated virus corresponded to the torradovirus RNA1 and RNA2, respectively; however, sequence comparisons revealed 64-83% identities with RNA1 and RNA2 sequences of ToTV, ToANV and ToMarV. Together, these results indicate that the chocolate-spot-associated virus is a member of a distinct torradovirus species and, thus, another member of the recently established genus Torradovirus in the family Secoviridae. The name tomato chocolate spot virus is proposed.
Collapse
Affiliation(s)
- O. Batuman
- Department of Plant Pathology, University of California Davis, Davis, CA 95616 USA
| | - Y.-W. Kuo
- Department of Plant Pathology, University of California Davis, Davis, CA 95616 USA
| | - M. Palmieri
- Department of Plant Protection, University of Valle de Guatemala, Guatemala City, Republic of Guatemala
| | - M. R. Rojas
- Department of Plant Pathology, University of California Davis, Davis, CA 95616 USA
| | - R. L. Gilbertson
- Department of Plant Pathology, University of California Davis, Davis, CA 95616 USA
| |
Collapse
|
25
|
Hanssen IM, Lapidot M, Thomma BPHJ. Emerging viral diseases of tomato crops. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2010; 23:539-48. [PMID: 20367462 DOI: 10.1094/mpmi-23-5-0539] [Citation(s) in RCA: 148] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Viral diseases are an important limiting factor in many crop production systems. Because antiviral products are not available, control strategies rely on genetic resistance or hygienic measures to prevent viral diseases, or on eradication of diseased crops to control such diseases. Increasing international travel and trade of plant materials enhances the risk of introducing new viruses and their vectors into production systems. In addition, changing climate conditions can contribute to a successful spread of newly introduced viruses or their vectors and establishment of these organisms in areas that were previously unfavorable. Tomato is economically the most important vegetable crop worldwide and many viruses infecting tomato have been described, while new viral diseases keep emerging. Pepino mosaic virus is a rapidly emerging virus which has established itself as one of the most important viral diseases in tomato production worldwide over recent years. Begomovirus species and other whitefly-transmitted viruses are invading into new areas, and several recently described new viruses such as Tomato torrado virus and new Tospovirus species are rapidly spreading over large geographic areas. In this article, emerging viruses of tomato crops are discussed.
Collapse
Affiliation(s)
- Inge M Hanssen
- Scientia Terrae Research Institute, Sint-Katelijne-Waver, Belgium
| | | | | |
Collapse
|
26
|
Chen LF, Rojas M, Kon T, Gamby K, Xoconostle-Cazares B, Gilbertson RL. A severe symptom phenotype in tomato in Mali is caused by a reassortant between a novel recombinant begomovirus (Tomato yellow leaf curl Mali virus) and a betasatellite. MOLECULAR PLANT PATHOLOGY 2009; 10:415-30. [PMID: 19400843 PMCID: PMC6640326 DOI: 10.1111/j.1364-3703.2009.00541.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Tomato production in West Africa has been severely affected by begomovirus diseases, including yellow leaf curl and a severe symptom phenotype, characterized by extremely stunted and distorted growth and small deformed leaves. Here, a novel recombinant begomovirus from Mali, Tomato yellow leaf curl Mali virus (TYLCMLV), is described that, alone, causes tomato yellow leaf curl disease or, in combination with a betasatellite, causes the severe symptom phenotype. TYLCMLV is an Old World monopartite begomovirus with a hybrid genome composed of sequences from Tomato yellow leaf curl virus-Mild (TYLCV-Mld) and Hollyhock leaf crumple virus (HoLCrV). A TYLCMLV infectious clone induced leaf curl and yellowing in tomato, leaf curl, crumpling and yellowing in Nicotiana benthamiana and common bean, mild symptoms in N. glutinosa, and a symptomless infection in Datura stramonium. In a field-collected sample from a tomato plant showing the severe symptom phenotype in Mali, TYLCMLV was detected together with a betasatellite, identified as Cotton leaf curl Gezira betasatellite (CLCuGB). Tomato plants co-agroinoculated with TYLCMLV and CLCuGB developed severely stunted and distorted growth and small crumpled leaves. These symptoms were more severe than those induced by TYLCMLV alone, and were similar to the severe symptom phenotype observed in the field in Mali and in other West African countries. TYLCMLV and CLCuGB also induced more severe symptoms than TYLCMLV in the other solanaceous hosts, but not in common bean. The increased symptom severity was associated with hyperplasia of phloem-associated cells, but relatively little increase in TYLCMLV DNA levels. In surveys of tomato virus diseases in West Africa, TYLCMLV was commonly detected in plants with leaf curl and yellow leaf curl symptoms, whereas CLCuGB was infrequently detected and always in association with the severe symptom phenotype. Together, these results indicate that TYLCMLV causes tomato yellow leaf curl disease throughout West Africa, whereas TYLCMLV and CLCuGB represent a reassortant that causes the severe symptom phenotype in tomato.
Collapse
Affiliation(s)
- Li-Fang Chen
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | | | | | | | | | | |
Collapse
|