Plant Viruses: From Ecology to Control

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Plant Microbe Interactions".

Deadline for manuscript submissions: closed (28 February 2021) | Viewed by 62370

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Special Issue Editors

Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Consejo Superior de Investigaciones Científicas – Universidad de Málaga (IHSM-CSIC-UMA), 29750 Algarrobo-Costa, Málaga, Spain
Interests: plant virology; emergent plant diseases; virus taxonomy; plant–pathogen interactions; vector insects
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
Interests: plant virology; emergent plant diseases; virus taxonomy; plant–pathogen interactions; insect vectors
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plant viruses cause many of the most important diseases threatening crops worldwide. Over the last quarter of a century, an increasing number of plant viruses have emerged in various parts of the world, especially in the tropics and subtropics. As is generally observed for plant viruses, most of the emerging viruses are transmitted horizontally by biological vectors, mainly insects. Reverse genetics using infectious clones—available for many plant viruses—has been used for identification of viral determinants involved in virus–host and virus–vector interactions. Although many studies have identified a number of factors involved in disease development and transmission, the precise mechanisms are unknown for most of the virus–plant–vector combinations. In most cases, the diverse outcomes resulting from virus–virus interactions are poorly understood. Although significant advances have been made towards understand the mechanisms involved in plant resistance to viruses, we are far from being able to apply this knowledge to protect cultivated plants from the all viral threats.

The aim of this Special Issue is to provide a platform for researchers interested in plant virology to share their recent results. To achieve this, we are inviting you to submit research articles, short communications and reviews related to the various aspects of plant virology: ecology, virus–plant host interactions, virus–vector interactions, virus–virus interactions, and control strategies—from classical genetic resistance to cutting-edge biotechnological approaches. Studies describing new viral genome sequences or presenting comparative transcriptomic analysis should provide novel insights into the biology of the virus to be considered for publication.

We look forward to assembling an issue that highlights some of the best current research in plant virology.

Dr. Jesús Navas-Castillo
Dr. Elvira Fiallo-Olivé
Guest Editors

Manuscript Submission Information

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Keywords

  • plant viruses
  • emergent viruses
  • ecology
  • virus–plant interactions
  • virus–vector interactions
  • virus–virus interactions
  • genetic resistance
  • control

Published Papers (16 papers)

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Editorial

Jump to: Research, Review

4 pages, 2236 KiB  
Editorial
Special Issue “Plant Viruses: From Ecology to Control”
by Jesús Navas-Castillo and Elvira Fiallo-Olivé
Microorganisms 2021, 9(6), 1136; https://doi.org/10.3390/microorganisms9061136 - 25 May 2021
Viewed by 1768
Abstract
Plant viruses cause many of the most important diseases threatening crops worldwide [...] Full article
(This article belongs to the Special Issue Plant Viruses: From Ecology to Control)
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Research

Jump to: Editorial, Review

15 pages, 3176 KiB  
Article
Adaptation and Codon-Usage Preference of Apple and Pear-Infecting Apple Stem Grooving Viruses
by Jaedeok Kim, Aamir Lal, Eui-Joon Kil, Hae-Ryun Kwak, Hwan-Su Yoon, Hong-Soo Choi, Mikyeong Kim, Muhammad Ali and Sukchan Lee
Microorganisms 2021, 9(6), 1111; https://doi.org/10.3390/microorganisms9061111 - 21 May 2021
Cited by 5 | Viewed by 2567
Abstract
Apple stem grooving virus (ASGV; genus Capillovirus) is an economically important virus. It has an approx. 6.5 kb, monopartite, linear, positive-sense, single-stranded RNA genome. The present study includes identification of 24 isolates—13 isolates from apple (Pyrus malus L.) and 11 isolates [...] Read more.
Apple stem grooving virus (ASGV; genus Capillovirus) is an economically important virus. It has an approx. 6.5 kb, monopartite, linear, positive-sense, single-stranded RNA genome. The present study includes identification of 24 isolates—13 isolates from apple (Pyrus malus L.) and 11 isolates from pear (Pyrus communis L.)—from different agricultural fields in South Korea. The coat protein (CP) gene of the corresponding 23 isolates were amplified, sequenced, and analyzed. The CP sequences showed phylogenetic separation based on their host species, and not on the geography, indicating host adaptation. Further analysis showed that the ASGV isolated in this study followed host adaptation influenced and preferred by the host codon-usage. Full article
(This article belongs to the Special Issue Plant Viruses: From Ecology to Control)
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17 pages, 2862 KiB  
Article
Use of High-Throughput Sequencing and Two RNA Input Methods to Identify Viruses Infecting Tomato Crops
by Ayoub Maachi, Covadonga Torre, Raquel N. Sempere, Yolanda Hernando, Miguel A. Aranda and Livia Donaire
Microorganisms 2021, 9(5), 1043; https://doi.org/10.3390/microorganisms9051043 - 12 May 2021
Cited by 8 | Viewed by 3483
Abstract
We used high-throughput sequencing to identify viruses on tomato samples showing virus-like symptoms. Samples were collected from crops in the Iberian Peninsula. Either total RNA or double-stranded RNA (dsRNA) were used as starting material to build the cDNA libraries. In total, seven virus [...] Read more.
We used high-throughput sequencing to identify viruses on tomato samples showing virus-like symptoms. Samples were collected from crops in the Iberian Peninsula. Either total RNA or double-stranded RNA (dsRNA) were used as starting material to build the cDNA libraries. In total, seven virus species were identified, with pepino mosaic virus being the most abundant one. The dsRNA input provided better coverage and read depth but missed one virus species compared with the total RNA input. By performing in silico analyses, we determined a minimum sequencing depth per sample of 0.2 and 1.5 million reads for dsRNA and rRNA-depleted total RNA inputs, respectively, to detect even the less abundant viruses. Primers and TaqMan probes targeting conserved regions in the viral genomes were designed and/or used for virus detection; all viruses were detected by qRT-PCR/RT-PCR in individual samples, with all except one sample showing mixed infections. Three virus species (Olive latent virus 1, Lettuce ring necrosis virus and Tomato fruit blotch virus) are herein reported for the first time in tomato crops in Spain. Full article
(This article belongs to the Special Issue Plant Viruses: From Ecology to Control)
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19 pages, 3561 KiB  
Article
Revealing the Complexity of Sweepovirus-Deltasatellite–Plant Host Interactions: Expanded Natural and Experimental Helper Virus Range and Effect Dependence on Virus-Host Combination
by Camila G. Ferro, F. Murilo Zerbini, Jesús Navas-Castillo and Elvira Fiallo-Olivé
Microorganisms 2021, 9(5), 1018; https://doi.org/10.3390/microorganisms9051018 - 10 May 2021
Cited by 7 | Viewed by 2189
Abstract
Sweepoviruses are begomoviruses (genus Begomovirus, family Geminiviridae) with ssDNA genomes infecting sweet potato and other species of the family Convolvulaceae. Deltasatellites (genus Deltasatellite, family Tolecusatellitidae) are small-size non-coding DNA satellites associated with begomoviruses. In this study, the genetic diversity [...] Read more.
Sweepoviruses are begomoviruses (genus Begomovirus, family Geminiviridae) with ssDNA genomes infecting sweet potato and other species of the family Convolvulaceae. Deltasatellites (genus Deltasatellite, family Tolecusatellitidae) are small-size non-coding DNA satellites associated with begomoviruses. In this study, the genetic diversity of deltasatellites associated with sweepoviruses infecting Ipomoea indica plants was analyzed by further sampling the populations where the deltasatellite sweet potato leaf curl deltasatellite 1 (SPLCD1) was initially found, expanding the search to other geographical areas in southern continental Spain and the Canary Islands. The sweepoviruses present in the samples coinfected with deltasatellites were also fully characterized by sequencing in order to define the range of viruses that could act as helper viruses in nature. Additionally, experiments were performed to assess the ability of a number of geminivirids (the monopartite tomato leaf deformation virus and the bipartite NW begomovirus Sida golden yellow vein virus, the bipartite OW begomovirus tomato leaf curl New Delhi virus, and the curtovirus beet curly top virus) to transreplicate SPLCD1 in their natural plant hosts or the experimental host Nicotiana benthamiana. The results show that SPLCD1 can be transreplicated by all the geminivirids assayed in N. benthamiana and by tomato leaf curl New Delhi virus in zucchini. The presence of SPLCD1 did not affect the symptomatology caused by the helper viruses, and its effect on viral DNA accumulation depended on the helper virus–host plant combination. Full article
(This article belongs to the Special Issue Plant Viruses: From Ecology to Control)
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17 pages, 1575 KiB  
Article
Resistant Sources and Genetic Control of Resistance to ToLCNDV in Cucumber
by Cristina Sáez, Laura G. M. Ambrosio, Silvia M. Miguel, José Vicente Valcárcel, María José Díez, Belén Picó and Carmelo López
Microorganisms 2021, 9(5), 913; https://doi.org/10.3390/microorganisms9050913 - 24 Apr 2021
Cited by 15 | Viewed by 3504
Abstract
Tomato leaf curl New Delhi virus (ToLCNDV) is a severe threat for cucurbit production worldwide. Resistance has been reported in several crops, but at present, there are no described accessions with resistance to ToLCNDV in cucumber (Cucumis sativus). C. sativus var. [...] Read more.
Tomato leaf curl New Delhi virus (ToLCNDV) is a severe threat for cucurbit production worldwide. Resistance has been reported in several crops, but at present, there are no described accessions with resistance to ToLCNDV in cucumber (Cucumis sativus). C. sativus var. sativus accessions were mechanically inoculated with ToLCNDV and screened for resistance, by scoring symptom severity, tissue printing, and PCR (conventional and quantitative). Severe symptoms and high load of viral DNA were found in plants of a nuclear collection of Spanish landraces and in accessions of C. sativus from different geographical origins. Three Indian accessions (CGN23089, CGN23423, and CGN23633) were highly resistant to the mechanical inoculation, as well as all plants of their progenies obtained by selfing. To study the inheritance of the resistance to ToLCNDV, plants of the CGN23089 accession were crossed with the susceptible accession BGV011742, and F1 hybrids were used to construct segregating populations (F2 and backcrosses), which were mechanically inoculated and evaluated for symptom development and viral load by qPCR. The analysis of the genetic control fit with a recessive monogenic inheritance model, and after genotyping with SNPs distributed along the C. sativus genome, a QTL associated with ToLCNDV resistance was identified in chromosome 2 of cucumber. Full article
(This article belongs to the Special Issue Plant Viruses: From Ecology to Control)
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15 pages, 4751 KiB  
Article
Nanopore Sequencing Is a Credible Alternative to Recover Complete Genomes of Geminiviruses
by Selim Ben Chehida, Denis Filloux, Emmanuel Fernandez, Oumaima Moubset, Murielle Hoareau, Charlotte Julian, Laurence Blondin, Jean-Michel Lett, Philippe Roumagnac and Pierre Lefeuvre
Microorganisms 2021, 9(5), 903; https://doi.org/10.3390/microorganisms9050903 - 23 Apr 2021
Cited by 17 | Viewed by 4692
Abstract
Next-generation sequencing (NGS), through the implementation of metagenomic protocols, has led to the discovery of thousands of new viruses in the last decade. Nevertheless, these protocols are still laborious and costly to implement, and the technique has not yet become routine for everyday [...] Read more.
Next-generation sequencing (NGS), through the implementation of metagenomic protocols, has led to the discovery of thousands of new viruses in the last decade. Nevertheless, these protocols are still laborious and costly to implement, and the technique has not yet become routine for everyday virus characterization. Within the context of CRESS DNA virus studies, we implemented two alternative long-read NGS protocols, one that is agnostic to the sequence (without a priori knowledge of the viral genome) and the other that use specific primers to target a virus (with a priori). Agnostic and specific long read NGS-based assembled genomes of two capulavirus strains were compared to those obtained using the gold standard technique of Sanger sequencing. Both protocols allowed the detection and accurate full genome characterization of both strains. Globally, the assembled genomes were very similar (99.5–99.7% identity) to the Sanger sequences consensus, but differences in the homopolymeric tracks of these sequences indicated a specific lack of accuracy of the long reads NGS approach that has yet to be improved. Nevertheless, the use of the bench-top sequencer has proven to be a credible alternative in the context of CRESS DNA virus study and could offer a new range of applications not previously accessible. Full article
(This article belongs to the Special Issue Plant Viruses: From Ecology to Control)
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19 pages, 3687 KiB  
Article
Virus Host Jumping Can Be Boosted by Adaptation to a Bridge Plant Species
by Sandra Martínez-Turiño, María Calvo, Leonor Cecilia Bedoya, Mingmin Zhao and Juan Antonio García
Microorganisms 2021, 9(4), 805; https://doi.org/10.3390/microorganisms9040805 - 11 Apr 2021
Cited by 5 | Viewed by 2439
Abstract
Understanding biological mechanisms that regulate emergence of viral diseases, in particular those events engaging cross-species pathogens spillover, is becoming increasingly important in virology. Species barrier jumping has been extensively studied in animal viruses, and the critical role of a suitable intermediate host in [...] Read more.
Understanding biological mechanisms that regulate emergence of viral diseases, in particular those events engaging cross-species pathogens spillover, is becoming increasingly important in virology. Species barrier jumping has been extensively studied in animal viruses, and the critical role of a suitable intermediate host in animal viruses-generated human pandemics is highly topical. However, studies on host jumping involving plant viruses have been focused on shifting intra-species, leaving aside the putative role of “bridge hosts” in facilitating interspecies crossing. Here, we take advantage of several VPg mutants, derived from a chimeric construct of the potyvirus Plum pox virus (PPV), analyzing its differential behaviour in three herbaceous species. Our results showed that two VPg mutations in a Nicotiana clevelandii-adapted virus, emerged during adaptation to the bridge-host Arabidopsis thaliana, drastically prompted partial adaptation to Chenopodium foetidum. Although both changes are expected to facilitate productive interactions with eIF(iso)4E, polymorphims detected in PPV VPg and the three eIF(iso)4E studied, extrapolated to a recent VPg:eIF4E structural model, suggested that two adaptation ways can be operating. Remarkably, we found that VPg mutations driving host-range expansion in two non-related species, not only are not associated with cost trade-off constraints in the original host, but also improve fitness on it. Full article
(This article belongs to the Special Issue Plant Viruses: From Ecology to Control)
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16 pages, 1501 KiB  
Article
Arabidopsis thaliana Genes Associated with Cucumber mosaic virus Virulence and Their Link to Virus Seed Transmission
by Nuria Montes, Alberto Cobos, Miriam Gil-Valle, Elena Caro and Israel Pagán
Microorganisms 2021, 9(4), 692; https://doi.org/10.3390/microorganisms9040692 - 27 Mar 2021
Cited by 10 | Viewed by 2907
Abstract
Virulence, the effect of pathogen infection on progeny production, is a major determinant of host and pathogen fitness as it affects host fecundity and pathogen transmission. In plant–virus interactions, ample evidence indicates that virulence is genetically controlled by both partners. However, the host [...] Read more.
Virulence, the effect of pathogen infection on progeny production, is a major determinant of host and pathogen fitness as it affects host fecundity and pathogen transmission. In plant–virus interactions, ample evidence indicates that virulence is genetically controlled by both partners. However, the host genetic determinants are poorly understood. Through a genome-wide association study (GWAS) of 154 Arabidopsis thaliana genotypes infected by Cucumber mosaic virus (CMV), we identified eight host genes associated with virulence, most of them involved in response to biotic stresses and in cell wall biogenesis in plant reproductive structures. Given that virulence is a main determinant of the efficiency of plant virus seed transmission, we explored the link between this trait and the genetic regulation of virulence. Our results suggest that the same functions that control virulence are also important for CMV transmission through seeds. In sum, this work provides evidence of a novel role for some previously known plant defense genes and for the cell wall metabolism in plant virus interactions. Full article
(This article belongs to the Special Issue Plant Viruses: From Ecology to Control)
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19 pages, 16344 KiB  
Article
Persistent Southern Tomato Virus (STV) Interacts with Cucumber Mosaic and/or Pepino Mosaic Virus in Mixed- Infections Modifying Plant Symptoms, Viral Titer and Small RNA Accumulation
by Laura Elvira González, Rosa Peiró, Luis Rubio and Luis Galipienso
Microorganisms 2021, 9(4), 689; https://doi.org/10.3390/microorganisms9040689 - 26 Mar 2021
Cited by 16 | Viewed by 4045
Abstract
Southern tomato virus (STV) is a persistent virus that was, at the beginning, associated with some tomato fruit disorders. Subsequent studies showed that the virus did not induce apparent symptoms in single infections. Accordingly, the reported symptoms could be induced by the interaction [...] Read more.
Southern tomato virus (STV) is a persistent virus that was, at the beginning, associated with some tomato fruit disorders. Subsequent studies showed that the virus did not induce apparent symptoms in single infections. Accordingly, the reported symptoms could be induced by the interaction of STV with other viruses, which frequently infect tomato. Here, we studied the effect of STV in co- and triple-infections with Cucumber mosaic virus (CMV) and Pepino mosaic virus (PepMV). Our results showed complex interactions among these viruses. Co-infections leaded to a synergism between STV and CMV or PepMV: STV increased CMV titer and plant symptoms at early infection stages, whereas PepMV only exacerbated the plant symptoms. CMV and PepMV co-infection showed an antagonistic interaction with a strong decrease of CMV titer and a modification of the plant symptoms with respect to the single infections. However, the presence of STV in a triple-infection abolished this antagonism, restoring the CMV titer and plant symptoms. The siRNAs analysis showed a total of 78 miRNAs, with 47 corresponding to novel miRNAs in tomato, which were expressed differentially in the plants that were infected with these viruses with respect to the control mock-inoculated plants. These miRNAs were involved in the regulation of important functions and their number and expression level varied, depending on the virus combination. The number of vsiRNAs in STV single-infected tomato plants was very small, but STV vsiRNAs increased with the presence of CMV and PepMV. Additionally, the rates of CMV and PepMV vsiRNAs varied depending on the virus combination. The frequencies of vsiRNAs in the viral genomes were not uniform, but they were not influenced by other viruses. Full article
(This article belongs to the Special Issue Plant Viruses: From Ecology to Control)
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14 pages, 1665 KiB  
Article
Yield Losses Caused by Barley Yellow Dwarf Virus-PAV Infection in Wheat and Barley: A Three-Year Field Study in South-Eastern Australia
by Narelle Nancarrow, Mohammad Aftab, Grant Hollaway, Brendan Rodoni and Piotr Trębicki
Microorganisms 2021, 9(3), 645; https://doi.org/10.3390/microorganisms9030645 - 19 Mar 2021
Cited by 22 | Viewed by 4422
Abstract
Barley yellow dwarf virus (BYDV) is transmitted by aphids and significantly reduces the yield and quality of cereals worldwide. Four experiments investigating the effects of barley yellow dwarf virus-PAV (BYDV-PAV) infection on either wheat or barley were conducted over three years (2015, 2017, [...] Read more.
Barley yellow dwarf virus (BYDV) is transmitted by aphids and significantly reduces the yield and quality of cereals worldwide. Four experiments investigating the effects of barley yellow dwarf virus-PAV (BYDV-PAV) infection on either wheat or barley were conducted over three years (2015, 2017, and 2018) under typical field conditions in South-Eastern Australia. Plants inoculated with BYDV-PAV using viruliferous aphids (Rhopalosiphum padi) were harvested at maturity then grain yield and yield components were measured. Compared to the non-inoculated control, virus infection severely reduced grain yield by up to 84% (1358 kg/ha) in wheat and 64% (1456 kg/ha) in barley. The yield component most affected by virus infection was grain number, which accounted for a large proportion of the yield loss. There were no significant differences between early (seedling stage) and later (early-tillering stage) infection for any of the parameters measured (plant height, biomass, yield, grain number, 1000-grain weight or grain size) for either wheat or barley. Additionally, this study provides an estimated yield loss value, or impact factor, of 0.91% (72 kg/ha) for each one percent increase in natural BYDV-PAV background infection. Yield losses varied considerably between experiments, demonstrating the important role of cultivar and environmental factors in BYDV epidemiology and highlighting the importance of conducting these experiments under varying conditions for specific cultivar–vector–virus combinations. Full article
(This article belongs to the Special Issue Plant Viruses: From Ecology to Control)
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9 pages, 1856 KiB  
Communication
Membrane Association and Topology of Citrus Leprosis Virus C2 Movement and Capsid Proteins
by Mikhail Oliveira Leastro, Juliana Freitas-Astúa, Elliot Watanabe Kitajima, Vicente Pallás and Jesús Á. Sánchez-Navarro
Microorganisms 2021, 9(2), 418; https://doi.org/10.3390/microorganisms9020418 - 17 Feb 2021
Cited by 3 | Viewed by 1897
Abstract
Although citrus leprosis disease has been known for more than a hundred years, one of its causal agents, citrus leprosis virus C2 (CiLV-C2), is poorly characterized. This study described the association of CiLV-C2 movement protein (MP) and capsid protein (p29) with biological membranes. [...] Read more.
Although citrus leprosis disease has been known for more than a hundred years, one of its causal agents, citrus leprosis virus C2 (CiLV-C2), is poorly characterized. This study described the association of CiLV-C2 movement protein (MP) and capsid protein (p29) with biological membranes. Our findings obtained by computer predictions, chemical treatments after membrane fractionation, and biomolecular fluorescence complementation assays revealed that p29 is peripherally associated, while the MP is integrally bound to the cell membranes. Topological analyses revealed that both the p29 and MP expose their N- and C-termini to the cell cytoplasmic compartment. The implications of these results in the intracellular movement of the virus were discussed. Full article
(This article belongs to the Special Issue Plant Viruses: From Ecology to Control)
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12 pages, 2905 KiB  
Article
Implication of the Whitefly Protein Vps Twenty Associated 1 (Vta1) in the Transmission of Cotton Leaf Curl Multan Virus
by Yao Chi, Li-Long Pan, Shu-Sheng Liu, Shahid Mansoor and Xiao-Wei Wang
Microorganisms 2021, 9(2), 304; https://doi.org/10.3390/microorganisms9020304 - 02 Feb 2021
Cited by 6 | Viewed by 2266
Abstract
Cotton leaf curl Multan virus (CLCuMuV) is one of the major casual agents of cotton leaf curl disease. Previous studies show that two indigenous whitefly species of the Bemisia tabaci complex, Asia II 1 and Asia II 7, are able to transmit CLCuMuV, [...] Read more.
Cotton leaf curl Multan virus (CLCuMuV) is one of the major casual agents of cotton leaf curl disease. Previous studies show that two indigenous whitefly species of the Bemisia tabaci complex, Asia II 1 and Asia II 7, are able to transmit CLCuMuV, but the molecular mechanisms underlying the transmission are poorly known. In this study, we attempted to identify the whitefly proteins involved in CLCuMuV transmission. First, using a yeast two-hybrid system, we identified 54 candidate proteins of Asia II 1 that putatively can interact with the coat protein of CLCuMuV. Second, we examined interactions between the CLCuMuV coat protein and several whitefly proteins, including vacuolar protein sorting-associated protein (Vps) twenty associated 1 (Vta1). Third, using RNA interference, we found that Vta1 positively regulated CLCuMuV acquisition and transmission by the Asia II 1 whitefly. In addition, we showed that the interaction between the CLCuMuV coat protein and Vta1 from the whitefly Middle East-Asia Minor (MEAM1), a poor vector of CLCuMuV, was much weaker than that between Asia II 1 Vta1 and the CLCuMuV coat protein. Silencing of Vta1 in MEAM1 did not affect the quantity of CLCuMuV acquired by the whitefly. Taken together, our results suggest that Vta1 may play an important role in the transmission of CLCuMuV by the whitefly. Full article
(This article belongs to the Special Issue Plant Viruses: From Ecology to Control)
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Review

Jump to: Editorial, Research

31 pages, 2532 KiB  
Review
A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses
by Denis Kutnjak, Lucie Tamisier, Ian Adams, Neil Boonham, Thierry Candresse, Michela Chiumenti, Kris De Jonghe, Jan F. Kreuze, Marie Lefebvre, Gonçalo Silva, Martha Malapi-Wight, Paolo Margaria, Irena Mavrič Pleško, Sam McGreig, Laura Miozzi, Benoit Remenant, Jean-Sebastien Reynard, Johan Rollin, Mike Rott, Olivier Schumpp, Sébastien Massart and Annelies Haegemanadd Show full author list remove Hide full author list
Microorganisms 2021, 9(4), 841; https://doi.org/10.3390/microorganisms9040841 - 14 Apr 2021
Cited by 33 | Viewed by 7074
Abstract
High-throughput sequencing (HTS) technologies have become indispensable tools assisting plant virus diagnostics and research thanks to their ability to detect any plant virus in a sample without prior knowledge. As HTS technologies are heavily relying on bioinformatics analysis of the huge amount of [...] Read more.
High-throughput sequencing (HTS) technologies have become indispensable tools assisting plant virus diagnostics and research thanks to their ability to detect any plant virus in a sample without prior knowledge. As HTS technologies are heavily relying on bioinformatics analysis of the huge amount of generated sequences, it is of utmost importance that researchers can rely on efficient and reliable bioinformatic tools and can understand the principles, advantages, and disadvantages of the tools used. Here, we present a critical overview of the steps involved in HTS as employed for plant virus detection and virome characterization. We start from sample preparation and nucleic acid extraction as appropriate to the chosen HTS strategy, which is followed by basic data analysis requirements, an extensive overview of the in-depth data processing options, and taxonomic classification of viral sequences detected. By presenting the bioinformatic tools and a detailed overview of the consecutive steps that can be used to implement a well-structured HTS data analysis in an easy and accessible way, this paper is targeted at both beginners and expert scientists engaging in HTS plant virome projects. Full article
(This article belongs to the Special Issue Plant Viruses: From Ecology to Control)
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18 pages, 1447 KiB  
Review
Geminiviral Triggers and Suppressors of Plant Antiviral Immunity
by Ruan M. Teixeira, Marco Aurélio Ferreira, Gabriel A. S. Raimundo and Elizabeth P. B. Fontes
Microorganisms 2021, 9(4), 775; https://doi.org/10.3390/microorganisms9040775 - 08 Apr 2021
Cited by 21 | Viewed by 3458
Abstract
Geminiviruses are circular single-stranded DNA plant viruses encapsidated into geminate virion particles, which infect many crops and vegetables and, hence, represent significant agricultural constraints worldwide. To maintain their broad-range host spectrum and establish productive infection, the geminiviruses must circumvent a potent plant antiviral [...] Read more.
Geminiviruses are circular single-stranded DNA plant viruses encapsidated into geminate virion particles, which infect many crops and vegetables and, hence, represent significant agricultural constraints worldwide. To maintain their broad-range host spectrum and establish productive infection, the geminiviruses must circumvent a potent plant antiviral immune system, which consists of a multilayered perception system represented by RNA interference sensors and effectors, pattern recognition receptors (PRR), and resistance (R) proteins. This recognition system leads to the activation of conserved defense responses that protect plants against different co-existing viral and nonviral pathogens in nature. Furthermore, a specific antiviral cell surface receptor signaling is activated at the onset of geminivirus infection to suppress global translation. This review highlighted these layers of virus perception and host defenses and the mechanisms developed by geminiviruses to overcome the plant antiviral immunity mechanisms. Full article
(This article belongs to the Special Issue Plant Viruses: From Ecology to Control)
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19 pages, 9508 KiB  
Review
The Global Dimension of Tomato Yellow Leaf Curl Disease: Current Status and Breeding Perspectives
by Zhe Yan, Anne-Marie A. Wolters, Jesús Navas-Castillo and Yuling Bai
Microorganisms 2021, 9(4), 740; https://doi.org/10.3390/microorganisms9040740 - 01 Apr 2021
Cited by 28 | Viewed by 8284
Abstract
Tomato yellow leaf curl disease (TYLCD) caused by tomato yellow leaf curl virus (TYLCV) and a group of related begomoviruses is an important disease which in recent years has caused serious economic problems in tomato (Solanum lycopersicum) production worldwide. Spreading of [...] Read more.
Tomato yellow leaf curl disease (TYLCD) caused by tomato yellow leaf curl virus (TYLCV) and a group of related begomoviruses is an important disease which in recent years has caused serious economic problems in tomato (Solanum lycopersicum) production worldwide. Spreading of the vectors, whiteflies of the Bemisia tabaci complex, has been responsible for many TYLCD outbreaks. In this review, we summarize the current knowledge of TYLCV and TYLV-like begomoviruses and the driving forces of the increasing global significance through rapid evolution of begomovirus variants, mixed infection in the field, association with betasatellites and host range expansion. Breeding for host plant resistance is considered as one of the most promising and sustainable methods in controlling TYLCD. Resistance to TYLCD was found in several wild relatives of tomato from which six TYLCV resistance genes (Ty-1 to Ty-6) have been identified. Currently, Ty-1 and Ty-3 are the primary resistance genes widely used in tomato breeding programs. Ty-2 is also exploited commercially either alone or in combination with other Ty-genes (i.e., Ty-1, Ty-3 or ty-5). Additionally, screening of a large collection of wild tomato species has resulted in the identification of novel TYLCD resistance sources. In this review, we focus on genetic resources used to date in breeding for TYLCVD resistance. For future breeding strategies, we discuss several leads in order to make full use of the naturally occurring and engineered resistance to mount a broad-spectrum and sustainable begomovirus resistance. Full article
(This article belongs to the Special Issue Plant Viruses: From Ecology to Control)
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30 pages, 3273 KiB  
Review
Variability, Functions and Interactions of Plant Virus Movement Proteins: What Do We Know So Far?
by Gaurav Kumar and Indranil Dasgupta
Microorganisms 2021, 9(4), 695; https://doi.org/10.3390/microorganisms9040695 - 27 Mar 2021
Cited by 18 | Viewed by 5017
Abstract
Of the various proteins encoded by plant viruses, one of the most interesting is the movement protein (MP). MPs are unique to plant viruses and show surprising structural and functional variability while maintaining their core function, which is to facilitate the intercellular transport [...] Read more.
Of the various proteins encoded by plant viruses, one of the most interesting is the movement protein (MP). MPs are unique to plant viruses and show surprising structural and functional variability while maintaining their core function, which is to facilitate the intercellular transport of viruses or viral nucleoprotein complexes. MPs interact with components of the intercellular channels, the plasmodesmata (PD), modifying their size exclusion limits and thus allowing larger particles, including virions, to pass through. The interaction of MPs with the components of PD, the formation of transport complexes and the recruitment of host cellular components have all revealed different facets of their functions. Multitasking is an inherent property of most viral proteins, and MPs are no exception. Some MPs carry out multitasking, which includes gene silencing suppression, viral replication and modulation of host protein turnover machinery. This review brings together the current knowledge on MPs, focusing on their structural variability, various functions and interactions with host proteins. Full article
(This article belongs to the Special Issue Plant Viruses: From Ecology to Control)
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