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Genetic Diversity of Plant Viruses and the Epidemiology of Plant-Virus-Induced...
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Genetic Diversity of Plant Viruses and the Epidemiology of Plant-Virus-Induced Diseases

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Protection and Biotic Interactions".

Deadline for manuscript submissions: closed (30 September 2021) | Viewed by 15677

Special Issue Editors

Prof. Dr. Beata Hasiów-Jaroszewska

E-Mail Website
Guest Editor
Institute of Plant Protection-National Research Institute, Department of Virology and Bacteriology, ul. Wł. Węgorka 20, 60-318 Poznań, Poland
Interests: evolution of plant viruses; host–pathogen interactions; subviral RNA particles; RNA interference
Special Issues, Collections and Topics in MDPI journals
Dr. Matthaios M. Mathioudakis

E-Mail Website
Guest Editor
Institute of Olive trees, Subtropical plants & Viticulture-Hellenic Agricultural Organization “DEMETER”, Laboratory of Plant Pathology, Karamanlis Ave. 167, Gr-73134 Chania, Crete, Greece
Interests: plant virus molecular characterization; plant virus diagnostics and epidemiology; plant-virus interactions; RNA silencing suppression
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Annual crop losses due to plant diseases are estimated worldwide at $60 billion. Although is difficult to estimate losses caused by plant viruses alone, viruses are considered to be the second greatest contributor to yield loss. The majority of plant viruses of economic importance are messenger‐type RNA viruses. RNA viruses have a great potential for genetic variation, rapid evolution, and adaptation as a consequence of high mutation rates and recombination events leading to new and in some cases more severe variants. The characterization of the genetic variability and structure of viral populations provides relevant information on the processes involved in virus evolution and epidemiology. Understanding the role of genetic diversity in controlling patterns of pathogen emergence and impact in nature has the potential to provide new insights for crop management. The knowledge about virus epidemiology, mechanisms of virus evolution, and factors that affect the emergence of new genetic variants are crucial for designing reliable diagnostic tools and developing efficient and durable disease-control strategies. This Special Issue of Plants will focus on studies regarding the variability of plant viruses, their epidemiology, and factors that promote the emergence of new virus species and variants.

Dr. Beata Hasiów-Jaroszewska
Dr. Matthaios M. Mathioudakis
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • genetic variability
  • evolution
  • epidemiology
  • plant viruses

Published Papers (5 papers)

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Research

9 pages, 1281 KiB  
Communication
A Novel Distinct Genetic Variant of Tomato Torrado Virus with Substantially Shorter RNA1-Specific 3’Untranslated Region (3’UTR)
by Marta Budziszewska and Przemysław Wieczorek
Plants 2021, 10(11), 2454; https://doi.org/10.3390/plants10112454 - 13 Nov 2021
Cited by 1 | Viewed by 1907
Abstract
Tomato torrado virus (ToTV) induces severe systemic necrosis in Solanum lycopersicum. This work aimed at describing the genetic variability of necrosis-inducing ToTV-Wal’17 collected in 2017, derived from the ToTV-Wal’03 after long-term passages in plants. Sequence analyses of the ToTV-Wal’17 indicated twenty-eight single [...] Read more.
Tomato torrado virus (ToTV) induces severe systemic necrosis in Solanum lycopersicum. This work aimed at describing the genetic variability of necrosis-inducing ToTV-Wal’17 collected in 2017, derived from the ToTV-Wal’03 after long-term passages in plants. Sequence analyses of the ToTV-Wal’17 indicated twenty-eight single nucleotide substitutions in coding sequence of both RNAs, twelve of which resulted in amino acid changes in viral polyproteins. Moreover the sequencing data revealed that the 3’UTR of ToTV-Wal’17 RNA1 was 394 nts shorter in comparison to Wal’03. The performed sequence analyses revealed that 3’UTR of RNA1 of ToTV-Wal’17 is the most divergent across all previously described European isolates. Full article
(This article belongs to the Special Issue Genetic Diversity of Plant Viruses and the Epidemiology of Plant-Virus-Induced Diseases)
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14 pages, 1567 KiB  
Article
Genetic Diversity, Pathogenicity and Pseudorecombination of Cucurbit-Infecting Begomoviruses in Malaysia
by Yu-Jeng Chen, Hsuan-Chun Lai, Chung-Cheng Lin, Zhuan Yi Neoh and Wen-Shi Tsai
Plants 2021, 10(11), 2396; https://doi.org/10.3390/plants10112396 - 6 Nov 2021
Cited by 7 | Viewed by 2716
Abstract
Cucurbits are important crops in the world. However, leaf curl disease constrains their production. Here, begomovirus diversity and pathogenicity associated with the disease in Malaysia were studied based on 49 begomovirus-detected out of 69 symptomatic plants from seven cucurbit crops in 15 locations [...] Read more.
Cucurbits are important crops in the world. However, leaf curl disease constrains their production. Here, begomovirus diversity and pathogenicity associated with the disease in Malaysia were studied based on 49 begomovirus-detected out of 69 symptomatic plants from seven cucurbit crops in 15 locations during 2016 and 2017. The presence of Squash leaf curl China virus (SLCCNV) and Tomato leaf curl New Delhi virus (ToLCNDV) were confirmed by virus detection by polymerase chain reaction, viral DNA sequence analysis and specific detection of the viral components. ToLCNDV Malaysian isolates were further distinguished into strains A, B, C and D. Virus co-infection was detected in bitter gourd, bottle gourd and squash. Among them, eight bitter gourd samples were detected without SLCCNV DNA-A. However, one bottle gourd and five squash samples were without ToLCNDV DNA-B. Pseudorecombination of ToLCNDV DNA-A and SLCCNV DNA-B was detected in two bitter gourd samples. The pathogenic viruses and pseudorecombinants were confirmed by agroinoculation. The viral DNA-B influencing on symptomology and host range was also confirmed. The results strengthen the epidemic of cucurbit-infecting begomovirus in Malaysia as well as Southeast Asia. Especially, the natural pseudorecombinant of begomovirus that extends host range and causes severe symptom implies a threat to crops. Full article
(This article belongs to the Special Issue Genetic Diversity of Plant Viruses and the Epidemiology of Plant-Virus-Induced Diseases)
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19 pages, 2370 KiB  
Article
Molecular Characterization of the Coat Protein Gene of Greek Apple Stem Pitting Virus Isolates: Evolution through Deletions, Insertions, and Recombination Events
by Matthaios M. Mathioudakis, Varvara I. Maliogka, Thierry Candresse, Osmar Nickel, Thor Vinicius Martins Fajardo, Daria Budzyńska, Beata Hasiów-Jaroszewska and Nikolaos I. Katis
Plants 2021, 10(5), 917; https://doi.org/10.3390/plants10050917 - 3 May 2021
Cited by 4 | Viewed by 2455
Abstract
A RT–PCR assay developed to amplify the full coat protein (CP) gene of apple stem pitting virus (ASPV) was evaluated using 180 Greek apple and pear samples and showed a broad detection range. This method was used to investigate the presence of ASPV [...] Read more.
A RT–PCR assay developed to amplify the full coat protein (CP) gene of apple stem pitting virus (ASPV) was evaluated using 180 Greek apple and pear samples and showed a broad detection range. This method was used to investigate the presence of ASPV in quince in Greece and showed a high incidence of 52%. The sequences of 14 isolates from various hosts with a distinct RFLP profile were determined. ASPV population genetics and the factors driving ASPV evolution were analyzed using the Greek ASPV sequences, novel sequences from Brazilian apple trees and Chinese botanical Pyrus species, and homologous sequences retrieved from GenBank. Fourteen variant types of Greek, Brazilian and botanical isolates, which differ in CP gene length and presence of indels, were identified. In addition, these analyses showed high intra- and inter-group variation among isolates from different countries and hosts, indicating the significant variability present in ASPV. Recombination events were detected in four isolates originating from Greek pear and quince and two from Brazilian apples. In a phylogenetic analysis, there was a tendency for isolates to cluster together based on CP gene length, the isolation host, and the detection method applied. Although there was no strict clustering based on geographical origin, most isolates from a given country tended to regroup in specific clusters. Interestingly, it was found that the phylogeny was correlated to the type, position, and pattern of indels, which represent hallmarks of specific lineages and indicate their possible role in virus diversification, rather than the CP size itself. Evidence of recombination between isolates from botanical and cultivated species and the clustering of isolates from botanical species and isolates from cultivated species suggest the existence of a possible undetermined transmission mechanism allowing the exchange of ASPV isolates between the cultivated and wild/ornamental hosts. Full article
(This article belongs to the Special Issue Genetic Diversity of Plant Viruses and the Epidemiology of Plant-Virus-Induced Diseases)
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12 pages, 1349 KiB  
Article
Molecular Characterization of Potato Virus Y (PVY) Using High-Throughput Sequencing: Constraints on Full Genome Reconstructions Imposed by Mixed Infection Involving Recombinant PVY Strains
by Miroslav Glasa, Richard Hančinský, Katarína Šoltys, Lukáš Predajňa, Jana Tomašechová, Pavol Hauptvogel, Michaela Mrkvová, Daniel Mihálik and Thierry Candresse
Plants 2021, 10(4), 753; https://doi.org/10.3390/plants10040753 - 12 Apr 2021
Cited by 8 | Viewed by 2895
Abstract
In recent years, high throughput sequencing (HTS) has brought new possibilities to the study of the diversity and complexity of plant viromes. Mixed infection of a single plant with several viruses is frequently observed in such studies. We analyzed the virome of 10 [...] Read more.
In recent years, high throughput sequencing (HTS) has brought new possibilities to the study of the diversity and complexity of plant viromes. Mixed infection of a single plant with several viruses is frequently observed in such studies. We analyzed the virome of 10 tomato and sweet pepper samples from Slovakia, all showing the presence of potato virus Y (PVY) infection. Most datasets allow the determination of the nearly complete sequence of a single-variant PVY genome, belonging to one of the PVY recombinant strains (N-Wi, NTNa, or NTNb). However, in three to-mato samples (T1, T40, and T62) the presence of N-type and O-type sequences spanning the same genome region was documented, indicative of mixed infections involving different PVY strains variants, hampering the automated assembly of PVY genomes present in the sample. The N- and O-type in silico data were further confirmed by specific RT-PCR assays targeting UTR-P1 and NIa genomic parts. Although full genomes could not be de novo assembled directly in this situation, their deep coverage by relatively long paired reads allowed their manual re-assembly using very stringent mapping parameters. These results highlight the complexity of PVY infection of some host plants and the challenges that can be met when trying to precisely identify the PVY isolates involved in mixed infection. Full article
(This article belongs to the Special Issue Genetic Diversity of Plant Viruses and the Epidemiology of Plant-Virus-Induced Diseases)
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25 pages, 27203 KiB  
Article
Genetic Diversity of Potyviruses Associated with Tulip Breaking Syndrome
by János Ágoston, Asztéria Almási, Katalin Salánki and László Palkovics
Plants 2020, 9(12), 1807; https://doi.org/10.3390/plants9121807 - 19 Dec 2020
Cited by 2 | Viewed by 4557
Abstract
Tulip breaking is economically the most important viral disease of modern-day tulip growing. It is characterized by irregular flame and feather-like patterns in the flowers and mosaic on the foliage. Thirty-two leaf samples were collected from cultivated tulip plants showing tulip breaking syndrome [...] Read more.
Tulip breaking is economically the most important viral disease of modern-day tulip growing. It is characterized by irregular flame and feather-like patterns in the flowers and mosaic on the foliage. Thirty-two leaf samples were collected from cultivated tulip plants showing tulip breaking syndrome from Hungary in 2017 and 2018. Virus identification was performed by serological (ELISA) and molecular (RT-PCR) methods. All samples proved to be infected with a potyvirus and evidence was provided that three potyvirus species could be identified in the samples: Lily mottle virus (LMoV), Tulip breaking virus (TBV) and Rembrandt tulip-breaking virus (ReTBV). Recombination prediction accomplished with Recombination Detection Program (RDP) v4.98 revealed potential intraspecies recombination in the case of TBV and LMoV. Phylogenetic analyses of the coat protein (CP) regions proved the monophyletic origin of these viruses and verified them as three different species according to current International Committee on Taxonomy of Viruses (ICTV) species demarcation criteria. Based on these results, we analyzed taxonomic relations concerning potyviruses associated with tulip breaking syndrome. We propose the elevation of ReTBV to species level, and emergence of two new subgroups in ReTBV. Full article
(This article belongs to the Special Issue Genetic Diversity of Plant Viruses and the Epidemiology of Plant-Virus-Induced Diseases)
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