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Journals
Viruses
Special Issues
Diversity and Coinfections of Plant or Fungal Viruses 2023
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Diversity and Coinfections of Plant or Fungal Viruses 2023

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Viruses of Plants, Fungi and Protozoa".

Deadline for manuscript submissions: closed (15 April 2024) | Viewed by 6140

Special Issue Editors

Dr. Islam Hamim

E-Mail Website
Guest Editor
1. Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh, Bangladesh
2. Laboratory of Plant Pathology, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
Interests: virology; plant pathology; insect/pollinator pathology; plant-microbe interactions; pesticide resistance; biodiversity and ecology of agriculture landscape
Special Issues, Collections and Topics in MDPI journals
Dr. Ken Komatsu

E-Mail Website
Guest Editor
Laboratory of Plant Pathology, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
Interests: plant pathology; plant virology; molecular biology
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Hiromitsu Moriyama

E-Mail Website
Guest Editor
Laboratory of Molecular and Cellular Biology, Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
Interests: plant protection science; applied microbiology; applied molecular cell biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The genetic background of a virus in an infected plant or fungus is not uniform. The highly heterogeneous nature of virus populations affects symptom expressions in a host. Indeed, a virus isolated from a single plant often exhibits genomic sequence differences within sub-isolates and can impact phenotypic changes in a host. Coinfection with another virus alters symptom expression in a host plant, resulting in more severe symptoms and, eventually, worse disease consequences. Coinfections among fungal viruses may be also generated by two or more viruses that are phylogenetically diverse, and are very frequent in the field, sometimes even in laboratory conditions.

Therefore, the goal of this Special Issue is to invite respective scientists to submit original research articles, short communications, case studies, and reviews regarding plant or fungal viruses. Manuscripts concerning a single virus or a mixture of viruses covering either individual or multiple host species are welcomed. The scope of this Special Issue includes, but is not limited to:

  • The detection, diversity, and biology of viruses;
  • Virus emergence, ecology, and evolution;
  • Diversity or co-infection or function of a virus or viruses;
  • Mechanisms of altered symptoms or phenotypic changes caused by interaction between different virus species or virus variants;
  • Pathogenesis and management of viruses or virus-like agents or virus variants.

Dr. Islam Hamim
Dr. Ken Komatsu
Prof. Dr. Hiromitsu Moriyama
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. Viruses is an international peer-reviewed open access monthly 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 2600 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

  • diagnosis
  • surveillance
  • molecular mechanism
  • viroid
  • subviral agents
  • mycoviruses
  • biological control
  • pesticide resistance
  • antiviral defense mechanism
  • population genetics
  • recombination
  • gene expressions
  • host range

Published Papers (6 papers)

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Research

24 pages, 740 KiB  
Article
Geminiviridae and Alphasatellitidae Diversity Revealed by Metagenomic Analysis of Susceptible and Tolerant Tomato Cultivars across Distinct Brazilian Biomes
by Izaías Araújo de Oliveira, Luciane de Nazaré Almeida dos Reis, Maria Esther de Noronha Fonseca, Felipe Fochat Silva Melo, Leonardo Silva Boiteux and Rita de Cássia Pereira-Carvalho
Viruses 2024, 16(6), 899; https://doi.org/10.3390/v16060899 - 1 Jun 2024
Viewed by 263
Abstract
The diversity of Geminiviridae and Alphasatellitidae species in tomatoes was assessed via high-throughput sequencing of 154 symptomatic foliar samples collected from 2002 to 2017 across seven Brazilian biomes. The first pool (BP1) comprised 73 samples from the North (13), Northeast (36), and South [...] Read more.
The diversity of Geminiviridae and Alphasatellitidae species in tomatoes was assessed via high-throughput sequencing of 154 symptomatic foliar samples collected from 2002 to 2017 across seven Brazilian biomes. The first pool (BP1) comprised 73 samples from the North (13), Northeast (36), and South (24) regions. Sixteen begomoviruses and one Topilevirus were detected in BP1. Four begomovirus-like contigs were identified as putative novel species (NS). NS#1 was reported in the semi-arid (Northeast) region and NS#2 and NS#4 in mild subtropical climates (South region), whereas NS#3 was detected in the warm and humid (North) region. The second pool (BP2) comprised 81 samples from Southeast (39) and Central–West (42) regions. Fourteen viruses and subviral agents were detected in BP2, including two topileviruses, a putative novel begomovirus (NS#5), and two alphasatellites occurring in continental highland areas. The five putative novel begomoviruses displayed strict endemic distributions. Conversely, tomato mottle leaf curl virus (a monopartite species) displayed the most widespread distribution occurring across the seven sampled biomes. The overall diversity and frequency of mixed infections were higher in susceptible (16 viruses + alphasatellites) in comparison to tolerant (carrying the Ty–1 or Ty–3 introgressions) samples, which displayed 9 viruses. This complex panorama reinforces the notion that the tomato-associated Geminiviridae diversity is yet underestimated in Neotropical regions. Full article
(This article belongs to the Special Issue Diversity and Coinfections of Plant or Fungal Viruses 2023)
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17 pages, 902 KiB  
Article
Diagnosis and Characterization of Plant Viruses Using HTS to Support Virus Management and Tomato Breeding
by Enrique González-Pérez, Elizabeth Chiquito-Almanza, Salvador Villalobos-Reyes, Jaime Canul-Ku and José Luis Anaya-López
Viruses 2024, 16(6), 888; https://doi.org/10.3390/v16060888 - 31 May 2024
Viewed by 223
Abstract
Viral diseases pose a significant threat to tomato crops (Solanum lycopersicum L.), one of the world’s most economically important vegetable crops. The limited genetic diversity of cultivated tomatoes contributes to their high susceptibility to viral infections. To address this challenge, tomato breeding [...] Read more.
Viral diseases pose a significant threat to tomato crops (Solanum lycopersicum L.), one of the world’s most economically important vegetable crops. The limited genetic diversity of cultivated tomatoes contributes to their high susceptibility to viral infections. To address this challenge, tomato breeding programs must harness the genetic resources found in native populations and wild relatives. Breeding efforts may aim to develop broad-spectrum resistance against the virome. To identify the viruses naturally infecting 19 advanced lines, derived from native tomatoes, high-throughput sequencing (HTS) of small RNAs and confirmation with PCR and RT-PCR were used. Single and mixed infections with tomato mosaic virus (ToMV), tomato golden mosaic virus (ToGMoV), and pepper huasteco yellow vein virus (PHYVV) were detected. The complete consensus genomes of three variants of Mexican ToMV isolates were reconstructed, potentially forming a new ToMV clade with a distinct 3’ UTR. The absence of reported mutations associated with resistance-breaking to ToMV suggests that the Tm-1, Tm-2, and Tm-22 genes could theoretically be used to confer resistance. However, the high mutation rates and a 63 nucleotide insertion in the 3’ UTR, as well as amino acid mutations in the ORFs encoding 126 KDa, 183 KDa, and MP of Mexican ToMV isolates, suggest that it is necessary to evaluate the capacity of these variants to overcome Tm-1, Tm-2, and Tm-22 resistance genes. This evaluation, along with the characterization of advanced lines using molecular markers linked to these resistant genes, will be addressed in future studies as part of the breeding strategy. This study emphasizes the importance of using HTS for accurate identification and characterization of plant viruses that naturally infect tomato germplasm based on the consensus genome sequences. This study provides crucial insights to select appropriate disease management strategies and resistance genes and guide breeding efforts toward the development of virus-resistant tomato varieties. Full article
(This article belongs to the Special Issue Diversity and Coinfections of Plant or Fungal Viruses 2023)
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14 pages, 4710 KiB  
Article
Characterization of Two Novel Single-Stranded RNA Viruses from Agroathelia rolfsii, the Causal Agent of Peanut Stem Rot
by Dongyang Yu, Qianqian Wang, Wanduo Song, Yanping Kang, Yong Lei, Zhihui Wang, Yuning Chen, Dongxin Huai, Xin Wang, Boshou Liao and Liying Yan
Viruses 2024, 16(6), 854; https://doi.org/10.3390/v16060854 - 27 May 2024
Viewed by 412
Abstract
Peanut stem rot is a soil-borne disease caused by Agroathelia rolfsii. It occurs widely and seriously affects the peanut yield in most peanut-producing areas. The mycoviruses that induce the hypovirulence of some plant pathogenic fungi are potential resources for the biological control [...] Read more.
Peanut stem rot is a soil-borne disease caused by Agroathelia rolfsii. It occurs widely and seriously affects the peanut yield in most peanut-producing areas. The mycoviruses that induce the hypovirulence of some plant pathogenic fungi are potential resources for the biological control of fungal diseases in plants. Thus far, few mycoviruses have been found in A. rolfsii. In this study, two mitoviruses, namely, Agroathelia rolfsii mitovirus 1 (ArMV1) and Agroathelia rolfsii mitovirus 2 (ArMV2), were identified from the weakly virulent A. rolfsii strain GP3-1, and they were also found in other A. rolfsii isolates. High amounts of ArMV1 and ArMV2in the mycelium could reduce the virulence of A. rolfsii strains. This is the first report on the existence of mitoviruses in A. rolfsii. The results of this study may provide insights into the classification and evolution of mitoviruses in A. rolfsii and enable the exploration of the use of mycoviruses as biocontrol agents for the control of peanut stem rot. Full article
(This article belongs to the Special Issue Diversity and Coinfections of Plant or Fungal Viruses 2023)
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18 pages, 5621 KiB  
Article
Exploring Tomato Fruit Viromes through Transcriptome Data Analysis
by Yeonhwa Jo, Hoseong Choi, Bong Choon Lee, Jin-Sung Hong, Sang-Min Kim and Won Kyong Cho
Viruses 2023, 15(11), 2139; https://doi.org/10.3390/v15112139 - 24 Oct 2023
Viewed by 1225
Abstract
This study delves into the complex landscape of viral infections in tomatoes (Solanum lycopersicum) using available transcriptome data. We conducted a virome analysis, revealing 219 viral contigs linked to four distinct viruses: tomato chlorosis virus (ToCV), southern tomato virus (STV), tomato [...] Read more.
This study delves into the complex landscape of viral infections in tomatoes (Solanum lycopersicum) using available transcriptome data. We conducted a virome analysis, revealing 219 viral contigs linked to four distinct viruses: tomato chlorosis virus (ToCV), southern tomato virus (STV), tomato yellow leaf curl virus (TYLCV), and cucumber mosaic virus (CMV). Among these, ToCV predominated in contig count, followed by STV, TYLCV, and CMV. A notable finding was the prevalence of coinfections, emphasizing the concurrent presence of multiple viruses in tomato plants. Despite generally low viral levels in fruit transcriptomes, STV emerged as the primary virus based on viral read count. We delved deeper into viral abundance and the contributions of RNA segments to replication. While initially focused on studying the impact of sound treatment on tomato fruit transcriptomes, the unexpected viral presence underscores the importance of considering viruses in plant research. Geographical variations in virome communities hint at potential forensic applications. Phylogenetic analysis provided insights into viral origins and genetic diversity, enhancing our understanding of the Korean tomato virome. In conclusion, this study advances our knowledge of the tomato virome, stressing the need for robust pest control in greenhouse-grown tomatoes and offering insights into virus management and crop protection. Full article
(This article belongs to the Special Issue Diversity and Coinfections of Plant or Fungal Viruses 2023)
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16 pages, 4180 KiB  
Article
Horizontal and Vertical Transmission of a Mycovirus Closely Related to the Partitivirus RhsV717 That Confers Hypovirulence in Rhizoctonia solani
by Aili Sun, Lianjing Zhao, Yang Sun, Yingrui Chen, Chengyun Li, Wenhan Dong and Genhua Yang
Viruses 2023, 15(10), 2088; https://doi.org/10.3390/v15102088 - 13 Oct 2023
Cited by 3 | Viewed by 1011
Abstract
Rhizoctonia solani virus717 (RhsV717) was isolated from the Rhizoctonia solani (R. solani) AG-2 strain Rhs717. This study isolated a virus designated as Rhizoctonia solani partitivirus BS-5 (RsPV-BS5) from the R. solani AG-3 strain BS-5, the causal agent of tobacco target spot [...] Read more.
Rhizoctonia solani virus717 (RhsV717) was isolated from the Rhizoctonia solani (R. solani) AG-2 strain Rhs717. This study isolated a virus designated as Rhizoctonia solani partitivirus BS-5 (RsPV-BS5) from the R. solani AG-3 strain BS-5, the causal agent of tobacco target spot disease. The virus was identified as a strain of RhsV717. Transmission electron microscopy (TEM) images showed that RsPV-BS5 had virus particles with a diameter of approximately 40 nm. Importantly, it can be horizontally transmitted through hyphal anastomosis and vertically transmitted via sexual basidiospores. Furthermore, this study demonstrated that RsPV-BS5 infection significantly impedes mycelial growth and induces hypovirulence in tobacco leaves. Thus, RsPV-BS5 presents a promising avenue for biocontrolling tobacco target spot disease. Transcriptome analysis unveiled differential expression of four genes related to cell wall-degrading enzymes between two isogenic strains, 06-2-15V and 06-2-15. These findings shed light on the molecular mechanism through which RsPV-BS5 reduces host pathogenicity. Full article
(This article belongs to the Special Issue Diversity and Coinfections of Plant or Fungal Viruses 2023)
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19 pages, 11019 KiB  
Article
Molecular Analysis of the Global Population of Potato Virus S Redefines Its Phylogeny, and Has Crop Biosecurity Implications
by Şerife Topkaya, Ali Çelik, Adyatma Irawan Santosa and Roger A. C. Jones
Viruses 2023, 15(5), 1104; https://doi.org/10.3390/v15051104 - 30 Apr 2023
Cited by 9 | Viewed by 2142
Abstract
In 2020, 264 samples were collected from potato fields in the Turkish provinces of Bolu, Afyon, Kayseri and Niğde. RT-PCR tests, with primers which amplified its coat protein (CP), detected potato virus S (PVS) in 35 samples. Complete CP sequences were obtained from [...] Read more.
In 2020, 264 samples were collected from potato fields in the Turkish provinces of Bolu, Afyon, Kayseri and Niğde. RT-PCR tests, with primers which amplified its coat protein (CP), detected potato virus S (PVS) in 35 samples. Complete CP sequences were obtained from 14 samples. Phylogenetic analysis using non-recombinant sequences of (i) the 14 CP’s, another 8 from Tokat province and 73 others from GenBank; and (ii) 130 complete ORF, RdRp and TGB sequences from GenBank, found that they fitted within phylogroups, PVSI, PVSII or PVSIII. All Turkish CP sequences were in PVSI, clustering within five subclades. Subclades 1 and 4 were in three to four provinces, whereas 2, 3 and 5 were in one province each. All four genome regions were under strong negative selection constraints (ω = 0.0603–0.1825). Considerable genetic variation existed amongst PVSI and PVSII isolates. Three neutrality test methods showed PVSIII remained balanced whilst PVSI and PVSII underwent population expansion. The high fixation index values assigned to all PVSI, PVSII and PVSIII comparisons supported subdivision into three phylogroups. As it spreads more readily by aphid and contact transmission, and may elicit more severe symptoms in potato, PVSII spread constitutes a biosecurity threat for countries still free from it. Full article
(This article belongs to the Special Issue Diversity and Coinfections of Plant or Fungal Viruses 2023)
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