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Plants Viroid/Viruses: Insight into Genome and Epidemiology
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Plants Viroid/Viruses: Insight into Genome and Epidemiology

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 (31 August 2022) | Viewed by 29359

Special Issue Editor

Dr. Ajay Kumar Mishra

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Guest Editor
Khalifa Centre for Genetic Engineering & Biotechnology, United Arab Emirates University, Al Ain P.O. Box 1555, United Arab Emirates
Interests: Parasitic RNA; long non-coding RNA in plant-viroid interaction; Molecular mechanism of viroid pathogenicity; Mediator complex in disease resistance against viroids
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Viruses and viroids are infectious pathogens, which as an invisible foe cause disruption in host physiology to induce plant diseases of economic and agronomic significance in many crops, thus representing a serious threat to global food security. The replication through a dsRNA intermediate within living plant cells or protoplasts is one of the unique and common properties shared by plant RNA viruses and viroids. In the course of interaction, virus or viroids render the blueprint in the form of their nucleic acid and exploit the structural materials (nucleic acid and proteins), the energy, and the cellular machinery of host plants for their replication and movement to adjacent and distant plant cells. The host range and spread of viruses/viroids through different modes of  transmission has increased dramatically in recent years. The climate change, international trade in agricultural products as well as reduced resilience in production systems due to decades of agricultural intensification have played major role. The profound progress in the last decades on uncovering the molecular dialog between viruses/viroids, came up with multidimensional strategies directly exploitable in crop improvement programs. In this context, epidemiology, molecular biology, genomics, breeding programs, and interaction with vector and host are important realm of studies, which offers insight into problem-solving and decision-making steps to tackle these traitors in sustainable agricultural production.

In this special issue, we aim to cover the virus or viroid-associated plant diseases and their impact on crop production, recent knowledge in virus or viroid pathogenicity, transport, transmission, effective control strategies, diagnostic techniques, plant resistances against viruses/viroids, crop improvement programs and global transcriptome or proteome or metabolome, transcription factors, small or long non-coding RNA profiling in response to virus or viroid infection. I cordially invite viroid/virus community researchers to contribute their discoveries and thoughts as a research article or review in this special issue.

Dr. Ajay Kumar Mishra
Guest Editor

Manuscript Submission Information

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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

  • Viruses
  • Viroids
  • Molecular evolution
  • Plant–virus/viroid interactions
  • Replication
  • Pathogenicity
  • Transmission
  • Diseases
  • Diagnosis
  • Disease Management

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Published Papers (7 papers)

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Research

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14 pages, 2821 KiB  
Article
Complete Genome Sequence of a Novel Monopartite Mastrevirus, Soybean Geminivirus B, Isolated from Soybean (Glycine max (L.) Merrill)
by Hoseong Choi, Yeonhwa Jo, Jinsung Hong, Hyunjung Chung, Sooyeon Choi, Sangmin Kim, Jeonghun Lee, Sanghyun Moh, Bongchoon Lee and Won Kyong Cho
Plants 2022, 11(13), 1768; https://doi.org/10.3390/plants11131768 - 3 Jul 2022
Cited by 3 | Viewed by 2466
Abstract
Soybean is one of the most important crops in Korea. To identify the viruses infecting soybean, we conducted RNA sequencing with samples displaying symptoms of viral disease. A contig displaying sequence similarity to the known Geminivirus was identified. A polymerase chain reaction (PCR) [...] Read more.
Soybean is one of the most important crops in Korea. To identify the viruses infecting soybean, we conducted RNA sequencing with samples displaying symptoms of viral disease. A contig displaying sequence similarity to the known Geminivirus was identified. A polymerase chain reaction (PCR) using two different pairs of back-to-back primers and rolling circle amplification (RCA) confirmed the complete genome of a novel virus named soybean geminivirus B (SGVB), consisting of a circular monopartite DNA genome measuring 2616 nucleotides (nt) in length. SGVB contains four open reading frames (ORFs) and three intergenic regions (IRs). IR1 includes a nonanucleotide origin of replication in the stem-loop structure. Phylogenetic and BLAST analyses demonstrated that SGVB could be a novel virus belonging to the genus Mastrevirus in the family Geminiviridae. We generated infectious clones for SGVB by adding a copy of the IR1 region of SGVB, comparing the V-ori in addition to the full-length genome of SGVB. Using the infectious clones, we observed chlorosis and leaf curling with a latent infection in the inoculated Nicotiana benthamiana plants, while none of the inoculated soybean plants showed any visible symptoms of disease. This study provides the complete genome sequence and infectious clones of a novel Mastrevirus referred to as SGVB from soybean in Korea. Full article
(This article belongs to the Special Issue Plants Viroid/Viruses: Insight into Genome and Epidemiology)
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8 pages, 782 KiB  
Article
Identification and Characterization of a Garlic Virus E Genome in Garlic (Allium sativum L.) Using High-Throughput Sequencing from India
by Malyaj R. Prajapati, Aakansha Manav, Jitender Singh, Pankaj Kumar, Amit Kumar, Ravindra Kumar, Satya Prakash and Virendra Kumar Baranwal
Plants 2022, 11(2), 224; https://doi.org/10.3390/plants11020224 - 15 Jan 2022
Cited by 10 | Viewed by 3333
Abstract
Garlic (Allium sativum L.) plants exhibiting mosaics, deformation, and yellow stripes symptoms were identified in Meerut City, Uttar Pradesh, India. To investigate the viruses in the garlic samples, the method of high-throughput sequencing (HTS) was used. Complete genome of the garlic virus [...] Read more.
Garlic (Allium sativum L.) plants exhibiting mosaics, deformation, and yellow stripes symptoms were identified in Meerut City, Uttar Pradesh, India. To investigate the viruses in the garlic samples, the method of high-throughput sequencing (HTS) was used. Complete genome of the garlic virus E (GarV-E) isolate (NCBI accession No. MW925710) was retrieved. The virus complete genome comprises 8450 nucleotides (nts), excluding the poly (A) tail at the 3′ terminus, with 5′ and 3′ untranslated regions (UTRs) of 99 and 384 nts, respectively, and ORFs encoding replicase with a conserved motif for RNA-dependent RNA polymerase (RdRP), TGB1, TGB2, TGB3, serine-rich protein, coat protein, and nucleic acid binding protein (NABP). The sequence homology shared 83.49–90.40% and 87.48–92.87% with those of GarV-E isolates available in NCBI at the nucleotide and amino acid levels, respectively. Phylogenetic analysis showed a close relationship of this isolate from India (MW925710) with GarV-E isolate YH (AJ292230) from Zhejiang, China. The presence of GarV-E was also confirmed by RT-PCR. The present study is the first report of GarV-E in garlic cultivar Yamuna Safed-3 grown in northern India. However, further studies are needed to confirm its role in symptom development, nationwide distribution, genetic diversity, and potential yield loss to the garlic in India. Full article
(This article belongs to the Special Issue Plants Viroid/Viruses: Insight into Genome and Epidemiology)
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13 pages, 2103 KiB  
Article
An Improved Method for the Extraction of Nucleic Acids from Plant Tissue without Grinding to Detect Plant Viruses and Viroids
by Tatsuji Hataya
Plants 2021, 10(12), 2683; https://doi.org/10.3390/plants10122683 - 6 Dec 2021
Cited by 2 | Viewed by 4708
Abstract
Gene amplification techniques such as polymerase chain reaction (PCR) are widely used for the diagnosis of plant diseases caused by viruses and viroids. It is preferable that sample preparation methods for PCR or reverse transcription (RT) PCR are rapid, straightforward, and inexpensive. We [...] Read more.
Gene amplification techniques such as polymerase chain reaction (PCR) are widely used for the diagnosis of plant diseases caused by viruses and viroids. It is preferable that sample preparation methods for PCR or reverse transcription (RT) PCR are rapid, straightforward, and inexpensive. We previously reported a method for the extraction of nucleic acids without mechanical tissue grinding using a buffer containing potassium ethyl xanthogenate (PEX) to detect viroid RNAs. In the present report, the previous PEX method was improved and simplified. In the simplified PEX (SPEX) method, the process of PEX buffer treatment for plant cell wall disruption is improved to one step of incubation at 80 °C for 10 min, instead of three steps that took more than 26 min at 65 °C in the previous method. Total nucleic acids could be extracted from fresh, frozen, or dried leaves of a cultivar or wild species of tobacco, tomato, citron, hop plants, and pericarps of persimmon fruits by the SPEX method. Several RNA viruses and viroids were successfully detected from the extracted nucleic acids together with an internal mRNA by RT-PCR. The SPEX method may be useful for detecting not only viruses and viroids, but also other plant pathogens. Full article
(This article belongs to the Special Issue Plants Viroid/Viruses: Insight into Genome and Epidemiology)
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15 pages, 3082 KiB  
Article
Transformation of Seed Non-Transmissible Hop Viroids in Nicotiana benthamiana Causes Distortions in Male Gametophyte Development
by Lenka Steinbachová, Jaroslav Matoušek, Gerhard Steger, Helena Matoušková, Sebastjan Radišek and David Honys
Plants 2021, 10(11), 2398; https://doi.org/10.3390/plants10112398 - 6 Nov 2021
Cited by 6 | Viewed by 2555
Abstract
Viroids are small, non-coding, parasitic RNAs that promote developmental distortions in sensitive plants. We analyzed pollen of Nicotiana benthamiana after infection and/or ectopic transformation with cDNAs of citrus bark cracking viroid (CBCVd), apple fruit crinkle viroid (AFCVd) and potato spindle tuber viroid (PSTVd) [...] Read more.
Viroids are small, non-coding, parasitic RNAs that promote developmental distortions in sensitive plants. We analyzed pollen of Nicotiana benthamiana after infection and/or ectopic transformation with cDNAs of citrus bark cracking viroid (CBCVd), apple fruit crinkle viroid (AFCVd) and potato spindle tuber viroid (PSTVd) variant AS1. These viroids were seed non-transmissible in N. benthamiana. All viroids propagated to high levels in immature anthers similar to leaves, while their levels were drastically reduced by approximately 3.6 × 103, 800 and 59 times in mature pollen of CBCVd, AFCVd and PSTVd infected N. benthamiana, respectively, in comparison to leaves. These results suggest similar elimination processes during male gametophyte development as in the Nicotiana tabacum we presented in our previous study. Mature pollen of N. benthamiana showed no apparent defects in infected plants although all three viroids induced strong pathological symptoms on leaves. While Nicotiana species have naturally bicellular mature pollen, we noted a rare occurrence of mature pollen with three nuclei in CBCVd-infected N. benthamiana. Changes in the expression of ribosomal marker proteins in AFCVd-infected pollen were detected, suggesting some changes in pollen metabolism. N. benthamiana transformed with 35S-driven viroid cDNAs showed strong symptoms including defects in pollen development. A large number of aborted pollen (34% and 62%) and a slight increase of young pollen grains (8% and 15%) were found in mature pollen of AFCVd and CBCVd transformants, respectively, in comparison to control plants (3.9% aborted pollen and 0.3% young pollen). Moreover, pollen grains with malformed nuclei or trinuclear pollen were found in CBCVd-transformed plants. Our results suggest that “forcing” overexpression of seed non-transmissible viroid led to strong pollen pathogenesis. Viroid adaptation to pollen metabolism can be assumed as an important factor for viroid transmissibility through pollen and seeds. Full article
(This article belongs to the Special Issue Plants Viroid/Viruses: Insight into Genome and Epidemiology)
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23 pages, 14362 KiB  
Article
The Influence of Hop Latent Viroid (HLVd) Infection on Gene Expression and Secondary Metabolite Contents in Hop (Humulus lupulus L.) Glandular Trichomes
by Josef Patzak, Alena Henychová, Karel Krofta, Petr Svoboda and Ivana Malířová
Plants 2021, 10(11), 2297; https://doi.org/10.3390/plants10112297 - 26 Oct 2021
Cited by 11 | Viewed by 3879
Abstract
Viroids are small infectious pathogens, composed of a short single-stranded circular RNA. Hop (Humulus lupulus L.) plants are hosts to four viroids from the family Pospiviroidae. Hop latent viroid (HLVd) is spread worldwide in all hop-growing regions without any visible symptoms [...] Read more.
Viroids are small infectious pathogens, composed of a short single-stranded circular RNA. Hop (Humulus lupulus L.) plants are hosts to four viroids from the family Pospiviroidae. Hop latent viroid (HLVd) is spread worldwide in all hop-growing regions without any visible symptoms on infected hop plants. In this study, we evaluated the influence of HLVd infection on the content and the composition of secondary metabolites in maturated hop cones, together with gene expression analyses of involved biosynthesis and regulation genes for Saaz, Sládek, Premiant and Agnus cultivars. We confirmed that the contents of alpha bitter acids were significantly reduced in the range from 8.8% to 34% by viroid infection. New, we found that viroid infection significantly reduced the contents of xanthohumol in the range from 3.9% to 23.5%. In essential oils of Saaz cultivar, the contents of monoterpenes, terpene epoxides and terpene alcohols were increased, but the contents of sesquiterpenes and terpene ketones were decreased. Secondary metabolites changes were supported by gene expression analyses, except essential oils. Last-step biosynthesis enzyme genes, namely humulone synthase 1 (HS1) and 2 (HS2) for alpha bitter acids and O-methytransferase 1 (OMT1) for xanthohumol, were down-regulated by viroid infection. We found that the expression of ribosomal protein L5 (RPL5) RPL5 and the splicing of transcription factor IIIA-7ZF were affected by viroid infection and a disbalance in proteosynthesis can influence transcriptions of biosynthesis and regulatory genes involved in of secondary metabolites biosynthesis. We suppose that RPL5/TFIIIA-7ZF regulatory cascade can be involved in HLVd replication as for other viroids of the family Pospiviroidae. Full article
(This article belongs to the Special Issue Plants Viroid/Viruses: Insight into Genome and Epidemiology)
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18 pages, 4256 KiB  
Article
Tolerance Even to Lethal Strain of Potato Spindle Tuber Viroid Found in Wild Tomato Species Can Be Introduced by Crossing
by Takashi Naoi and Tatsuji Hataya
Plants 2021, 10(3), 575; https://doi.org/10.3390/plants10030575 - 18 Mar 2021
Cited by 6 | Viewed by 3434
Abstract
To date, natural resistance or tolerance, which can be introduced into crops by crossing, to potato spindle tuber viroid (PSTVd) has not been reported. Additionally, responses to PSTVd infection in many wild tomato species, including some species that can be crossed with PSTVd-susceptible [...] Read more.
To date, natural resistance or tolerance, which can be introduced into crops by crossing, to potato spindle tuber viroid (PSTVd) has not been reported. Additionally, responses to PSTVd infection in many wild tomato species, including some species that can be crossed with PSTVd-susceptible cultivated tomatoes (Solanum lycopersicum var. lycoperaicum), have not been ascertained. The aim of this study was to evaluate responses to PSTVd infection including resistance and tolerance. Accordingly, we inoculated several cultivated and wild tomato species with intermediate and lethal strains of PSTVd. None of the host plants exhibited sufficient resistance to PSTVd to render systemic infection impossible; however, these plants displayed other responses, including tolerance. Further analysis of PSTVd accumulation revealed low accumulation of PSTVd in two wild species, exhibiting high tolerance, even to the lethal strain. Additionally, F1 hybrids generated by crossing a PSTVd-sensitive wild tomato (Solanum lycopersicum var. cerasiforme) with these wild relatives also exhibited tolerance to the lethal PSTVd strain, which is accompanied by low PSTVd accumulation during early infection. These results indicate that the tolerance toward PSTVd in wild species is a dominant trait and can be utilized for tomato breeding by crossing. Full article
(This article belongs to the Special Issue Plants Viroid/Viruses: Insight into Genome and Epidemiology)
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Review

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23 pages, 439 KiB  
Review
Mechanisms of Microbial Plant Protection and Control of Plant Viruses
by Lakshmaiah Manjunatha, Hosahatti Rajashekara, Leela Saisree Uppala, Dasannanamalige Siddesh Ambika, Balanagouda Patil, Kodegandlu Subbanna Shankarappa, Vishnu Sukumari Nath, Tiptur Rooplanaik Kavitha and Ajay Kumar Mishra
Plants 2022, 11(24), 3449; https://doi.org/10.3390/plants11243449 - 9 Dec 2022
Cited by 24 | Viewed by 6416
Abstract
Plant viral diseases are major constraints causing significant yield losses worldwide in agricultural and horticultural crops. The commonly used methods cannot eliminate viral load in infected plants. Many unconventional methods are presently being employed to prevent viral infection; however, every time, these methods [...] Read more.
Plant viral diseases are major constraints causing significant yield losses worldwide in agricultural and horticultural crops. The commonly used methods cannot eliminate viral load in infected plants. Many unconventional methods are presently being employed to prevent viral infection; however, every time, these methods are not found promising. As a result, it is critical to identify the most promising and sustainable management strategies for economically important plant viral diseases. The genetic makeup of 90 percent of viral diseases constitutes a single-stranded RNA; the most promising way for management of any RNA viruses is through use ribonucleases. The scope of involving beneficial microbial organisms in the integrated management of viral diseases is of the utmost importance and is highly imperative. This review highlights the importance of prokaryotic plant growth-promoting rhizobacteria/endophytic bacteria, actinomycetes, and fungal organisms, as well as their possible mechanisms for suppressing viral infection in plants via cross-protection, ISR, and the accumulation of defensive enzymes, phenolic compounds, lipopeptides, protease, and RNase activity against plant virus infection. Full article
(This article belongs to the Special Issue Plants Viroid/Viruses: Insight into Genome and Epidemiology)
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