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Agronomy
Special Issues
Molecular Evolution of Plant RNA Viruses
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Molecular Evolution of Plant RNA Viruses

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Pest and Disease Management".

Deadline for manuscript submissions: closed (30 August 2023) | Viewed by 4353

Special Issue Editor

Prof. Dr. Xuefeng Yuan

E-Mail Website
Guest Editor
College of Plant Protection, Shandong Agricultural University, 61 Daizong Street, Tai 'an City, China
Interests: the control of plant viral diseases; the regulation of viral gene expression
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plant viruses are obligate parasites that rely on the host cell for their survival and replication. Viruses undergo continuous evolution for optimal propagation in hosts. Mutation is believed to be the most important way to cause evolution. In addition, recombination, reassortment, and gene rearrangement also increase the variability of virus genome. The molecular evolution of important viral nucleotide, amino acid, RNA structure or genome level may alter the fitness of viral genome and subsequent interaction with the host. A deep understanding of the molecular evolution of plant RNA viruses will contribute to the control of viral diseases. This Special Issue aims to publish cutting-edge research on the molecular evolution of plant RNA viruses, including economically important emerging viruses, genome replication and viral protein translation, the interaction between plant RNA viruses and their host, the mechanisms of viral evolution and so on. We welcome comprehensive reviews, full-text research articles, and short communications.

Prof. Dr. Xuefeng Yuan
Guest Editor

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. Agronomy 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

  • plant RNA viruses
  • viral evolution
  • mutation
  • recombination
  • viral variety
  • fitness

Published Papers (3 papers)

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Research

14 pages, 2358 KiB  
Article
Probing the RNA Structure of a Satellite RNA of Cucumber Mosaic Virus Using SHAPE Method
by Zhifei Liu, Xinran Cao, Chengming Yu and Xuefeng Yuan
Agronomy 2023, 13(8), 1990; https://doi.org/10.3390/agronomy13081990 - 27 Jul 2023
Viewed by 892
Abstract
Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) is a widely used technique for RNA structure analysis using N-methylisatoic anhydride (NMIA) treatment that has been proven to be applicable to different types of RNA templates. In this study, we performed the structural analysis [...] Read more.
Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) is a widely used technique for RNA structure analysis using N-methylisatoic anhydride (NMIA) treatment that has been proven to be applicable to different types of RNA templates. In this study, we performed the structural analysis of the viral satellite RNA of cucumber mosaic virus TA-Tb (satCMV TA-Tb) using the SHAPE method. In the preliminary experiment, we optimized the protocol of SHAPE method for analyzing satCMV TA-Tb by determining a suitable quantity of template RNA. This optimization effectively reduced the appearance of a large number of intense bands in the NMIA-untreated sample lane, along with a strong overall background signal that prevented the clear elucidation of the RNA structure. SHAPE analysis indicated the presence of non-structured, single-stranded flexible regions throughout satCMV TA-Tb with prominent flexible stretches located around nucleotide positions 145 to 200. The positions of these flexible regions were particularly consistent with a secondary structure of satCMV TA-Tb predicted by mfold software v.2.3, which consisted of five 5′- and 3′-proximal stem-loops and one internal large multi-branched stem-loop. Sequence alignment and secondary RNA structure prediction of other satCMV sequences that are phylogenetically the same group with satCMV TA-Tb also suggested the presence of 5′- and 3′-proximal stem-loop structures. Our data provide the structural basis for elucidating the mechanism by which satCMV TA-Tb regulates the pathogenicity and replication of its helper virus. Full article
(This article belongs to the Special Issue Molecular Evolution of Plant RNA Viruses)
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14 pages, 9977 KiB  
Article
A Novel Isolate of Bean Common Mosaic Virus Isolated from Crownvetch (Securigera varia L. Lassen)
by Daniel Mihálik, Simona Grešíková, Richard Hančinský, Pavel Cejnar, Michaela Havrlentová and Ján Kraic
Agronomy 2023, 13(7), 1677; https://doi.org/10.3390/agronomy13071677 - 22 Jun 2023
Cited by 1 | Viewed by 1124
Abstract
Bean common mosaic virus from the genus Potyvirus has a wide range of hosts and a very negative impact on cultivated crops from the genus Phaseolus. The risk of viral infection of economically important crops increases even if the carriers of the [...] Read more.
Bean common mosaic virus from the genus Potyvirus has a wide range of hosts and a very negative impact on cultivated crops from the genus Phaseolus. The risk of viral infection of economically important crops increases even if the carriers of the virus are related plant species growing on agroecological interfaces. Such plant species have emerged as new hosts for BCMV, usually harboring novel genetic variants of the virus. A novel genetic variant of BCMV was isolated from a symptomatic crownvetch plant, where the presence of this virus was confirmed via Western blot analysis and via amino acid identities in peptide fragments of CI, HC-pro, and CP proteins using the nanoLC-ESI-Q-TOF. The novel BCMV SVK isolate differed from the most genetically similar one in 0.91% of nucleotides and 1.55% of amino acids. The highest number of amino acid substitutions (8.8% of amino acids) was in the P1 protein, followed by CP (2.44% of amino acids). Minor substitutions were in Hc-pro, CI, and Nib proteins. The symptomatic crownvetch plant was confirmed as a new host and carrier of the novel BCMV isolate. Full article
(This article belongs to the Special Issue Molecular Evolution of Plant RNA Viruses)
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9 pages, 5482 KiB  
Communication
Biological and Molecular Characterization of Clover Yellow Vein Virus Infecting Trifolium repens in China
by Zhengnan Li, Lei Xu, Pingping Sun, Mo Zhu, Lei Zhang, Bin Zhang and Shuang Song
Agronomy 2023, 13(5), 1193; https://doi.org/10.3390/agronomy13051193 - 24 Apr 2023
Cited by 1 | Viewed by 1660
Abstract
White clover (Trifolium repens L.) is an important perennial legume forage and ornamental plant, and is widely distributed and cultivated in the world. Recently, white clover plants showing symptoms of leaf mosaic and redding were observed in Hohhot, Inner Mongolia of China. [...] Read more.
White clover (Trifolium repens L.) is an important perennial legume forage and ornamental plant, and is widely distributed and cultivated in the world. Recently, white clover plants showing symptoms of leaf mosaic and redding were observed in Hohhot, Inner Mongolia of China. In this work, flexuous filamentous viral particles of about 700 × 13 nm in size were observed in the symptomatic leaf samples. The infection of clover yellow vein virus (ClYVV) was confirmed by small RNA sequencing and RT-PCR validation. Mechanical inoculation assays showed that this ClYVV isolate (ClYVV-IM) can infect a range of herbaceous species, including Nicotiana benthamiana, N. occidentalis, Chenopodium quinoa, C. amaranticolor, Vicia faba, Vigna unguiculata, and Solanum lycopersicum, causing various symptoms. The complete genome sequence of ClYVV-IM consists of 9565 nt and shared sequence identities, ranging from 83.05% to 96.30%, with those of the other ClYVV isolates published in GenBank. Phylogenetic analyses based on the polyprotein nucleotide and amino acid sequences clustered 15 ClYVV isolates into two groups and ClYVV-IM located in Group I. Two potential recombination events located at 914–2970 nt and 5153–5694 nt were detected in the genome of ClYVV-IM. To our knowledge, this is the first report of occurrence and complete genome of ClYVV infecting white clover in China. Full article
(This article belongs to the Special Issue Molecular Evolution of Plant RNA Viruses)
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