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Different Aspects of Plant Viral Metagenomics
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Different Aspects of Plant Viral Metagenomics

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 July 2024) | Viewed by 4671

Special Issue Editor

Dr. Eva Varallyay

E-Mail Website
Guest Editor
Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, 2100 Godollo, Hungary
Interests: plant virus diagnostics using small RNA HTS; grapevine; fruit trees
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Over the last two years, the COVID pandemic has changed how we think about viruses. We became more aware that viruses are all around us and at any point, they can threaten our ordinary life. However, for virologists already aware of the exceptional variance of viruses, this was not a surprise. In the last decade, high-throughput sequencing (HTS) methods have become available and made it possible to uncover viromes of different living organisms. HTS-based metagenomics revealed the presence of hundreds of viruses whose existence had never been described and/or anticipated.

This Special Issue of MDPI Plants will collect original research and reviews describing viromes of both crop and wild plants together with technical aspects of these research studies. I believe that this collection could complement our knowledge about the existence of particular viruses in different geographical locations and hosts and allow us to investigate their variation and distribution in field-collected samples, widening our knowledge about the metaviromes of plant ecosystems.

I believe that this Special Issue will interest researchers and plant protection engineers, and help the decision makers to take rationale plant protection measures to prevent the spread of invading pathogens around the globe.

Dr. Eva Varallyay
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. 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

  • metavirome
  • plant virus
  • HTS
  • crop
  • weed
  • vector

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Published Papers (3 papers)

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Research

12 pages, 1034 KiB  
Article
Olive Leaf Mottling Virus: A New Member of the Genus Olivavirus
by Ana Belén Ruiz-García, Thierry Candresse, José Malagón, Manuel Ruiz-Torres, Sergio Paz, Ana Pérez-Sierra and Antonio Olmos
Plants 2024, 13(16), 2290; https://doi.org/10.3390/plants13162290 - 17 Aug 2024
Viewed by 1178
Abstract
Studies of the virome of olive trees with symptoms of leaf mottling by high-throughput sequencing (HTS) revealed the presence of a new virus. Full coding genome sequences of two isolates were determined and consisted of a single RNA segment of 16,516 nt and [...] Read more.
Studies of the virome of olive trees with symptoms of leaf mottling by high-throughput sequencing (HTS) revealed the presence of a new virus. Full coding genome sequences of two isolates were determined and consisted of a single RNA segment of 16,516 nt and 16,489, respectively. The genomic organization contained 10 open reading frames (ORFs) from 5′ to 3′: ORF1a, ORF1b (RdRp), ORF2 (p22), ORF3 (p7), ORF4 (HSP70h), ORF5 (HSP90h), ORF6 (CP), ORF7 (p19), ORF8 (p12), ORF9 (p23) and ORF10 (p9). Phylogenetic analyses clustered this virus in the genus Olivavirus, family Closteroviridae, with the closest species being Olivavirus flaviolae, commonly named olive leaf yellowing-associated virus (OLYaV). However, amino acid sequences of all taxonomically relevant proteins showed, in all cases, a divergence higher than 25% between OLYaV and the new virus, indicating that it represents a new species in the genus Olivavirus for which the common name of olive leaf mottling virus (OLMV) is proposed. This study represents an advance in the genus Olivavirus and provides new insights into the olive virome. Full article
(This article belongs to the Special Issue Different Aspects of Plant Viral Metagenomics)
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12 pages, 1783 KiB  
Article
Cannabis Virome Reconstruction and Antiviral RNAi Characterization through Small RNA Sequencing
by Niccolo’ Miotti, Natalia Sukhikh, Nathalie Laboureau, Paola Casati and Mikhail M. Pooggin
Plants 2023, 12(23), 3925; https://doi.org/10.3390/plants12233925 - 21 Nov 2023
Cited by 2 | Viewed by 1340
Abstract
Viral infections pose an emerging threat to hemp (Cannabis sativa) cultivation. We used Illumina small (s)RNA sequencing for virome reconstruction and characterization of antiviral RNA interference (RNAi) in monoecious and dioecious hemp varieties, which exhibited different virus-like symptoms. Through de novo [...] Read more.
Viral infections pose an emerging threat to hemp (Cannabis sativa) cultivation. We used Illumina small (s)RNA sequencing for virome reconstruction and characterization of antiviral RNA interference (RNAi) in monoecious and dioecious hemp varieties, which exhibited different virus-like symptoms. Through de novo and reference-based sRNA assembly, we identified and reconstructed Cannabis cryptic virus (family Partitiviridae), Cannabis sativa mitovirus 1 (Mitoviridae) and Grapevine line pattern virus (Bromoviridae) as well as a novel virus tentatively classified into Partitiviridae. Members of both Partitiviridae and Bromoviridae were targeted by antiviral RNAi, generating 21 nt and, less abundant, 22 nt sRNAs from both strands of the entire virus genome, suggesting the involvement of Dicer-like (DCL) 4 and DCL2 in viral sRNA biogenesis, respectively. Mitovirus sRNAs represented predominantly the positive-sense strand and had a wider size range, with the 21 nt class being most abundant on both strands. For all viruses, 21 and 22 nt sRNAs had predominantly 5′-terminal uridine or cytosine, suggesting their binding to antiviral Argonaute (AGO) 1 and AGO5, respectively. As no clear association of any virus with symptoms was observed, further studies should clarify if these viruses individually or in combination can cause hemp diseases. Full article
(This article belongs to the Special Issue Different Aspects of Plant Viral Metagenomics)
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12 pages, 284 KiB  
Article
The First Virome of a Russian Vineyard
by Svetlana Vinogradova, Elena Porotikova, Emiliya Navrotskaya, Zsuzsanna Nagyne Galbacs, Sébastien Massart and Eva Varallyay
Plants 2023, 12(18), 3292; https://doi.org/10.3390/plants12183292 - 18 Sep 2023
Cited by 5 | Viewed by 1634
Abstract
Among other pathogens, more than 80 viruses infect grapevine. The aim of this work was to study the virome diversity of grapevine viruses and mycoviruses of a vineyard using high-throughput sequencing technologies. The grapevine virome was studied in symptomatic vines of the Rkatsiteli [...] Read more.
Among other pathogens, more than 80 viruses infect grapevine. The aim of this work was to study the virome diversity of grapevine viruses and mycoviruses of a vineyard using high-throughput sequencing technologies. The grapevine virome was studied in symptomatic vines of the Rkatsiteli cultivar (V. vinifera) collected at the vineyards of the Krasnodar Krai in Russia. Ribosomal-depleted total RNA and isolated small RNAs were used for library preparation and high-throughput sequencing. Six grapevine-infecting viruses and two viroids were validated by RT-PCR and analyzed phylogenetically. We identified the presence of grapevine leafroll-associated virus 3, grapevine Pinot gris virus, grapevine virus T, grapevine rupestris stem-pitting-associated virus, grapevine fleck virus, and grapevine rupestris vein feathering virus, as well as two viroids, grapevine yellow speckle viroid 1 and hop stunt viroid. We also studied the mycovirome of the vineyard and identified nine viruses with single-stranded positive-sense RNA genomes: alternaria arborescens mitovirus 1, botrytis cinerea mitovirus 1, botrytis cinerea mitovirus 2, botrytis cinerea mitovirus 3, botrytis cinerea mitovirus 4, sclerotinia sclerotiorum mitovirus 3, botrytis cinerea hypovirus 1, grapevine-associated narnavirus 1, and botrytis virus F. In addition, we identified botrytis cinerea hypovirus 1 satellite-like RNA and two single-stranded negative-sense RNA viruses. This is the first study of grapevine mycoviruses in Russia. The obtained result will contribute to the development of biocontrol strategies in the future. Full article
(This article belongs to the Special Issue Different Aspects of Plant Viral Metagenomics)
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