Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
7.1
4.7
Journals
Viruses
Special Issues
Plant Virus Metagenomics
share announcement

Plant Virus Metagenomics

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 (31 December 2023) | Viewed by 7449

Special Issue Editor

Prof. Dr. Renyi Liu

E-Mail Website
Guest Editor
Center for Agroforestry Mega Data Science, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
Interests: plant viruses; bioinformatics; plant genomics; plant metabolomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

With the advances in sequencing technologies and reduced costs involved, metagenomics has become an indispensable tool in various aspects of plant virus research, namely in the identification and characterization of novel viruses, virus diversity and evolution, viral pathogenesis, and virus–host interactions, as well as in RNA silencing, virus detection and diagnosis.

This Special Issue on plant virus metagenomics invites authors to submit original research or review articles that involve the application of metagenomics in any aspect of plant virus research. Researchers are encouraged to submit novel applications of advanced sequencing technologies and to develop bioinformatics tools and databases related to plant virus metagenomics.

Prof. Dr. Renyi Liu
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. 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

  • virus metagenomics
  • plant viruses
  • identification of novel viruses
  • plant–virus interaction

Published Papers (5 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

18 pages, 2443 KiB  
Article
Multiple Infections with Viruses of the Family Tymoviridae in Czech Grapevines
by Marcela Komínková, Karima Ben Mansour, Petr Komínek, Jana Brožová and Radomíra Střalková
Viruses 2024, 16(3), 343; https://doi.org/10.3390/v16030343 - 23 Feb 2024
Viewed by 633
Abstract
This study focused on the viruses of the Tymoviridae family that infect grapevines in the Czech Republic. Complete sequences of GFkV (grapevine fleck virus) and GRGV (grapevine red globe virus) from the genus Maculavirus and GRVFV (grapevine rupestris vein feathering virus) and GSyV-1 [...] Read more.
This study focused on the viruses of the Tymoviridae family that infect grapevines in the Czech Republic. Complete sequences of GFkV (grapevine fleck virus) and GRGV (grapevine red globe virus) from the genus Maculavirus and GRVFV (grapevine rupestris vein feathering virus) and GSyV-1 (grapevine Syrah virus 1) from the genus Marafivirus were obtained using high-throughput sequencing of small RNAs and total RNAs. Mixed infections with these viruses were observed, as well as several variants of these viruses in the same plant. Phylogenetic analysis showed the position of the newly obtained virus isolates within the Tymoviridae family. Recombinant analysis provided evidence of single and multiple intraspecific recombinations in GRGV, GSyV-1, and GRVFV. Additionally, GAMaV, a grapevine virus from the genus Marafivirus, was reported for the first time in the Czech Republic. Full article
(This article belongs to the Special Issue Plant Virus Metagenomics)
►▼ Show Figures

Graphical abstract

34 pages, 4383 KiB  
Article
Meta-Transcriptomic Analysis Uncovers the Presence of Four Novel Viruses and Multiple Known Virus Genera in a Single Hibiscus rosa-sinensis Plant in Colombia
by Avijit Roy, Sam Grinstead, Guillermo Leon Martínez, Juan Carlos Campos Pinzón, Schyler O. Nunziata, Chellappan Padmanabhan and John Hammond
Viruses 2024, 16(2), 267; https://doi.org/10.3390/v16020267 - 07 Feb 2024
Viewed by 986
Abstract
Hibiscus is not native to Colombia but well suited to its arid soil and dry climates. A single hibiscus plant from Risaralda, showing black spots on upper and lower sides of its leaves, was collected for virome analysis using meta-transcriptomic high-throughput sequencing technology. [...] Read more.
Hibiscus is not native to Colombia but well suited to its arid soil and dry climates. A single hibiscus plant from Risaralda, showing black spots on upper and lower sides of its leaves, was collected for virome analysis using meta-transcriptomic high-throughput sequencing technology. Bioinformatic analysis identified 12.5% of the total reads in the Ribo-Zero cDNA library which mapped to viral genomes. BLAST searches revealed the presence of carlavirus, potexvirus, and of known members of the genera Betacarmovirus, Cilevirus, Nepovirus, and Tobamovirus in the sample; confirmed by RT-PCR with virus-specific primers followed by amplicon sequencing. Furthermore, in silico analysis suggested the possibility of a novel soymovirus, and a new hibiscus strain of citrus leprosis virus C2 in the mixed infection. Both RNA dependent RNA polymerase and coat protein gene sequences of the potex and carla viruses shared less than 72% nucleotide and 80% amino acid identities with any alphaflexi- and betaflexi-virus sequences available in GenBank, identifying three novel carlavirus and one potexvirus species in the Hibiscus rosa-sinensis plant. The detection of physalis vein necrosis nepovirus and passion fruit green spot cilevirus in hibiscus are also new reports from Colombia. Overall, the meta-transcriptome analysis identified the complex virome associated with the black spot symptoms on hibiscus leaves and demonstrated the diversity of virus genera tolerated in the mixed infection of a single H. rosa-sinensis plant. Full article
(This article belongs to the Special Issue Plant Virus Metagenomics)
►▼ Show Figures

Figure 1

28 pages, 8408 KiB  
Article
Grapevine Virome of the Don Ampelographic Collection in Russia Has Concealed Five Novel Viruses
by Daria Belkina, Daria Karpova, Elena Porotikova, Ilya Lifanov and Svetlana Vinogradova
Viruses 2023, 15(12), 2429; https://doi.org/10.3390/v15122429 - 14 Dec 2023
Viewed by 1641
Abstract
In this study, an analysis of the virome of 51 grapevines from the Don ampelographic collection named after Ya. I. Potapenko (Russia) was performed using high-throughput sequencing of total RNA. A total of 20 previously described grapevine viruses and 4 viroids were identified. [...] Read more.
In this study, an analysis of the virome of 51 grapevines from the Don ampelographic collection named after Ya. I. Potapenko (Russia) was performed using high-throughput sequencing of total RNA. A total of 20 previously described grapevine viruses and 4 viroids were identified. The most detected were grapevine rupestris stem pitting-associated virus (98%), hop stunt viroid (98%), grapevine Pinot gris virus (96%), grapevine yellow speckle viroid 1 (94%), and grapevine fleck virus (GFkV, 80%). Among the economically significant viruses, the most present were grapevine leafroll-associated virus 3 (37%), grapevine virus A (24%), and grapevine leafroll-associated virus 1 (16%). For the first time in Russia, a grapevine-associated tymo-like virus (78%) was detected. After a bioinformatics analysis, 123 complete or nearly complete viral genomes and 64 complete viroid genomes were assembled. An analysis of the phylogenetic relationships with reported global isolates was performed. We discovered and characterized the genomes of five novel grapevine viruses: bipartite dsRNA grapevine alphapartitivirus (genus Alphapartitivirus, family Partitiviridae), bipartite (+) ssRNA grapevine secovirus (genus Fabavirus, family Secoviridae) and three (+) ssRNA grapevine umbra-like viruses 2, -3, -4 (which phylogenetically occupy an intermediate position between representatives of the genus Umbravirus and umbravirus-like associated RNAs). Full article
(This article belongs to the Special Issue Plant Virus Metagenomics)
►▼ Show Figures

Figure 1

19 pages, 2685 KiB  
Article
Area Wide Monitoring of Plant and Honey Bee (Apis mellifera) Viruses in Blueberry (Vaccinium corymbosum) Agroecosystems Facilitated by Honey Bee Pollination
by Eunseo Lee, Raj Vansia, James Phelan, Andrea Lofano, Adam Smith, Aiming Wang, Guillaume J. Bilodeau, Stephen F. Pernal, M. Marta Guarna, Michael Rott and Jonathan S. Griffiths
Viruses 2023, 15(5), 1209; https://doi.org/10.3390/v15051209 - 20 May 2023
Cited by 3 | Viewed by 2126
Abstract
Healthy agroecosystems are dependent on a complex web of factors and inter-species interactions. Flowers are hubs for pathogen transmission, including the horizontal or vertical transmission of plant-viruses and the horizontal transmission of bee-viruses. Pollination by the European honey bee (Apis mellifera) [...] Read more.
Healthy agroecosystems are dependent on a complex web of factors and inter-species interactions. Flowers are hubs for pathogen transmission, including the horizontal or vertical transmission of plant-viruses and the horizontal transmission of bee-viruses. Pollination by the European honey bee (Apis mellifera) is critical for industrial fruit production, but bees can also vector viruses and other pathogens between individuals. Here, we utilized commercial honey bee pollination services in blueberry (Vaccinium corymbosum) farms for a metagenomics-based bee and plant virus monitoring system. Following RNA sequencing, viruses were identified by mapping reads to a reference sequence database through the bioinformatics portal Virtool. In total, 29 unique plant viral species were found at two blueberry farms in British Columbia (BC). Nine viruses were identified at one site in Ontario (ON), five of which were not identified in BC. Ilarviruses blueberry shock virus (BlShV) and prune dwarf virus (PDV) were the most frequently detected viruses in BC but absent in ON, while nepoviruses tomato ringspot virus and tobacco ringspot virus were common in ON but absent in BC. BlShV coat protein (CP) nucleotide sequences were nearly identical in all samples, while PDV CP sequences were more diverse, suggesting multiple strains of PDV circulating at this site. Ten bee-infecting viruses were identified, with black queen cell virus frequently detected in ON and BC. Area-wide bee-mediated pathogen monitoring can provide new insights into the diversity of viruses present in, and the health of, bee-pollination ecosystems. This approach can be limited by a short sampling season, biased towards pollen-transmitted viruses, and the plant material collected by bees can be very diverse. This can obscure the origin of some viruses, but bee-mediated virus monitoring can be an effective preliminary monitoring approach. Full article
(This article belongs to the Special Issue Plant Virus Metagenomics)
►▼ Show Figures

Figure 1

12 pages, 4186 KiB  
Article
Identification and Characterization of a Novel Quanzhou Mulberry Virus from Mulberry (Morus alba)
by Jia Wei, Lei Chen, Zilong Xu, Peigang Liu, Yan Zhu, Tianbao Lin, Lu Yang, Yuan Huang and Zhiqiang Lv
Viruses 2023, 15(5), 1131; https://doi.org/10.3390/v15051131 - 09 May 2023
Viewed by 1299
Abstract
In this study, we discovered a new virus named Quanzhou mulberry virus (QMV), which was identified from the leaves of an ancient mulberry tree. This tree is over 1300 years old and is located at Fujian Kaiyuan Temple, a renowned cultural heritage site [...] Read more.
In this study, we discovered a new virus named Quanzhou mulberry virus (QMV), which was identified from the leaves of an ancient mulberry tree. This tree is over 1300 years old and is located at Fujian Kaiyuan Temple, a renowned cultural heritage site in China. We obtained the complete genome sequence of QMV using RNA sequencing followed by rapid amplification of complementary DNA ends (RACE). The QMV genome is 9256 nucleotides (nt) long and encodes five open reading frames (ORFs). Its virion was made of icosahedral particles. Phylogenetic analysis suggests that it belongs to the unclassified Riboviria. An infectious clone for QMV was generated and agroinfiltrated into Nicotiana benthamiana and mulberry, resulting in no visible disease symptoms. However, systemic movement of the virus was only observed in mulberry seedlings, suggesting that it has a host-specific pattern of movement. Our findings provide a valuable reference for further studies on QMV and related viruses, contributing to the understanding of viral evolution and biodiversity in mulberry. Full article
(This article belongs to the Special Issue Plant Virus Metagenomics)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-5
Back to TopTop