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Viruses
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Genomics in Plant Viral Research
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Genomics in Plant Viral Research

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 January 2022) | Viewed by 33189

Special Issue Editors

Dr. Solomon Maina

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Guest Editor
Plant Biosecurity Research and Diagnostics, NSW Department of Primary Industries | Biosecurity & Food Safety, Elizabeth Macarthur Agricultural Institute, Menangle, NSW 2568, Australia
Interests: plant viruses; high throughput sequencing; virus recombination and phylogeny; virus bioinformatics; biosecurity; emerging genomics diagnostic methods
Prof. Dr. Brendan Rodoni

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Guest Editor
Agriculture Victoria and School of Applied Systems Biology, La Trobe University, AgriBio Centre, 5 Ring Rd, La Trobe University, Bundoora, VIC 3083, Australia
Interests: biosecurity; plant viruses; genomics and diagnostic

Special Issue Information

Dear Colleagues,

Emerging and re-emerging plant viruses present a major concern for food security and public health globally. Global pandemics such as CoVid-19 underscore the need of applying genomics and epidemiology approaches in detecting, identifying, and tracing viruses within their pathosystem. Similarly, the emergence and re-emergence of plant viruses from native vegetation to cultivated crops has enormous consequences towards global food security and public health at large. As such, novel robust cost-effective genomics-based diagnostic and epidemiological analysis offer an opportunity to decipher viral populations in both non- and cultivated plants, assess their potential biosecurity threat, and implement effective management measures. Over the last decade, high-throughput sequencing and bioinformatics have become a core component of virus research underpinning genomics epidemiology.

This Special Issue invites novel original papers, reviews, and opinion articles that explore (i) the development and application of novel cutting-edge sequencing approaches to better understand or manage plant viruses from non and cultivated plant origins through discovery, transmission, evolution, and genomics epidemiology, (ii) new methods or technologies, exploring transboundary, biosecurity threats such as border screening, prevention, and control of emerging and re-emerging plant viruses. In addition, due to the scale and complexity of HTS, virus genomics, bioinformatics analyses and interpretation, a paradigm shift is required in designing future standards or recommendations in plant virus genome-based diagnostic approaches. In this regard, novel original papers, reviews, and opinion articles exploring potential quality management systems of the HTS that can be adopted globally will be highly regarded.

Dr. Solomon Maina
Prof. Brendan Rodoni
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.

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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 viruses
  • high-throughput sequencing
  • genomics epidemiology
  • biosecurity

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Published Papers (9 papers)

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Editorial

Jump to: Research, Review, Other

4 pages, 184 KiB  
Editorial
Genomics in Plant Viral Research
by Solomon Maina and Brendan Rodoni
Viruses 2022, 14(4), 668; https://doi.org/10.3390/v14040668 - 24 Mar 2022
Cited by 2 | Viewed by 2176
Abstract
Plant viruses constitute a large group of pathogens causing damaging diseases in many agricultural and horticultural crops around the world [...] Full article
(This article belongs to the Special Issue Genomics in Plant Viral Research)

Research

Jump to: Editorial, Review, Other

12 pages, 2430 KiB  
Article
Metatranscriptomic Sequencing Suggests the Presence of Novel RNA Viruses in Rice Transmitted by Brown Planthopper
by Shufen Chao, Haoran Wang, Qing Yan, Long Chen, Guoqing Chen, Yihong Wu, Baozhong Meng, Lixin Jin, Xudong Zhu and Guozhong Feng
Viruses 2021, 13(12), 2464; https://doi.org/10.3390/v13122464 - 9 Dec 2021
Cited by 6 | Viewed by 2837
Abstract
Viral pathogens are a major threat to stable crop production. Using a backcross strategy, we find that integrating a dominant brown planthopper (BPH) resistance gene Bph3 into a high-yield and BPH-susceptible indica rice variety significantly enhances BPH resistance. However, when Bph3-carrying backcross [...] Read more.
Viral pathogens are a major threat to stable crop production. Using a backcross strategy, we find that integrating a dominant brown planthopper (BPH) resistance gene Bph3 into a high-yield and BPH-susceptible indica rice variety significantly enhances BPH resistance. However, when Bph3-carrying backcross lines are infested with BPH, these BPH-resistant lines exhibit sterile characteristics, displaying panicle enclosure and failure of seed production at their mature stage. As we suspected, BPH-mediated viral infections could cause the observed sterile symptoms, and we characterized rice-infecting viruses using deep metatranscriptomic sequencing. Our analyses revealed eight novel virus species and five known viruses, including a highly divergent virus clustered within a currently unclassified family. Additionally, we characterized rice plant antiviral responses using small RNA sequencing. The results revealed abundant virus-derived small interfering RNAs in sterile rice plants, providing evidence for Dicer-like and Argonaute-mediated immune responses in rice plants. Together, our results provide insights into the diversity of viruses in rice plants, and our findings suggest that multiple virus infections occur in rice plants. Full article
(This article belongs to the Special Issue Genomics in Plant Viral Research)
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19 pages, 3497 KiB  
Article
A Bipartite Geminivirus with a Highly Divergent Genomic Organization Identified in Olive Trees May Represent a Novel Evolutionary Direction in the Family Geminiviridae
by Patrick Materatski, Susan Jones, Mariana Patanita, Maria Doroteia Campos, António Bento Dias, Maria do Rosário Félix and Carla M. R. Varanda
Viruses 2021, 13(10), 2035; https://doi.org/10.3390/v13102035 - 9 Oct 2021
Cited by 11 | Viewed by 2578
Abstract
Olea europaea Geminivirus (OEGV) was recently identified in olive in Italy through HTS. In this work, we used HTS to show the presence of an OEGV isolate in Portuguese olive trees and suggest the evolution direction of OEGV. The bipartite genome (DNA-A and [...] Read more.
Olea europaea Geminivirus (OEGV) was recently identified in olive in Italy through HTS. In this work, we used HTS to show the presence of an OEGV isolate in Portuguese olive trees and suggest the evolution direction of OEGV. The bipartite genome (DNA-A and DNA-B) of the OEGV-PT is similar to Old World begomoviruses in length, but it lacks a pre-coat protein (AV2), which is a typical feature of New World begomoviruses (NW). DNA-A genome organization is closer to NW, containing four ORFs; three in complementary-sense AC1/Rep, AC2/TrAP, AC3/REn and one in virion-sense AV1/CP, but no AC4, typical of begomoviruses. DNA-B comprises two ORFs; MP in virion sense with higher similarity to the tyrosine phosphorylation site of NW, but in opposite sense to begomoviruses; BC1, with no known conserved domains in the complementary sense and no NSP typical of bipartite begomoviruses. Our results show that OEGV presents the longest common region among the begomoviruses, and the TATA box and four replication-associated iterons in a completely new arrangement. We propose two new putative conserved regions for the geminiviruses CP. Lastly, we highlight unique features that may represent a new evolutionary direction for geminiviruses and suggest that OEGV-PT evolution may have occurred from an ancient OW monopartite Begomovirus that lost V2 and C4, gaining functions on cell-to-cell movement by acquiring a DNA-B component. Full article
(This article belongs to the Special Issue Genomics in Plant Viral Research)
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15 pages, 5078 KiB  
Article
Metagenomic Analysis of Marigold: Mixed Infection Including Two New Viruses
by Hang Yin, Zheng Dong, Xulong Wang, Shuhao Lu, Fei Xia, Annihaer Abuduwaili, Yang Bi and Yongqiang Li
Viruses 2021, 13(7), 1254; https://doi.org/10.3390/v13071254 - 28 Jun 2021
Cited by 4 | Viewed by 3516
Abstract
Marigold plants with symptoms of mosaic, crinkle, leaf curl and necrosis were observed and small RNA and ribo-depleted total RNA deep sequencing were conducted to identify the associated viruses. Broad bean wilt virus 2, cucumber mosaic virus, turnip mosaic virus, a new potyvirus [...] Read more.
Marigold plants with symptoms of mosaic, crinkle, leaf curl and necrosis were observed and small RNA and ribo-depleted total RNA deep sequencing were conducted to identify the associated viruses. Broad bean wilt virus 2, cucumber mosaic virus, turnip mosaic virus, a new potyvirus tentatively named marigold mosaic virus (MMV) and a new partitivirus named as marigold cryptic virus (MCV) were finally identified. Complete genome sequence analysis showed MMV was 9811 nt in length, encoding a large polyprotein with highest aa sequence identity (57%) with the putative potyvirus polygonatumkingianum virus 1. Phylogenetic analysis with the definite potyviruses based on the polyprotein sequence showed MMV clustered closest to plum pox virus. The complete genome of MCV comprised of dsRNA1 (1583 bp) and dsRNA2 (1459 bp), encoding the RNA-dependent RNA polymerase (RdRp), and coat protein (CP), respectively. MCV RdRp shared the highest (75.7%) aa sequence identity with the unclassified partitivirus ambrosia cryptic virus 2, and 59.0%, 57.1%, 56.1%, 54.5% and 33.7% with the corresponding region of the definite delta-partitiviruses, pepper cryptic virus 2, beet cryptic virus 3, beet cryptic virus 2, pepper cryptic virus 1 and fig cryptic virus, respectively. Phylogenetic analysis based on the RdRp aa sequence showed MCV clustered into the delta-partitivirus group. These findings enriched our knowledge of viruses infecting marigold, but the association of the observed symptom and the identified viruses and the biological characterization of the new viruses should be further investigated. Full article
(This article belongs to the Special Issue Genomics in Plant Viral Research)
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14 pages, 1545 KiB  
Article
Synthesis and Characterization of a Full-Length Infectious cDNA Clone of Tomato Mottle Mosaic Virus
by Liqin Tu, Shuhua Wu, Danna Gao, Yong Liu, Yuelin Zhu and Yinghua Ji
Viruses 2021, 13(6), 1050; https://doi.org/10.3390/v13061050 - 1 Jun 2021
Cited by 9 | Viewed by 3628
Abstract
Tomato mottle mosaic virus (ToMMV) is a noteworthy virus which belongs to the Virgaviridae family and causes serious economic losses in tomato. Here, we isolated and cloned the full-length genome of a ToMMV Chinese isolate (ToMMV-LN) from a naturally infected tomato (Solanum [...] Read more.
Tomato mottle mosaic virus (ToMMV) is a noteworthy virus which belongs to the Virgaviridae family and causes serious economic losses in tomato. Here, we isolated and cloned the full-length genome of a ToMMV Chinese isolate (ToMMV-LN) from a naturally infected tomato (Solanum lycopersicum L.). Sequence analysis showed that ToMMV-LN contains 6399 nucleotides (nts) and is most closely related to a ToMMV Mexican isolate with a sequence identity of 99.48%. Next, an infectious cDNA clone of ToMMV was constructed by a homologous recombination approach. Both the model host N. benthamiana and the natural hosts tomato and pepper developed severe symptoms upon agroinfiltration with pToMMV, which had a strong infectivity. Electron micrographs indicated that a large number of rigid rod-shaped ToMMV virions were observed from the agroinfiltrated N. benthamiana leaves. Finally, our results also confirmed that tomato plants inoculated with pToMMV led to a high infection rate of 100% in 4–5 weeks post-infiltration (wpi), while pepper plants inoculated with pToMMV led to an infection rate of 40–47% in 4–5 wpi. This is the first report of the development of a full-length infectious cDNA clone of ToMMV. We believe that this infectious clone will enable further studies of ToMMV genes function, pathogenicity and virus–host interaction. Full article
(This article belongs to the Special Issue Genomics in Plant Viral Research)
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15 pages, 886 KiB  
Article
Targeted Genome Sequencing (TG-Seq) Approaches to Detect Plant Viruses
by Solomon Maina, Linda Zheng and Brendan C. Rodoni
Viruses 2021, 13(4), 583; https://doi.org/10.3390/v13040583 - 30 Mar 2021
Cited by 17 | Viewed by 3913
Abstract
Globally, high-throughput sequencing (HTS) has been used for virus detection in germplasm certification programs. However, sequencing costs have impeded its implementation as a routine diagnostic certification tool. In this study, the targeted genome sequencing (TG-Seq) approach was developed to simultaneously detect multiple (four) [...] Read more.
Globally, high-throughput sequencing (HTS) has been used for virus detection in germplasm certification programs. However, sequencing costs have impeded its implementation as a routine diagnostic certification tool. In this study, the targeted genome sequencing (TG-Seq) approach was developed to simultaneously detect multiple (four) viral species of; Pea early browning virus (PEBV), Cucumber mosaic virus (CMV), Bean yellow mosaic virus (BYMV) and Pea seedborne mosaic virus (PSbMV). TG-Seq detected all the expected viral amplicons within multiplex PCR (mPCR) reactions. In contrast, the expected PCR amplicons were not detected by gel electrophoresis (GE). For example, for CMV, GE only detected RNA1 and RNA2 while TG-Seq detected all the three RNA components of CMV. In an mPCR to amplify all four viruses, TG-Seq readily detected each virus with more than 732,277 sequence reads mapping to each amplicon. In addition, TG-Seq also detected all four amplicons within a 10−8 serial dilution that were not detectable by GE. Our current findings reveal that the TG-Seq approach offers significant potential and is a highly sensitive targeted approach for detecting multiple plant viruses within a given biological sample. This is the first study describing direct HTS of plant virus mPCR products. These findings have major implications for grain germplasm healthy certification programs and biosecurity management in relation to pathogen entry into Australia and elsewhere. Full article
(This article belongs to the Special Issue Genomics in Plant Viral Research)
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19 pages, 4866 KiB  
Article
Molecular Characteristics of Jujube Yellow Mottle-Associated Virus Infecting Jujube (Ziziphus jujuba Mill.) Grown at Aksu in Xinjiang of China
by Jiashu Guo, Yanxiang Wang, Guoping Wang, Jian Hong, Zuokun Yang, Jianyu Bai and Ni Hong
Viruses 2021, 13(1), 25; https://doi.org/10.3390/v13010025 - 25 Dec 2020
Cited by 10 | Viewed by 3591
Abstract
Chinese jujube (Ziziphus jujuba Mill.) is a native fruit crop in China. Leaf mottle and dapple fruit disease is prevalent in cultivated jujube plants grown at Aksu in Xinjiang Uygur Autonomous Region of China. Jujube yellow mottle-associated virus (JYMaV), a tentative member [...] Read more.
Chinese jujube (Ziziphus jujuba Mill.) is a native fruit crop in China. Leaf mottle and dapple fruit disease is prevalent in cultivated jujube plants grown at Aksu in Xinjiang Uygur Autonomous Region of China. Jujube yellow mottle-associated virus (JYMaV), a tentative member in the genus Emaravirus, was recently identified from mottle-diseased jujube plants grown in Liaoning Province in China, but its incidence and genetic diversity in China is unknown. In this study, the genome sequences of three JYMaV isolates from two jujube cultivars and one jujube variant were determined by high-throughput sequencing (HTS) for small RNA and rRNA-depleted RNA coupled with RT-PCR assays. Comparison of these sequences together with sequences of the viral RNA segments derived by primer set 3C/5H-based RT-PCR revealed that genetic diversity was present in the virus populations and high sequence variation occurred at the non-translational regions of each of the viral genomic segments. Field investigation confirmed the close association of the virus with leaf mottle symptoms of jujube plants. Furthermore, this study revealed that P5 encoded in the viral RNA5 displayed a nuclear localization feature differing from the plasmodesma (PD) subcellular localization of the virus movement protein (P4), and the two proteins could interact with each other in the BiFC assays. Our study provides a snapshot of JYMaV genetic diversity in its natural hosts. Full article
(This article belongs to the Special Issue Genomics in Plant Viral Research)
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Review

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68 pages, 10163 KiB  
Review
Virus Diseases of Cereal and Oilseed Crops in Australia: Current Position and Future Challenges
by Roger A. C. Jones, Murray Sharman, Piotr Trębicki, Solomon Maina and Benjamin S. Congdon
Viruses 2021, 13(10), 2051; https://doi.org/10.3390/v13102051 - 12 Oct 2021
Cited by 23 | Viewed by 6188
Abstract
This review summarizes research on virus diseases of cereals and oilseeds in Australia since the 1950s. All viruses known to infect the diverse range of cereal and oilseed crops grown in the continent’s temperate, Mediterranean, subtropical and tropical cropping regions are included. Viruses [...] Read more.
This review summarizes research on virus diseases of cereals and oilseeds in Australia since the 1950s. All viruses known to infect the diverse range of cereal and oilseed crops grown in the continent’s temperate, Mediterranean, subtropical and tropical cropping regions are included. Viruses that occur commonly and have potential to cause the greatest seed yield and quality losses are described in detail, focusing on their biology, epidemiology and management. These are: barley yellow dwarf virus, cereal yellow dwarf virus and wheat streak mosaic virus in wheat, barley, oats, triticale and rye; Johnsongrass mosaic virus in sorghum, maize, sweet corn and pearl millet; turnip yellows virus and turnip mosaic virus in canola and Indian mustard; tobacco streak virus in sunflower; and cotton bunchy top virus in cotton. The currently less important viruses covered number nine infecting nine cereal crops and 14 infecting eight oilseed crops (none recorded for rice or linseed). Brief background information on the scope of the Australian cereal and oilseed industries, virus epidemiology and management and yield loss quantification is provided. Major future threats to managing virus diseases effectively include damaging viruses and virus vector species spreading from elsewhere, the increasing spectrum of insecticide resistance in insect and mite vectors, resistance-breaking virus strains, changes in epidemiology, virus and vectors impacts arising from climate instability and extreme weather events, and insufficient industry awareness of virus diseases. The pressing need for more resources to focus on addressing these threats is emphasized and recommendations over future research priorities provided. Full article
(This article belongs to the Special Issue Genomics in Plant Viral Research)
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Other

13 pages, 239 KiB  
Opinion
Post-COVID-19 Action: Guarding Africa’s Crops against Viral Epidemics Requires Research Capacity Building That Unifies a Trio of Transdisciplinary Interventions
by Francis O. Wamonje
Viruses 2020, 12(11), 1276; https://doi.org/10.3390/v12111276 - 9 Nov 2020
Cited by 2 | Viewed by 2926
Abstract
The COVID-19 pandemic has shown that understanding the genomics of a virus, diagnostics and breaking virus transmission is essential in managing viral pandemics. The same lessons can apply for plant viruses. There are plant viruses that have severely disrupted crop production in multiple [...] Read more.
The COVID-19 pandemic has shown that understanding the genomics of a virus, diagnostics and breaking virus transmission is essential in managing viral pandemics. The same lessons can apply for plant viruses. There are plant viruses that have severely disrupted crop production in multiple countries, as recently seen with maize lethal necrosis disease in eastern and southern Africa. High-throughput sequencing (HTS) is needed to detect new viral threats. Equally important is building local capacity to develop the tools required for rapid diagnosis of plant viruses. Most plant viruses are insect-vectored, hence, biological insights on virus transmission are vital in modelling disease spread. Research in Africa in these three areas is in its infancy and disjointed. Despite intense interest, uptake of HTS by African researchers is hampered by infrastructural gaps. The use of whole-genome information to develop field-deployable diagnostics on the continent is virtually inexistent. There is fledgling research into plant-virus-vector interactions to inform modelling of viral transmission. The gains so far have been modest but encouraging, and therefore must be consolidated. For this, I propose the creation of a new Research Centre for Africa. This bold investment is needed to secure the future of Africa’s crops from insect-vectored viral diseases. Full article
(This article belongs to the Special Issue Genomics in Plant Viral Research)
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