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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 (30 November 2022) | Viewed by 31001

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Prof. Dr. Zongtao Sun

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State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
Interests: next-generation sequencing; plant viruses; new viruses; host–virus interaction
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Prof. Dr. Mengji Cao

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Citrus Research Institute, Southwest University, Chongqing 400712, China
Interests: plant viruses; viromics; citrus viruses
Special Issues, Collections and Topics in MDPI journals

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Dear Colleagues,

Next-generation sequencing (NGS) is a newly advanced tool for all viral discovery and identification, genome sequencing, and the ecology of viral diseases. NGS technologies provide an unbiased and efficient way to obtain a large amount of data about complete virus genomes. The advantages of NGS also include the characterization, distribution, and accumulation of virus small RNAs (vsRNAs) and viroid-derived small RNAs (vd-sRNAs), the identification of new viruses, the quantification of host gene expression, and the extension to decipher the virus strain differentiation. NGS analysis may provide a window to know the evolutionary history of various plant viruses and viroids. The developments of the bioinformatics tools for NGS analysis could facilitate the progress of disease diagnosis.

The purpose of this Special Issue is to collect articles (reviews, original research, and short communications) on, but not limited to, the identification of new viruses and host–virus interaction using the NGS method.

Prof. Dr. Zongtao Sun
Prof. Dr. Mengji Cao
Guest Editors

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Keywords

next-generation sequencing
plant viruses
new viruses
host–virus interaction

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Related Special Issue

Next-Generation Sequencing in Plant Virology 2.0 in Viruses (9 articles)

Published Papers (11 papers)

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Research

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17 pages, 3759 KiB

Open AccessArticle

Concerning the Etiology of Syrah Decline: A Fresh Perspective on an Old and Complex Issue Facing the Global Grape and Wine Industry

by Huogen Xiao, Olivia Roscow, Julia Hooker, Caihong Li, Hans J. Maree and Baozhong Meng

Viruses 2023, 15(1), 23; https://doi.org/10.3390/v15010023 - 21 Dec 2022

Cited by 2 | Viewed by 2309

Abstract

Syrah decline, first identified in Southern France in the 1990s, has become a major concern in the global grape and wine industry. This disease mainly affects Syrah (Shiraz) grapevines. Characteristic symptoms include the bright and uniform reddening of leaves throughout the canopy in late summer or early fall; the appearance of abnormalities on the trunk, mainly at the graft union (swelling, pits, grooves, and necrosis); and a reduction in vine vigor, yield and berry quality. Diseased vines may die a few years after disease onset. Damages to the vine are even more pronounced in cool climate regions such as Ontario (Canada), where the affected vines are subjected to very cold and prolonged winters, leading to large numbers of vine deaths. Despite the extensive efforts of the global grape research community over the past few decades, the etiology of this disease remains unclear. In this study, we conducted extensive analyses of viruses in declining Syrah vines identified in commercial vineyards in the Niagara region (Ontario, Canada) through high-throughput sequencing, PCR, RT-PCR and the profiling of genetic variants of select viruses. Multiple viruses and viral strains, as well as three viroids, were identified. However, an unequivocal causal relationship cannot be established between Syrah decline and any of these viruses, although the possibility that certain virus or genetic variants, or both in combination, may contribute to the disease cannot be excluded. Gleaning all information that is available to date, we feel that the traditional approach and an insistence on finding a single cause for such a complex disorder in a woody perennial fruit crop involving grafting will prove to be futile. We hope that this study offers new conceptual perspectives on the etiology of this economically important but enigmatic disease complex that affects the global grape and wine industry. Full article

(This article belongs to the Special Issue Next-Generation Sequencing in Plant Virology)

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14 pages, 4947 KiB

Open AccessArticle

Identification of Three Viruses Infecting Mulberry Varieties

by Lei Chen, Zi-Long Xu, Pei-Gang Liu, Yan Zhu, Tian-Bao Lin, Tian-Yan Li, Zhi-Qiang Lv and Jia Wei

Viruses 2022, 14(11), 2564; https://doi.org/10.3390/v14112564 - 19 Nov 2022

Cited by 3 | Viewed by 2367

Abstract

Viruses-mediated genome editing in plants is a powerful strategy to develop plant cultivars with important and novel agricultural traits. Mulberry alba is an important economic tree species that has been cultivated in China for more than 5000 years. So far, only a few viruses have been identified from mulberry trees, and their application potential is largely unknown. Therefore, mining more virus resources from the mulberry tree can pave the way for the establishment of useful engineering tools. In this study, eight old mulberry plants were gathered in seven geographic areas for virome analysis. Based on transcriptome analysis, we discovered three viruses associated with mulberries: Citrus leaf blotch virus isolate mulberry alba 2 (CLBV-ML2), Mulberry-associated virga-like virus (MaVLV), and Mulberry-associated narna-like virus (MaNLV). The genome of CLBV-ML2 was completely sequenced and exhibited high homology with Citriviruses, considered to be members of the genus Citrivirus, while the genomes of MaVLV and MaNLV were nearly completed lacking the 5′ and 3′ termini sequences. We tentatively consider MaVLV to be members of the family Virgaviridae and MaNLV to be members of the genus Narnavirus based on the results of phylogenetic trees. The infection experiments showed that CLBV-ML2 could be detected in the inoculated seedlings of both N. benthamiana and Morus alba, while MaVLV could only be detected in N. benthamiana. All of the infected seedlings did not show obvious symptoms. Full article

(This article belongs to the Special Issue Next-Generation Sequencing in Plant Virology)

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20 pages, 2184 KiB

Open AccessArticle

Detection of Apple Hammerhead Viroid, Apple Luteovirus 1 and Citrus Concave Gum-Associated Virus in Apple Propagation Materials and Orchards in the Czech Republic and Hungary

by Eva Várallyay, Jaroslava Přibylová, Zsuzsanna Nagyne Galbacs, Almash Jahan, Tunde Varga, Josef Špak, Ondřej Lenz, Jana Fránová, Jiří Sedlák and Igor Koloniuk

Viruses 2022, 14(11), 2347; https://doi.org/10.3390/v14112347 - 25 Oct 2022

Cited by 4 | Viewed by 2520

Abstract

Grafting cultivars onto rootstocks is a widely used practice by the apple industry predominantly aimed at faster fruit bearing. Using high-throughput sequencing, we revealed the presence of recently described viral agents, namely apple hammerhead viroid (AHVd), apple luteovirus 1 (ALV-1), and citrus concave gum-associated virus (CCGaV), in germplasm collections and production orchards in the Czech Republic and Hungary. The HTS results were validated with RT-(q)PCR, and Northern blotting techniques. To obtain further insight about the presence of these agents, RT-PCR based surveys were carried out and showed their widespread presence alone or in mixed infections. The pathogens were present both in production areas and in feral samples. In addition, rootstock-to-scion transmission of ALV-1 and CCGaV was confirmed using commercial rootstock materials. Phylogenetic relationships based on partial sequences of distinct variants were also investigated. Furthermore, the rosy apple aphid was found to be ALV-1-positive, suggesting that it might be a potential vector of the virus. Full article

(This article belongs to the Special Issue Next-Generation Sequencing in Plant Virology)

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16 pages, 5922 KiB

Open AccessArticle

Discovery and Characterization of a Novel Umbravirus from Paederia scandens Plants Showing Leaf Chlorosis and Yellowing Symptoms

by Lianshun Zheng, Shuai Fu, Yi Xie, Yang Han, Xueping Zhou and Jianxiang Wu

Viruses 2022, 14(8), 1821; https://doi.org/10.3390/v14081821 - 19 Aug 2022

Cited by 2 | Viewed by 2098

Abstract

Umbraviruses are a special class of plant viruses that do not encode any viral structural proteins. Here, a novel umbravirus that has been tentatively named Paederia scandens chlorosis yellow virus (PSCYV) was discovered through RNA-seq in Paederia scandens plants showing leaf chlorosis and yellowing symptoms. The PSCYV genome is a 4301 nt positive-sense, single strand RNA that contains four open reading frames (ORFs), i.e., ORF1–4, that encode P1–P4 proteins, respectively. Together, ORF1 and ORF2 are predicted to encode an additional protein, RdRp, through a −1 frameshift mechanism. The P3 protein encoded by ORF3 was predicted to be the viral long-distance movement protein. P4 was determined to function as the viral cell-to-cell movement protein (MP) and transcriptional gene silencing (TGS) suppressor. Both P1 and RdRp function as weak post-transcriptional gene silencing (PTGS) suppressors of PSCYV. The PVX-expression system indicated that all viral proteins may be symptom determinants of PSCYV. Phylogenetic analysis indicated that PSCYV is evolutionarily related to members of the genus Umbravirus in the family Tombusviridae. Furthermore, a cDNA infectious clone of PSCYV was successfully constructed and used to prove that PSCYV can infect both Paederia scandens and Nicotiana benthamiana plants through mechanical inoculation, causing leaf chlorosis and yellowing symptoms. These findings have broadened our understanding of umbraviruses and their host range. Full article

(This article belongs to the Special Issue Next-Generation Sequencing in Plant Virology)

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18 pages, 4243 KiB

Open AccessArticle

Comparative Transcriptome Analysis of CMV or 2b-Deficient CMV-Infected dcl2dcl4 Reveals the Effects of Viral Infection on Symptom Induction in Arabidopsis thaliana

by Qian Xu, Li Shen, Liying Jin, Meng Wang, Fenghan Chang and Zhongxin Guo

Viruses 2022, 14(7), 1582; https://doi.org/10.3390/v14071582 - 21 Jul 2022

Viewed by 2121

Abstract

Due to the impaired antiviral RNAi, the dcl2dcl4 (dcl2/4) mutant is highly susceptible to viruses deficient of the viral suppressor of the RNA silencing (VSR) contrast to wild-type Arabidopsis. It was found that more severe disease symptoms were induced in dcl2/4 infected with VSR-deficient CMV (CMV-Δ2b or CMV-2aTΔ2b) compared to wild-type Arabidopsis infected with intact CMV. In order to investigate the underlying mechanism, comparative transcriptome analysis was performed with Col-0 and dcl2/4 that were infected by CMV, CMV-Δ2b and CMV-2aTΔ2b, respectively. Our analysis showed that the systematic infection of CMV, CMV-Δ2b and CMV-2aTΔ2b could cause hypoxia response and reduce photosynthesis. Asymptomatic infections of CMV-Δ2b or CMV-2aTΔ2b in Columbia (Col-0) promoted the expression of cell division-related genes and suppressed the transcription of metabolism and acquired resistance genes. On the other hand, immunity and resistance genes were highly induced, but photosynthesis and polysaccharide metabolism-related genes were suppressed in diseased plants. More interestingly, cell wall reorganization was specifically caused in modestly diseased Col-0 infected by CMV and a strong activation of SA signaling were correspondingly induced in severely diseased dcl2/4 by CMV or CMV mutants. Thus, our research revealed the nature of the Arabidopsis–CMV interaction at the transcriptome level and could provide new clues in symptom development and antiviral defense in plants. Full article

(This article belongs to the Special Issue Next-Generation Sequencing in Plant Virology)

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11 pages, 1546 KiB

Open AccessArticle

Molecular Characterization of a Novel Polerovirus Infecting Soybean in China

by Tengzhi Xu, Lei Lei, Yong Fu, Xiaolan Yang, Hao Luo, Xiangru Chen, Xiaomao Wu, Yaqin Wang and Meng-ao Jia

Viruses 2022, 14(7), 1428; https://doi.org/10.3390/v14071428 - 29 Jun 2022

Cited by 3 | Viewed by 2381

Abstract

Poleroviruses are positive-sense, single-stranded viruses. In this study, we describe the identification of a novel polerovirus isolated from soybean displaying curled leaves. The complete viral genome sequence was identified using high-throughput sequencing and confirmed using rapid amplification of cDNA ends (RACE), RT-PCR and Sanger sequencing. Its genome organization is typical of the members of genus Polerovirus, containing seven putative open reading frames (ORFs). The full genome is composed of single-stranded RNA of 5822 nucleotides in length, with the highest nucleotide sequence identity (79.07% with 63% coverage) for cowpea polerovirus 2 (CPPV2). Amino acid sequence identities of the protein products between the virus and its relatives are below the threshold determined by the International Committee of Taxonomy of Viruses (ICTV) for species demarcation, and this strongly supports this virus’ status as a novel species, for which the name soybean chlorotic leafroll virus (SbCLRV) is proposed. Recombination analysis identified a recombination event in the ORF5 of the 3’ portion in the genome. Phylogenetic analyses of the genome and encoded protein sequences revealed that the new virus is closely related to phasey bean mild yellows virus, CPPV2 and siratro latent polerovirus. Subsequently, we demonstrated the infectivity of SbCLRV in Nicotiana benthamiana via infectious cDNA clone generation and agroinoculation. Full article

(This article belongs to the Special Issue Next-Generation Sequencing in Plant Virology)

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12 pages, 2666 KiB

Open AccessArticle

Examination of the Virome of Taro Plants Affected by a Lethal Disease, the Alomae-Bobone Virus Complex, in Papua New Guinea

by Alejandro Olmedo-Velarde, Jarin Loristo, Alexandra Kong, Philip Waisen, Koon-Hui Wang, John Hu and Michael Melzer

Viruses 2022, 14(7), 1410; https://doi.org/10.3390/v14071410 - 28 Jun 2022

Cited by 6 | Viewed by 2240

Abstract

Alomae-bobone virus complex (ABVC) is a lethal but still understudied disease that is limited to the Solomon Islands and Papua New Guinea. The only virus clearly associated to ABVC is Colocasia bobone disease-associated virus (CBDaV). Taro (Colocasia esculenta) plants with and without symptoms of ABVC disease were sampled from two locations in Papua New Guinea and examined for viruses using high-throughput sequencing (HTS). Similar to previous reports, isolates of CBDaV were present only in symptomatic plants, further supporting its role in the disease. The only other viruses consistently present in symptomatic plants were badnaviruses: taro bacilliform virus (TaBV) and/or taro bacilliform CH virus (TaBCHV). If ABVC requires co-infection by multiple viruses, CBDaV and badnavirus infection appears to be the most likely combination. The complete genomes of two isolates of CBDaV and TaBCHV, and single isolates of TaBV and dasheen mosaic virus, were obtained in this study, furthering our knowledge of the genetic diversity of these relatively understudied taro viruses. HTS data also provided evidence for an agent similar to umbra-like viruses that we are tentatively designating it as Colocasia umbra-like virus (CULV). Full article

(This article belongs to the Special Issue Next-Generation Sequencing in Plant Virology)

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25 pages, 1782 KiB

Open AccessArticle

Virome of Grapevine Germplasm from the Anapa Ampelographic Collection (Russia)

by Darya Shvets, Elena Porotikova, Kirill Sandomirsky and Svetlana Vinogradova

Viruses 2022, 14(6), 1314; https://doi.org/10.3390/v14061314 - 15 Jun 2022

Cited by 15 | Viewed by 3489

Abstract

Grapevine germplasm collections are unique repositories of grape cultivars; therefore, it is necessary to minimize their infection with pathogens, including viruses, and develop various programs to maintain them in a virus-free state. In our study, we examined the virome of the largest Russian grapevine germplasm collection, the Anapa Ampelographic Collection, using high-throughput sequencing of total RNAs. As a result of bioinformatics analysis and validation of its results by reverse transcription PCR (RT-PCR) and quantitative RT-PCR (RT-qPCR), we identified 20 viruses and 3 viroids in 47 libraries. All samples were infected with 2 to 12 viruses and viroids, including those that cause economically significant diseases: leafroll, fleck, and rugose wood complex. For the first time in Russia, we detected Grapevine virus B (GVB), Grapevine virus F (GVF), Grapevine asteroid mosaic-associated virus (GAMaV), Grapevine Red Globe virus (GRGV), Grapevine satellite virus (GV-Sat), Grapevine virga-like virus (GVLV), Grapevine-associated jivivirus 1 (GaJV-1) and Vitis cryptic virus (VCV). A new putative representative of the genus Umbravirus with the provisional name Grapevine umbra-like virus (GULV) was also identified in Russian grape samples. Full article

(This article belongs to the Special Issue Next-Generation Sequencing in Plant Virology)

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9 pages, 8982 KiB

Open AccessCommunication

Diverse Novel Viruses Coinfecting the Tropical Ornamental Plant Polyscias balfouriana in China

by Yuxin Ma, Haiyan Che, Shengfeng Gao, Yating Lin and Shifang Li

Viruses 2022, 14(6), 1120; https://doi.org/10.3390/v14061120 - 24 May 2022

Viewed by 2095

Abstract

The viromic profile of Polyscias balfouriana cv. Marginata, a perennial woody and ornamental plant, was determined using ribosomal RNA-depleted total RNA (rRNA-depleted totRNA) sequencing. Five viruses (i.e., polyscias mosaic virus, PoMV; one potential novel rhabdovirus; and three novel viruses of Betaflexiviridae and Closteroviridae) were detected and prevalence-surveyed in Hainan province, China. The genomes of polyscias capillovirus 1 (PCaV-1) and polyscias citrivirus 1 (PCiV-1) of family Betaflexiviridae were completed, and the genomes of polyscias crinivirus 1 (PCrV-1) of Closteroviridae were nearly completed lacking the 5′ and 3′ termini. PCaV-1 shares 68% genome nucleotide (nt) identity and 66% replicase (Rep) amino acid (aa) identity with homologues in apple stem grooving virus (ASGV). PCiV-1 shares 65% genome nt identity and 64% Rep aa identity with homologs in citrus leaf blotch virus (CLBV). Meeting the species demarcation criteria, PCaV-1 and PCiV-1 were considered to be new species in genera Capillovirus and Citrivirus, respectively. PCrV-1 shares high genome nt identity (62%), heat shock protein 70-like protein (HSP70h) and RNA-dependent RNA polymerase (RdRp) aa identity (78–80%) with homologues in tomato chlorosis virus (ToCV). We tentatively consider PCrV-1 to be an unclassified member of the Crinivirus genus. PoMV, PCaV-1, PCiV-1, and PCrV-1 are the prevalent viruses with >73% occurrence in the Xinglong Tropical Botanical Garden, Hainan, China. Full article

(This article belongs to the Special Issue Next-Generation Sequencing in Plant Virology)

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17 pages, 3783 KiB

Open AccessArticle

Genome-Wide Identification and Gene Expression Analysis of the OTU DUB Family in Oryza sativa

by Qiannan Liu, Tingyun Yan, Xiaoxiang Tan, Zhongyan Wei, Yanjun Li, Zongtao Sun, Hehong Zhang and Jianping Chen

Viruses 2022, 14(2), 392; https://doi.org/10.3390/v14020392 - 14 Feb 2022

Cited by 7 | Viewed by 2754

Abstract

Ovarian tumor domain (OTU)-containing deubiquitinating enzymes (DUBs) are an essential DUB to maintain protein stability in plants and play important roles in plant growth development and stress response. However, there is little genome-wide identification and analysis of the OTU gene family in rice. In this study, we identified 20 genes of the OTU family in rice genome, which were classified into four groups based on the phylogenetic analysis. Their gene structures, conserved motifs and domains, chromosomal distribution, and cis elements in promoters were further studied. In addition, OTU gene expression patterns in response to plant hormone treatments, including SA, MeJA, NAA, BL, and ABA, were investigated by RT-qPCR analysis. The results showed that the expression profile of OsOTU genes exhibited plant hormone-specific expression. Expression levels of most of the rice OTU genes were significantly changed in response to rice stripe virus (RSV), rice black-streaked dwarf virus (RBSDV), Southern rice black-streaked dwarf virus (SRBSDV), and Rice stripe mosaic virus (RSMV). These results suggest that the rice OTU genes are involved in diverse hormone signaling pathways and in varied responses to virus infection, providing new insights for further functional study of OsOTU genes. Full article

(This article belongs to the Special Issue Next-Generation Sequencing in Plant Virology)

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Review

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20 pages, 4460 KiB

Open AccessReview

Plant Virus-Derived Vectors for Plant Genome Engineering

by Muhammad Arslan Mahmood, Rubab Zahra Naqvi, Saleem Ur Rahman, Imran Amin and Shahid Mansoor

Viruses 2023, 15(2), 531; https://doi.org/10.3390/v15020531 - 14 Feb 2023

Cited by 13 | Viewed by 4685

Abstract

Advances in genome engineering (GE) tools based on sequence-specific programmable nucleases have revolutionized precise genome editing in plants. However, only the traditional approaches are used to deliver these GE reagents, which mostly rely on Agrobacterium-mediated transformation or particle bombardment. These techniques have been successfully used for the past decades for the genetic engineering of plants with some limitations relating to lengthy time-taking protocols and transgenes integration-related regulatory concerns. Nevertheless, in the era of climate change, we require certain faster protocols for developing climate-smart resilient crops through GE to deal with global food security. Therefore, some alternative approaches are needed to robustly deliver the GE reagents. In this case, the plant viral vectors could be an excellent option for the delivery of GE reagents because they are efficient, effective, and precise. Additionally, these are autonomously replicating and considered as natural specialists for transient delivery. In the present review, we have discussed the potential use of these plant viral vectors for the efficient delivery of GE reagents. We have further described the different plant viral vectors, such as DNA and RNA viruses, which have been used as efficient gene targeting systems in model plants, and in other important crops including potato, tomato, wheat, and rice. The achievements gained so far in the use of viral vectors as a carrier for GE reagent delivery are depicted along with the benefits and limitations of each viral vector. Moreover, recent advances have been explored in employing viral vectors for GE and adapting this technology for future research. Full article

(This article belongs to the Special Issue Next-Generation Sequencing in Plant Virology)

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