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State-of-the-Art Plant Virus Research in China

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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 (31 December 2022) | Viewed by 25074

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Prof. Dr. Feng Li

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College of Horticultural Sciences and Forestry, Huazhong Agricultural University, Wuhan 430070, China
Interests: plant-virus interaction; RNA silencing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plant viruses impose serious threats to agriculture in China, and there is a big consortium of scientists working on basic plant virology and its applications in engineering viral-resistant crops. In the past few years, numerous important advancements have been achieved by Chinese scientists in elucidating mechanisms of viral pathogenesis, plant resistance to viral infection, and trilateral plant–virus–vector interactions. Many useful viral vectors for forward genetics and gene editing have also been developed which have made significant contributions to dissecting genetic mechanisms in plants. New advancements have also been seen in the discovery of new viral and viroid pathogens in crops, as well as the ecology of known viruses among important crops in China. All these new achievements have provided essential information and knowledge for agricultural researchers to engineering viral-resistant crops for deployment in specific areas. In this special issue, we welcome submissions for comprehensive reviews or new research advancements in—but not limited to—all the above mentioned areas.

Prof. Dr. Feng Li
Guest Editor

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Keywords

RNA silencing
autophage
viral suppressor of RNA silencing
pathogenesis
resistance
R gene
crop
insect
VIGS
gene editing

Published Papers (12 papers)

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Research

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11 pages, 1878 KiB

Open AccessArticle

Development of Dot-ELISA and Colloidal Gold Immunochromatographic Strip for Rapid and Super-Sensitive Detection of Plum Pox Virus in Apricot Trees

by Mengmeng Guo, Duo Qi, Jinxi Dong, Saiyu Dong, Xiuling Yang, Yajuan Qian, Xueping Zhou and Jianxiang Wu

Viruses 2023, 15(1), 169; https://doi.org/10.3390/v15010169 - 05 Jan 2023

Cited by 6 | Viewed by 1519

Abstract

Plum pox virus (PPV) is a causal agent of the stone fruit tree sharka disease that often causes enormous economic losses. Due to its worldwide distribution and economic importance, rapid and reliable diagnostic technologies are becoming increasingly important for successful management of sharka disease. In this study, we have produced two super-sensitive and specific anti-PPV monoclonal antibodies (i.e., MAbs 13H4 and 4A11). Using these two MAbs, we have now developed a dot enzyme-linked immunosorbent assay (dot-ELISA) and a colloidal gold immunochromatographic strip (CGICS) assay. These two technologies can be used to quickly and reliably detect PPV. The results of these sensitivity assays confirmed that the dot-ELISA and CGICS assays could detect PPV infection in apricot tree leaf crude extracts diluted up to 1:5120 and 1:6400 (w/v), respectively. Further analyses using field-collected apricot tree leaf samples showed that the detection endpoint of the dot-ELISA was ~26 times above that obtained through RT-PCR, and the CGICS was as sensitive as RT-PCR. This present study is to broaden the knowledge about detection limits of dot-ELISA and CGICS for PPV monitoring. We consider that these newly developed dot-ELISA and CGICS are particularly useful for large scale PPV surveys in fields. Full article

(This article belongs to the Special Issue State-of-the-Art Plant Virus Research in China)

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16 pages, 5517 KiB

Open AccessArticle

A Conserved, Serine-Rich Protein Plays Opposite Roles in N-Mediated Immunity against TMV and N-Triggered Cell Death

by Qingling Zhang, Jubin Wang, Xi Zhang, Yingtian Deng and Feng Li

Viruses 2023, 15(1), 26; https://doi.org/10.3390/v15010026 - 21 Dec 2022

Cited by 4 | Viewed by 1412

Abstract

Plant nucleotide-binding, leucine-rich, repeat-containing proteins (NLRs) play important roles in plant immunity. NLR expression and function are tightly regulated by multiple mechanisms. In this study, a conserved serine/arginine-rich protein (SR protein) was identified through the yeast one-hybrid screening of a tobacco cDNA library using DNA fragments from the N gene, an NLR that confers immunity to tobacco mosaic virus (TMV). This SR protein showed an interaction with a 3′ genomic regulatory sequence (GRS) and has a potential role in regulating the alternative splicing of N. Thus, it was named SR regulator for N, abbreviated SR4N. Further study showed that SR4N plays a positive role in N-mediated cell death but a negative role in N protein accumulation. SR4N also promotes multiple virus replications in co-expression experiments, and this enhancement may not function through RNA silencing suppression, as it did not enhance 35S-GFP expression in co-infiltration experiments. Bioinformatic and molecular studies revealed that SR4N belongs to the SR2Z subtype of the SR protein family, which was conserved in both dicots and monocots, and its roles in repressing viral immunity and triggering cell death were also conserved. Our study revealed new roles for SR2Z family proteins in plant immunity against viruses. Full article

(This article belongs to the Special Issue State-of-the-Art Plant Virus Research in China)

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12 pages, 3147 KiB

Open AccessArticle

A New Biotin Labeling and High-Molecular-Weight RNA Northern Method and Its Application in Viral RNA Detection

by Xi Zhang, Qingling Zhang, Long Cheng, Dan Liu, Hongzheng Wang, Yingjia Zhou, Liqun Ma, Jubin Wang and Feng Li

Viruses 2022, 14(12), 2664; https://doi.org/10.3390/v14122664 - 28 Nov 2022

Cited by 2 | Viewed by 1856

Abstract

Viruses cause severe crop losses. Studying the interaction between viruses and plants is very important for development of control measures. Northern blot is a well-accepted but very challenging technique to monitor the infection of viruses. Here, we modified the high-molecular-weight (hmw)RNA Northern blot experiment process, utilizing vertical electrophoresis to separate the RNA with denatured agarose gel. This protocol is compatible with regular equipment for Western blots and small RNA Northern blots and requires less input of total RNA. A new method to label the probe with biotin was also developed, which requires commonly used T4 DNA polymerase and detects viral RNA with high sensitivity. These new protocols made hmwRNA Northern blot cost-effective and easy-to-operate, very suitable for studying virus–host interactions. Full article

(This article belongs to the Special Issue State-of-the-Art Plant Virus Research in China)

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14 pages, 2647 KiB

Open AccessArticle

Occurrence and Molecular Variability of the Main Kiwifruit Viruses in the Sichuan Province of China

by Jing Shang, Qi Jia, Lei Zhang, Siqi Zhang, Junbo Du, Wenming Wang and Jing Shui

Viruses 2022, 14(11), 2460; https://doi.org/10.3390/v14112460 - 06 Nov 2022

Cited by 1 | Viewed by 1220

Abstract

Viruses cause important yield losses in kiwifruit. Here, we studied the occurrence and population structure of the major kiwifruit viruses in the Sichuan province of China. RT-PCR results showed the presence of Actinidia virus A (AcVA), Actinidia virus B (AcVB), Actinidia chlorotic ringspot-associated virus (AcCRaV), and the cucumber mosaic virus (CMV). AcCRaV was widely distributed, followed by CMV. These two viruses were often detected in co-infection with AcVA and AcVB. The virus detection rate was positively correlated with vine age. Four phylogenetic groups of AcVA and AcVB were identified, with AcVA isolates clustering mainly in subgroup I, and AcVB isolates clustering mainly in subgroups II, III, and IV. All CMV isolates clustered in subgroup II, and AcCRaV isolates clustered in subgroup IA. The genome of AcVA and AcCRaV was under negative selection pressure, while the genome of AcVB and CMV was under positive selection pressure. All the viruses, except AcVB, were in a state of expansion. The full-length genome of the most widely distributed AcCRaV isolate in kiwifruits in the Sichuan province was characterized by sequencing. Unique eight-nucleotide (TTTTTGAT) repeats were found in the 5′-terminal non-coding region of the AcCRaV RNA3 in a possible association with reduced disease symptoms. This is the first study of kiwifruit viruses in Sichuan. Full article

(This article belongs to the Special Issue State-of-the-Art Plant Virus Research in China)

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14 pages, 5485 KiB

Open AccessArticle

The N-Terminal α-Helix of Potato Virus X-Encoded RNA-Dependent RNA Polymerase Is Required for Membrane Association and Multimerization

by Xue Jiang, Yameng Luan, Mengzhu Chai, Yingshuai Yang, Yuting Wang, Wenjia Deng, Yonggang Li, Xiaofei Cheng and Xiaoyun Wu

Viruses 2022, 14(9), 1907; https://doi.org/10.3390/v14091907 - 28 Aug 2022

Cited by 1 | Viewed by 1601

Abstract

Positive-sense single-stranded RNA viruses replicate in virus-induced membranous organelles for maximum efficiency and immune escaping. The replication of potato virus X (PVX) takes place on the endoplasmic reticulum (ER); however, how PVX-encoded RNA-dependent RNA polymerase (RdRp) is associated with the ER is still unknown. A proline-kinked amphipathic α-helix was recently found in the MET domain of RdRp. In this study, we further illustrate that the first α-helix of the MET domain is also required for ER association. Moreover, we found that the MET domain forms multimers on ER and the first α-helix is essential for multimerization. These results suggest that the RdRp of PVX adopts more than one hydrophobic motif for membrane association and for multimerization. Full article

(This article belongs to the Special Issue State-of-the-Art Plant Virus Research in China)

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14 pages, 3005 KiB

Open AccessArticle

Selection and Validation of Reference Genes for Gene Expression Studies Using Quantitative Real-Time PCR in Prunus Necrotic Ringspot Virus-Infected Cucumis sativus

by Zhenfei Dong, Binhui Zhan and Shifang Li

Viruses 2022, 14(6), 1269; https://doi.org/10.3390/v14061269 - 10 Jun 2022

Cited by 2 | Viewed by 1686

Abstract

Several members of the genus Ilarvirus infect fruit trees and are distributed worldwide. Prunus necrotic ringspot virus (PNRSV) is one of the most prevalent viruses, causing significant losses. Cucumissativus can be infected by several ilarviruses, leading to obvious symptoms, including PNRSV, which suggests that cucumbers could be good hosts for the study of the pathogenesis of ilarviruses. Real-time quantitative PCR is an optimal choice for studying gene expression because of its simplicity and its fast and high sensitivity, while its accuracy is highly dependent on the stability of the reference genes. In this study, we assessed the stability of eleven reference genes with geNorm, NormFinder, ΔCt method, BestKeeper, and the ranking software, RefFinder. The results indicated that the combined use of EF1α and F-BOX was the most accurate normalization method. In addition, the host genes AGO1, AGO4, and RDR6 were selected to test the reliability of the reference genes. This study provides useful information for gene expression analysis during PNRSV infection and will facilitate gene expression studies associated with ilarvirus infection. Full article

(This article belongs to the Special Issue State-of-the-Art Plant Virus Research in China)

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18 pages, 6466 KiB

Open AccessArticle

Discovery and Genomic Function of a Novel Rice Dwarf-Associated Bunya-like Virus

by Dan Wang, Shuai Fu, Hongyue Wu, Mengji Cao, Li Liu, Xueping Zhou and Jianxiang Wu

Viruses 2022, 14(6), 1183; https://doi.org/10.3390/v14061183 - 29 May 2022

Cited by 6 | Viewed by 1885

Abstract

Bunyaviruses cause diseases in vertebrates, arthropods, and plants. Here, we used high-throughput RNA-seq to identify a bunya-like virus in rice plants showing the dwarfing symptom, which was tentatively named rice dwarf-associated bunya-like virus (RDaBV). The RDaBV genome consists of L, M, and S segments. The L segment has 6562 nt, and encodes an RdRp with a conserved Bunya_RdRp super family domain. The M segment has 1667 nt and encodes a nonstructural protein (NS). The complementary strand of the 1120 nt S segment encodes a nucleocapsid protein (N), while its viral strand encodes a small nonstructural protein (NSs). The amino acid (aa) sequence identities of RdRp, NS, and N between RDaBV and viruses from the family Discoviridae were the highest. Surprisingly, the RDaBV NSs protein did not match any viral proteins. Phylogenetic analysis based on RdRp indicated that RDaBV is evolutionarily close to viruses in the family Discoviridae. The PVX-expressed system indicated that RDaBV N and NS may be symptom determinants of RDaBV. Our movement complementation and callose staining experiment results confirmed that RDaBV NSs is a viral movement protein in plants, while an agro-infiltration experiment found that RDaBV NS is an RNA silencing suppressor. Thus, we determined that RDaBV is a novel rice-infecting bunya-like virus. Full article

(This article belongs to the Special Issue State-of-the-Art Plant Virus Research in China)

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21 pages, 5661 KiB

Open AccessArticle

Identification and Characterization of Two Novel Noda-like Viruses from Rice Plants Showing the Dwarfing Symptom

by Yi Xie, Shuai Fu, Li Xie, Yaqin Wang, Mengji Cao, Xueping Zhou and Jianxiang Wu

Viruses 2022, 14(6), 1159; https://doi.org/10.3390/v14061159 - 27 May 2022

Cited by 2 | Viewed by 1755

Abstract

Nodaviruses are small bipartite RNA viruses and are considered animal viruses. Here, we identified two novel noda-like viruses (referred to as rice-associated noda-like virus 1 (RNLV1) and rice-associated noda-like virus 2 (RNLV2)) in field-collected rice plants showing a dwarfing phenotype through RNA-seq. RNLV1 genome consists of 3335 nt RNA1 and 1769 nt RNA2, and RNLV2 genome consists of 3279 nt RNA1 and 1525 nt RNA2. Three conserved ORFs were identified in each genome of the two novel viruses, encoding an RNA-dependent RNA polymerase, an RNA silencing suppressor, and a capsid protein, respectively. The results of sequence alignment, protein domain prediction, and evolutionary analysis indicate that these two novel viruses are clearly different from the known nodaviruses, especially the CPs. We have also determined that the B2 protein encoded by the two new noda-like viruses can suppress RNA silencing in plants. Two reverse genetic systems were constructed and used to show that RNLV1 RNA1 can replicate in plant cells and RNLV1 can replicate in insect Sf9 cells. We have also found two unusual peptidase family A21 domains in the RNLV1 CP, and RNLV1 CP can self-cleave in acidic environments. These findings provide new knowledge of novel nodaviruses. Full article

(This article belongs to the Special Issue State-of-the-Art Plant Virus Research in China)

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14 pages, 3741 KiB

Open AccessArticle

Synonymous Codon Usage Analysis of Three Narcissus Potyviruses

by Zhen He, Shiwen Ding, Jiyuan Guo, Lang Qin and Xiaowei Xu

Viruses 2022, 14(5), 846; https://doi.org/10.3390/v14050846 - 19 Apr 2022

Cited by 5 | Viewed by 2071

Abstract

Narcissus degeneration virus (NDV), narcissus late season yellows virus (NLSYV) and narcissus yellow stripe virus (NYSV), which belong to the genus Potyvirus of the family Potyviridae, cause significant losses in the ornamental value and quality of narcissus. Several previous studies have explored the genetic diversity and evolution rate of narcissus viruses, but the analysis of the synonymous codons of the narcissus viruses is still unclear. Herein, the coat protein (CP) of three viruses is used to analyze the viruses’ phylogeny and codon usage pattern. Phylogenetic analysis showed that NYSV, NDV and NLSYV isolates were divided into five, three and five clusters, respectively, and these clusters seemed to reflect the geographic distribution. The effective number of codon (ENC) values indicated a weak codon usage bias in the CP coding region of the three narcissus viruses. ENC-plot and neutrality analysis showed that the codon usage bias of the three narcissus viruses is all mainly influenced by natural selection compared with the mutation pressure. The three narcissus viruses shared the same best optimal codon (CCA) and the synonymous codon prefers to use codons ending with A/U, compared to C/G. Our study shows the codon analysis of different viruses on the same host for the first time, which indicates the importance of the evolutionary-based design to control these viruses. Full article

(This article belongs to the Special Issue State-of-the-Art Plant Virus Research in China)

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11 pages, 2330 KiB

Open AccessArticle

Genome Editing of Rice eIF4G Loci Confers Partial Resistance to Rice Black-Streaked Dwarf Virus

by Wei Wang, Shuhui Ma, Peng Hu, Yinghua Ji and Feng Sun

Viruses 2021, 13(10), 2100; https://doi.org/10.3390/v13102100 - 18 Oct 2021

Cited by 15 | Viewed by 3051

Abstract

Rice black-streaked dwarf disease, caused by rice black-streaked dwarf virus (RBSDV), is a serious constraint in Chinese rice production. Breeding disease-resistant varieties through multigene aggregation is considered an effective way to control diseases, but few disease-resistant resources have been characterized thus far. To develop novel resources for resistance to RBSDV through CRISPR/Cas9-mediated genome editing, a guide RNA sequence targeting exon 1 of eIF4G was designed and cloned into a binary vector, pHUE401. This recombinant vector was used to generate mutations in the rice cultivar Nipponbare via Agrobacterium-mediated transformation. This approach produced heritable homozygous mutations in the transgene-free T1 generation. Sequence analysis of the eIF4G target region from T1 transgenic plants identified 3 bp deletion mutants, and analysis of the predicted amino acid sequence identified one amino acid deletion in mutants that possess near full-length eIF4G. Furthermore, our data suggest that eIF4G may plays an important role in rice normal development, as there were no eIF4G knock-out homozygous mutants in T1 generation plants. When homozygous mutant lines were inoculated with RBSDV, they exhibited enhanced tolerance to virus infection, without visibly affecting plant growth and development. However, the eif4g mutant plants showed the same sensitivity to rice stripe virus (RSV) infection as wild-type plants. Notably, the wild-type and mutant N-termini of eIF4G interacted directly with RBSDV P8 in yeast and in planta. Additionally, compared to wild-type plants, the eIF4G transcript level was reduced twofold in the mutant plants. These results indicate that site-specific mutation of rice eIF4G successfully conferred partial resistance specific to RBSDV associated with less transcription of eIF4G in mutants. Therefore, this study demonstrates that the novel eIF4G alleles generated by CRISPR/Cas9 represent valuable disease-resistant resources that can be used to develop RBSDV-resistant varieties. Full article

(This article belongs to the Special Issue State-of-the-Art Plant Virus Research in China)

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Review

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15 pages, 1042 KiB

Open AccessReview

Plant Defense and Viral Counter-Defense during Plant–Geminivirus Interactions

by Jianhang Zhang, Mengyuan Ma, Yule Liu and Asigul Ismayil

Viruses 2023, 15(2), 510; https://doi.org/10.3390/v15020510 - 12 Feb 2023

Cited by 4 | Viewed by 2254

Abstract

Geminiviruses are the largest family of plant viruses that cause severe diseases and devastating yield losses of economically important crops worldwide. In response to geminivirus infection, plants have evolved ingenious defense mechanisms to diminish or eliminate invading viral pathogens. However, increasing evidence shows that geminiviruses can interfere with plant defense response and create a suitable cell environment by hijacking host plant machinery to achieve successful infections. In this review, we discuss recent findings about plant defense and viral counter-defense during plant–geminivirus interactions. Full article

(This article belongs to the Special Issue State-of-the-Art Plant Virus Research in China)

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18 pages, 923 KiB

Open AccessReview

RNAi-Based Antiviral Innate Immunity in Plants

by Liying Jin, Mengna Chen, Meiqin Xiang and Zhongxin Guo

Viruses 2022, 14(2), 432; https://doi.org/10.3390/v14020432 - 20 Feb 2022

Cited by 14 | Viewed by 3570

Abstract

Multiple antiviral immunities were developed to defend against viral infection in hosts. RNA interference (RNAi)-based antiviral innate immunity is evolutionarily conserved in eukaryotes and plays a vital role against all types of viruses. During the arms race between the host and virus, many viruses evolve viral suppressors of RNA silencing (VSRs) to inhibit antiviral innate immunity. Here, we reviewed the mechanism at different stages in RNAi-based antiviral innate immunity in plants and the counteractions of various VSRs, mainly upon infection of RNA viruses in model plant Arabidopsis. Some critical challenges in the field were also proposed, and we think that further elucidating conserved antiviral innate immunity may convey a broad spectrum of antiviral strategies to prevent viral diseases in the future. Full article

(This article belongs to the Special Issue State-of-the-Art Plant Virus Research in China)

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