Query：
学者姓名：郭忠新
Refining：
Year
Type
Indexed by
Source
Complex
Co-Author
Language
Clean All
Abstract ：
Rice viruses seriously threaten rice cultivation and cause significant economic losses, but they have not yet been systematically identified, with only 20 rice-infecting viruses reported. Here, we perform a large-scale analysis of 17,115 RNA-seq libraries spanning 24 Oryza species across 51 countries. Using de novo assembly and homology-based methods, we identify 810 complete or near-complete viruses, including 276 known viruses and 534 novel viruses. Given the high divergence and atypical genome organizations of novel viruses, more than a half of them are tentatively assigned to 1 new order, 61 new families, and at least 104 new genera. Utilizing homology-independent approaches, we additionally identify 49 divergent RNA-dependent RNA polymerases (RdRPs), which are confirmed by protein structural alignment. Furthermore, we analyze the metadata of related Sequence Read Archive (SRA) libraries and estimated viral abundance in each library, leading to the screening of 427 viruses closely associated with rice plants. Overall, our study vastly expands the viral diversity in rice plants, providing insights for the prevention and control of viral disease.
Cite：
Copy from the list or Export to your reference management。
| GB/T 7714 | Zhu, Yu , Raza, Ali , Bai, Qing et al. In-depth analysis of 17,115 rice transcriptomes reveals extensive viral diversity in rice plants [J]. | NATURE COMMUNICATIONS , 2025 , 16 (1) . |
| MLA | Zhu, Yu et al. "In-depth analysis of 17,115 rice transcriptomes reveals extensive viral diversity in rice plants" . | NATURE COMMUNICATIONS 16 . 1 (2025) . |
| APA | Zhu, Yu , Raza, Ali , Bai, Qing , Zou, Chengwu , Niu, Jiangshuai , Guo, Zhongxin et al. In-depth analysis of 17,115 rice transcriptomes reveals extensive viral diversity in rice plants . | NATURE COMMUNICATIONS , 2025 , 16 (1) . |
| Export to | NoteExpress RIS BibTex |
Version ：
Abstract ：
Pandemics originating from zoonotic viruses have posed significant threats to human health and agriculture. Recent discoveries have revealed that wild-rice plants also harbour viral pathogens capable of severely impacting rice production, a cornerstone food crop. In this study, we conducted virome analysis on similar to 1000 wild-rice individual colonies and discovered a novel single-strand positive-sense RNA virus prevalent in these plants. Through comprehensive genomic characterization and comparative sequence analysis, this virus was classified as a new species in the genus Polerovirus, designated Rice less tiller virus (RLTV). Our investigations elucidated that RLTV could be transmitted from wild rice to cultivated rice via a specific insect vector, the aphid Rhopalosiphum padi, causing less tiller disease symptoms in rice plants. We generated an infectious cDNA clone for RLTV and demonstrated systemic infection of rice cultivars and induction of severe disease symptoms following mechanical inoculation or stable genetic transformation. We further illustrated transmission of RLTV from stable transgenic lines to healthy rice plants by the aphid vector, leading to the development of disease symptoms. Notably, our database searches showed that RLTV and another polerovirus isolated from a wild plant species are widely circulating not only in wild rice but also cultivated rice around the world. Our findings provide strong evidence for a wild plant origin for rice viruses and underscore the imminent threat posed by aphid-transmitted rice Polerovirus to rice cultivar.
Keyword ：
aphid aphid growth growth pathogens pathogens Polerovirus Polerovirus rice virus rice virus wild rice wild rice
Cite：
Copy from the list or Export to your reference management。
| GB/T 7714 | Yan, Wenkai , Zhu, Yu , Zou, Chengwu et al. Virome Characterization of Native Wild-Rice Plants Discovers a Novel Pathogenic Rice Polerovirus With World-Wide Circulation [J]. | PLANT CELL AND ENVIRONMENT , 2024 , 48 (2) : 1005-1020 . |
| MLA | Yan, Wenkai et al. "Virome Characterization of Native Wild-Rice Plants Discovers a Novel Pathogenic Rice Polerovirus With World-Wide Circulation" . | PLANT CELL AND ENVIRONMENT 48 . 2 (2024) : 1005-1020 . |
| APA | Yan, Wenkai , Zhu, Yu , Zou, Chengwu , Liu, Wencheng , Jia, Bei , Niu, Jiangshuai et al. Virome Characterization of Native Wild-Rice Plants Discovers a Novel Pathogenic Rice Polerovirus With World-Wide Circulation . | PLANT CELL AND ENVIRONMENT , 2024 , 48 (2) , 1005-1020 . |
| Export to | NoteExpress RIS BibTex |
Version ：
Abstract ：
Evolutionarily conserved antiviral RNA interference (RNAi) mediates a primary antiviral innate immunity preventing infection of broad-spectrum viruses in plants. However, the detailed mechanism in plants is still largely unknown, especially in important agricultural crops, including tomato. Varieties of pathogenic viruses evolve to possess viral suppressors of RNA silencing (VSRs) to suppress antiviral RNAi in the host. Due to the prevalence of VSRs, it is still unknown whether antiviral RNAi truly functions to prevent invasion by natural wild-type viruses in plants and animals. In this research, for the first time we applied CRISPR-Cas9 to generate ago2a, ago2b, or ago2ab mutants for two differentiated Solanum lycopersicum AGO2s, key effectors in antiviral RNAi. We found that AGO2a but not AGO2b was significantly induced to inhibit the propagation of not only VSR-deficient Cucumber mosaic virus (CMV) but also wild-type CMV-Fny in tomato; however, neither AGO2a nor AGO2b regulated disease induction after infection with either virus. Our findings firstly reveal a prominent role of AGO2a in antiviral RNAi innate immunity in tomato and demonstrate that antiviral RNAi evolves to defend against infection of natural wild-type CMV-Fny in tomato. However, AGO2a-mediated antiviral RNAi does not play major roles in promoting tolerance of tomato plants to CMV infection for maintaining health.
Cite：
Copy from the list or Export to your reference management。
| GB/T 7714 | Zhao, Liling , Chen, Yingfang , Xiao, Xingming et al. AGO2a but not AGO2b mediates antiviral defense against infection of wild-type cucumber mosaic virus in tomato [J]. | HORTICULTURE RESEARCH , 2023 , 10 (5) . |
| MLA | Zhao, Liling et al. "AGO2a but not AGO2b mediates antiviral defense against infection of wild-type cucumber mosaic virus in tomato" . | HORTICULTURE RESEARCH 10 . 5 (2023) . |
| APA | Zhao, Liling , Chen, Yingfang , Xiao, Xingming , Gao, Haiying , Cao, Jiamin , Zhang, Zhongkai et al. AGO2a but not AGO2b mediates antiviral defense against infection of wild-type cucumber mosaic virus in tomato . | HORTICULTURE RESEARCH , 2023 , 10 (5) . |
| Export to | NoteExpress RIS BibTex |
Version ：
Abstract ：
Author summaryEmerging and re-emerging dangerous viruses cause epidemics or pandemics to threaten human and economically important crops and animals. Some of the most dangerous human viruses have zoonotic origins from wild animals. Native plants may also host new endemic viruses that can spread to cause epidemics in cultivated rice, one of the most important staple plants in the world. In the research, we discovered Rice tiller inhibition virus (RTIV), a new insect-borne positive-strand RNA virus, from Asian wild rice plants through metagenomic sequencing, and demonstrated that RTIV could be transmitted by a wide-distributed specific species of aphids to cultivated rice and inhibited tillering, an important agronomic trait of rice plants. We further rescued RTIV by developing infectious clone and confirmed that it can be a dangerous aphid-transmitted viral pathogen of cultivated rice plants. Thus, not only a rare aphid-transmitted viral pathogen of rice plants was discovered in the research, our findings also indicate that novel pathogenic viruses could spread out from native plants to threaten important crop plants. A major threat to rice production is the disease epidemics caused by insect-borne viruses that emerge and re-emerge with undefined origins. It is well known that some human viruses have zoonotic origins from wild animals. However, it remains unknown whether native plants host uncharacterized endemic viruses with spillover potential to rice (Oryza sativa) as emerging pathogens. Here, we discovered rice tiller inhibition virus (RTIV), a novel RNA virus species, from colonies of Asian wild rice (O. rufipogon) in a genetic reserve by metagenomic sequencing. We identified the specific aphid vector that is able to transmit RTIV and found that RTIV would cause low-tillering disease in rice cultivar after transmission. We further demonstrated that an infectious molecular clone of RTIV initiated systemic infection and causes low-tillering disease in an elite rice variety after Agrobacterium-mediated inoculation or stable plant transformation, and RTIV can also be transmitted from transgenic rice plant through its aphid vector to cause disease. Finally, global transcriptome analysis indicated that RTIV may disturb defense and tillering pathway to cause low tillering disease in rice cultivar. Thus, our results show that new rice viral pathogens can emerge from native habitats, and RTIV, a rare aphid-transmitted rice viral pathogen from native wild rice, can threaten the production of rice cultivar after spillover.
Cite：
Copy from the list or Export to your reference management。
| GB/T 7714 | Yan, Wenkai , Zhu, Yu , Liu, Wencheng et al. Discovery of aphid-transmitted Rice tiller inhibition virus from native plants through metagenomic sequencing [J]. | PLOS PATHOGENS , 2023 , 19 (3) . |
| MLA | Yan, Wenkai et al. "Discovery of aphid-transmitted Rice tiller inhibition virus from native plants through metagenomic sequencing" . | PLOS PATHOGENS 19 . 3 (2023) . |
| APA | Yan, Wenkai , Zhu, Yu , Liu, Wencheng , Zou, Chengwu , Jia, Bei , Chen, Zhong-Qi et al. Discovery of aphid-transmitted Rice tiller inhibition virus from native plants through metagenomic sequencing . | PLOS PATHOGENS , 2023 , 19 (3) . |
| Export to | NoteExpress RIS BibTex |
Version ：
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.
Keyword ：
antiviral innate immunity antiviral innate immunity RNAi RNAi small RNA small RNA virus virus VSR VSR
Cite：
Copy from the list or Export to your reference management。
| GB/T 7714 | Jin, Liying , Chen, Mengna , Xiang, Meiqin et al. RNAi-Based Antiviral Innate Immunity in Plants [J]. | VIRUSES-BASEL , 2022 , 14 (2) . |
| MLA | Jin, Liying et al. "RNAi-Based Antiviral Innate Immunity in Plants" . | VIRUSES-BASEL 14 . 2 (2022) . |
| APA | Jin, Liying , Chen, Mengna , Xiang, Meiqin , Guo, Zhongxin . RNAi-Based Antiviral Innate Immunity in Plants . | VIRUSES-BASEL , 2022 , 14 (2) . |
| Export to | NoteExpress RIS BibTex |
Version ：
Abstract ：
Melanization in the hemolymph of arthropods is a conserved defense strategy against infection by invading pathogens. Numerous plant viruses are persistently transmitted by insect vectors, and must overcome hemolymph melanization. Here, we determine that the plant rhabdovirus rice stripe mosaic virus (RSMV) has evolved to evade the antiviral melanization response in the hemolymph in leafhopepr vectors. After virions enter vector hemolymph cells, viral nucleoprotein N is initially synthesized and directly interacts with prophenoloxidase (PPO), a core component of the melanization pathway and this process strongly activates the expression of PPO. Furthermore, such interaction could effectively inhibit the proteolytic cleavage of the zymogen PPO to active phenoloxidase (PO), finally suppressing hemolymph melanization. The knockdown of PPO expression or treatment with the PO inhibitor also suppresses hemolymph melanization and causes viral excessive accumulation, finally causing a high insect mortality rate. Consistent with this function, microinjection of N into leafhopper vectors attenuates melanization and promotes viral infection. These findings demonstrate that RSMV N serves as the effector to attenuate hemolymph melanization and facilitate viral persistent propagation in its insect vector. Our findings provide the insights in the understanding of ongoing arms race of insect immunity defense and viral counter-defense.
Keyword ：
leafhopper leafhopper melanization melanization prophenoloxidases (PPO) prophenoloxidases (PPO) rice stripe mosaic virus rice stripe mosaic virus viral infection viral infection
Cite：
Copy from the list or Export to your reference management。
| GB/T 7714 | Zhang, Ruonan , Zhang, Xiao-Feng , Chi, Yunhua et al. Nucleoprotein of a Rice Rhabdovirus Serves as the Effector to Attenuate Hemolymph Melanization and Facilitate Viral Persistent Propagation in its Leafhopper Vector [J]. | FRONTIERS IN IMMUNOLOGY , 2022 , 13 . |
| MLA | Zhang, Ruonan et al. "Nucleoprotein of a Rice Rhabdovirus Serves as the Effector to Attenuate Hemolymph Melanization and Facilitate Viral Persistent Propagation in its Leafhopper Vector" . | FRONTIERS IN IMMUNOLOGY 13 (2022) . |
| APA | Zhang, Ruonan , Zhang, Xiao-Feng , Chi, Yunhua , Xu, Yuanyuan , Chen, Hongyan , Guo, Zhongxin et al. Nucleoprotein of a Rice Rhabdovirus Serves as the Effector to Attenuate Hemolymph Melanization and Facilitate Viral Persistent Propagation in its Leafhopper Vector . | FRONTIERS IN IMMUNOLOGY , 2022 , 13 . |
| Export to | NoteExpress RIS BibTex |
Version ：
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-Delta 2b or CMV-2aT Delta 2b) 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-Delta 2b and CMV-2aT Delta 2b, respectively. Our analysis showed that the systematic infection of CMV, CMV-Delta 2b and CMV-2aT Delta 2b could cause hypoxia response and reduce photosynthesis. Asymptomatic infections of CMV-Delta 2b or CMV-2aT Delta 2b 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.
Keyword ：
4) 4) Arabidopsis thaliana Arabidopsis thaliana cucumber mosaic virus (CMV) cucumber mosaic virus (CMV) dcl2dcl4 (dcl2 dcl2dcl4 (dcl2 transcriptome transcriptome
Cite：
Copy from the list or Export to your reference management。
| GB/T 7714 | Xu, Qian , Shen, Li , Jin, Liying et al. Comparative Transcriptome Analysis of CMV or 2b-Deficient CMV-Infected dcl2dcl4 Reveals the Effects of Viral Infection on Symptom Induction in Arabidopsis thaliana [J]. | VIRUSES-BASEL , 2022 , 14 (7) . |
| MLA | Xu, Qian et al. "Comparative Transcriptome Analysis of CMV or 2b-Deficient CMV-Infected dcl2dcl4 Reveals the Effects of Viral Infection on Symptom Induction in Arabidopsis thaliana" . | VIRUSES-BASEL 14 . 7 (2022) . |
| APA | Xu, Qian , Shen, Li , Jin, Liying , Wang, Meng , Chang, Fenghan , Guo, Zhongxin . Comparative Transcriptome Analysis of CMV or 2b-Deficient CMV-Infected dcl2dcl4 Reveals the Effects of Viral Infection on Symptom Induction in Arabidopsis thaliana . | VIRUSES-BASEL , 2022 , 14 (7) . |
| Export to | NoteExpress RIS BibTex |
Version ：
Abstract ：
RNA-directed DNA methylation (RdDM) functions in de novo meth-ylation in CG, CHG, and CHH contexts. Here, we performed map -based cloning of OsNRPE1, which encodes the largest subunit of RNA polymerase V (Pol V), a key regulator of gene silencing and reproductive development in rice. We found that rice Pol V is re-quired for CHH methylation on RdDM loci by transcribing long non-coding RNAs. Pol V influences the accumulation of 24-nucleotide small interfering RNAs (24-nt siRNAs) in a locus-specific manner. Bio-synthesis of 24-nt siRNAs on loci with high CHH methylation levels and low CG and CHG methylation levels tends to depend on Pol V. In contrast, low methylation levels in the CHH context and high meth-ylation levels in CG and CHG contexts predisposes 24-nt siRNA ac-cumulation to be independent of Pol V. H3K9me1 and H3K9me2 tend to be enriched on Pol V-independent 24-nt siRNA loci, whereas various active histone modifications are enriched on Pol V-dependent 24-nt siRNA loci. DNA methylation is required for 24-nt siRNAs biosynthesis on Pol V-dependent loci but not on Pol V-independent loci. Our results reveal the function of rice Pol V for long noncoding RNA production, DNA methylation, 24-nt siRNA accumulation, and reproductive development.
Keyword ：
OsNRPE1 OsNRPE1 rice rice RNA polymerase V RNA polymerase V siRNA siRNA
Cite：
Copy from the list or Export to your reference management。
| GB/T 7714 | Zheng, Kezhi , Wang, Lili , Zeng, Longjun et al. The effect of RNA polymerase V on 24-nt siRNA accumulation depends on DNA methylation contexts and histone modifications in rice [J]. | PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA , 2021 , 118 (30) . |
| MLA | Zheng, Kezhi et al. "The effect of RNA polymerase V on 24-nt siRNA accumulation depends on DNA methylation contexts and histone modifications in rice" . | PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 118 . 30 (2021) . |
| APA | Zheng, Kezhi , Wang, Lili , Zeng, Longjun , Xu, Dachao , Guo, Zhongxin , Gao, Xiquan et al. The effect of RNA polymerase V on 24-nt siRNA accumulation depends on DNA methylation contexts and histone modifications in rice . | PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA , 2021 , 118 (30) . |
| Export to | NoteExpress RIS BibTex |
Version ：
Abstract ：
In plants, RNA-directed DNA methylation (RdDM) is a de novo DNA methylation pathway that is responsible for transcriptional silencing of repetitive elements. Here, the authors characterized a new RdDM factor, RDM15, and show that it is required for RdDM-dependent DNA methylation and siRNA accumulation at a subset of RdDM target loci. In plants, RNA-directed DNA methylation (RdDM) is a well-known de novo DNA methylation pathway that involves two plant-specific RNA polymerases, Pol IV and Pol V. In this study, we discovered and characterized an RdDM factor, RDM15. Through DNA methylome and genome-wide siRNA analyses, we show that RDM15 is required for RdDM-dependent DNA methylation and siRNA accumulation at a subset of RdDM target loci. We show that RDM15 contributes to Pol V-dependent downstream siRNA accumulation and interacts with NRPE3B, a subunit specific to Pol V. We also show that the C-terminal tudor domain of RDM15 specifically recognizes the histone 3 lysine 4 monomethylation (H3K4me1) mark. Structure analysis of RDM15 in complex with the H3K4me1 peptide showed that the RDM15 tudor domain specifically recognizes the monomethyllysine through an aromatic cage and a specific hydrogen bonding network; this chemical feature-based recognition mechanism differs from all previously reported monomethyllysine recognition mechanisms. RDM15 and H3K4me1 have similar genome-wide distribution patterns at RDM15-dependent RdDM target loci, establishing a link between H3K4me1 and RDM15-mediated RdDM in vivo. In summary, we have identified and characterized a histone H3K4me1-specific binding protein as an RdDM component, and structural analysis of RDM15 revealed a chemical feature-based lower methyllysine recognition mechanism.
Cite：
Copy from the list or Export to your reference management。
| GB/T 7714 | Niu, Qingfeng , Song, Zhe , Tang, Kai et al. A histone H3K4me1-specific binding protein is required for siRNA accumulation and DNA methylation at a subset of loci targeted by RNA-directed DNA methylation [J]. | NATURE COMMUNICATIONS , 2021 , 12 (1) . |
| MLA | Niu, Qingfeng et al. "A histone H3K4me1-specific binding protein is required for siRNA accumulation and DNA methylation at a subset of loci targeted by RNA-directed DNA methylation" . | NATURE COMMUNICATIONS 12 . 1 (2021) . |
| APA | Niu, Qingfeng , Song, Zhe , Tang, Kai , Chen, Lixian , Wang, Lisi , Ban, Ting et al. A histone H3K4me1-specific binding protein is required for siRNA accumulation and DNA methylation at a subset of loci targeted by RNA-directed DNA methylation . | NATURE COMMUNICATIONS , 2021 , 12 (1) . |
| Export to | NoteExpress RIS BibTex |
Version ：
Abstract ：
Geminivirus infection induces the expression of a plant imprinted E3 ligase gene, leading to the proteosomal degradation of DNA methyltransferases and epigenetic activation of viral gene transcription. Flowering plants and mammals contain imprinted genes that are primarily expressed in the endosperm and placenta in a parent-of-origin manner. In this study, we show that early activation of the geminivirus genes C2 and C3 in Arabidopsis (Arabidopsis thaliana) plants, encoding a viral suppressor of RNA interference and a replication enhancer protein, respectively, is correlated with the transient vegetative expression of VARIANT IN METHYLATION5 (VIM5), an endosperm imprinted gene that is conserved in diverse plant species. VIM5 is a ubiquitin E3 ligase that directly targets the DNA methyltransferases MET1 and CMT3 for degradation by the ubiquitin-26S proteasome proteolytic pathway. Infection with Beet severe curly top virus induced VIM5 expression in rosette leaf tissues, possibly via the expression of the viral replication initiator protein, leading to the early activation of C2 and C3 coupled with reduced symmetric methylation in the C2-3 promoter and the onset of disease symptoms. These findings demonstrate how this small DNA virus recruits a host imprinted gene for the epigenetic activation of viral gene transcription. Our findings reveal a distinct strategy used by plant pathogens to exploit the host machinery in order to inhibit methylation-mediated defense responses when establishing infection.
Cite：
Copy from the list or Export to your reference management。
| GB/T 7714 | Chen, Zhong-Qi , Zhao, Jian-Hua , Chen, Qian et al. DNA Geminivirus Infection Induces an Imprinted E3 Ligase Gene to Epigenetically Activate Viral Gene Transcription [J]. | PLANT CELL , 2020 , 32 (10) : 3256-3272 . |
| MLA | Chen, Zhong-Qi et al. "DNA Geminivirus Infection Induces an Imprinted E3 Ligase Gene to Epigenetically Activate Viral Gene Transcription" . | PLANT CELL 32 . 10 (2020) : 3256-3272 . |
| APA | Chen, Zhong-Qi , Zhao, Jian-Hua , Chen, Qian , Zhang, Zhong-Hui , Li, Jie , Guo, Zhong-Xin et al. DNA Geminivirus Infection Induces an Imprinted E3 Ligase Gene to Epigenetically Activate Viral Gene Transcription . | PLANT CELL , 2020 , 32 (10) , 3256-3272 . |
| Export to | NoteExpress RIS BibTex |
Version ：
Export
| Results： |
Selected to |
| Format： |
