{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T18:44:43Z","timestamp":1787942683419,"version":"build-2784847793"},"reference-count":120,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2026,1,29]],"date-time":"2026-01-29T00:00:00Z","timestamp":1769644800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32320103010"],"award-info":[{"award-number":["32320103010"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Basic Research Center, The Agricultural Science and Technology Innovation Program","award":["CAAS-BRC-CB-2025-02"],"award-info":[{"award-number":["CAAS-BRC-CB-2025-02"]}]},{"name":"Open Funds of the State Key Laboratory of Plant Environmental Resilience","award":["SKLPERKF2602"],"award-info":[{"award-number":["SKLPERKF2602"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Plant RNA interference (RNAi) is a fundamental antiviral defense that relies on coordinated activities of DICER-like endonucleases (DCLs), Argonaute proteins (AGOs) and RNA-dependent RNA polymerases (RDRs). Over the past decades, studies using model and crop species have uncovered complex and often redundant roles for DCLs and RDRs in generating and amplifying virus-derived small interfering RNAs (vsiRNAs), in addition to connections with transcriptional gene silencing (TGS) and epigenetic defenses against DNA viruses. Concurrently, plant viruses have evolved diverse counterstrategies\u2014proteinaceous RNA silencing suppressors (RSSs), exoribonuclease (XRN)-resistant noncoding RNAs, and indirect manipulation of host pathways\u2014to evade RNAi. Driven by the co-evolutionary arms race, plants have developed sophisticated counter-countermeasures that modulate or overcome viral anti-RNAi activity. Accumulated evidence suggests that plants encode host factor genes that are activated to degrade or sequester viral components such as RSSs against viral infection. On the other hand, plants have also evolved endogenous host modulators of antiviral RNAi that can either reinforce the antiviral response or be co-opted by viruses to antagonize it, representing a furious dynamic molecular battling mechanism. Here, we review recent advances in the molecular functions of DCLs and RDRs across species, summarize newly discovered viral counter-defenses (including RNA-based suppressors), and discuss host counter-countermeasures. We research key areas\u2014such as the roles of RDR\u03b3-class proteins, RTL1 (RNase three-like 1)-mediated competition with DCLs, and the mechanistic impact of viral noncoding RNAs\u2014and outline translational opportunities for improving virus resistance in crops through breeding, biotechnological approaches, and RNA-based applications.<\/jats:p>","DOI":"10.3390\/v18020184","type":"journal-article","created":{"date-parts":[[2026,1,29]],"date-time":"2026-01-29T16:08:17Z","timestamp":1769702897000},"page":"184","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Advances in Plant Antiviral RNAi: From Host DCLs\/RDRs to Diversified Viral Counteracting Strategies"],"prefix":"10.3390","volume":"18","author":[{"given":"Xue","family":"Li","sequence":"first","affiliation":[{"name":"State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fuan","family":"Pan","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5311-7331","authenticated-orcid":false,"given":"Xueping","family":"Zhou","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2233-0652","authenticated-orcid":false,"given":"Aiming","family":"Wang","sequence":"additional","affiliation":[{"name":"London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7360-1884","authenticated-orcid":false,"given":"Richard","family":"Kormelink","sequence":"additional","affiliation":[{"name":"Laboratory of Virology, Wageningen University and Research, 6700 AA Wageningen, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fangfang","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,1,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1094\/PHYTO-10-22-0358-IA","article-title":"Transgene silencing, RNA interference, and the antiviral defense mechanism directed by small interfering RNAs","volume":"113","author":"Ding","year":"2023","journal-title":"Phytopathology"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1016\/j.cell.2007.07.039","article-title":"Antiviral immunity directed by small RNAs","volume":"130","author":"Ding","year":"2007","journal-title":"Cell"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1016\/j.tplants.2010.09.001","article-title":"Virus-derived small interfering RNAs at the core of plant-virus interactions","volume":"15","author":"Llave","year":"2010","journal-title":"Trends Plant Sci."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Jin, L., Chen, M., Xiang, M., and Guo, Z. (2022). RNAi-based antiviral innate immunity in plants. Viruses, 14.","DOI":"10.3390\/v14020432"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1038\/nrg2504","article-title":"Small silencing RNAs: An expanding universe","volume":"10","author":"Ghildiyal","year":"2009","journal-title":"Nat. Rev. Genet."},{"key":"ref_6","first-page":"e70022","article-title":"Plant defense strategies: The dual armor of disease resistance and tolerance","volume":"2","author":"Tang","year":"2025","journal-title":"New Plant Prot."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.tplants.2023.10.014","article-title":"Plant-virus arms race beyond RNA interference","volume":"29","author":"Ge","year":"2024","journal-title":"Trends Plant Sci."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1625","DOI":"10.1105\/tpc.110.082305","article-title":"The 21-nucleotide, but not 22-nucleotide, viral secondary small interfering RNAs direct potent antiviral defense by two cooperative argonautes in Arabidopsis thaliana","volume":"23","author":"Wang","year":"2011","journal-title":"Plant Cell"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1073\/pnas.0904086107","article-title":"RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana","volume":"107","author":"Wang","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1016\/j.pbi.2015.06.013","article-title":"Antiviral roles of plant ARGONAUTES","volume":"27","author":"Carbonell","year":"2015","journal-title":"Curr. Opin. Plant Biol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1126\/science.1128214","article-title":"Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense","volume":"313","author":"Deleris","year":"2006","journal-title":"Science"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"5167","DOI":"10.1128\/JVI.00272-08","article-title":"Structural and genetic requirements for the biogenesis of tobacco rattle virus-derived small interfering RNAs","volume":"82","author":"Donaire","year":"2008","journal-title":"J. Virol."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Garcia-Ruiz, H., Carbonell, A., Hoyer, J.S., Fahlgren, N., Gilbert, K.B., Takeda, A., Giampetruzzi, A., Garcia Ruiz, M.T., McGinn, M.G., and Lowery, N. (2015). Roles and programming of Arabidopsis ARGONAUTE proteins during Turnip mosaic virus infection. PLoS Pathog., 11.","DOI":"10.1371\/journal.ppat.1004755"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1105\/tpc.109.073056","article-title":"Arabidopsis RNA-dependent RNA polymerases and dicer-like proteins in antiviral defense and small interfering RNA biogenesis during Turnip Mosaic Virus infection","volume":"22","author":"Takeda","year":"2010","journal-title":"Plant Cell"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"14732","DOI":"10.1073\/pnas.0805760105","article-title":"Arabidopsis DRB4, AGO1, AGO7, and RDR6 participate in a DCL4-initiated antiviral RNA silencing pathway negatively regulated by DCL1","volume":"105","author":"Qu","year":"2008","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/j.gene.2012.02.009","article-title":"Genome-wide identification of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families and their expression analyses in response to viral infection and abiotic stresses in Solanum lycopersicum","volume":"501","author":"Bai","year":"2012","journal-title":"Gene"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Liu, X., Lu, T., Dou, Y., Yu, B., and Zhang, C. (2014). Identification of RNA silencing components in soybean and sorghum. BMC Bioinform., 15.","DOI":"10.1186\/1471-2105-15-4"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Mosharaf, M.P., Rahman, H., Ahsan, M.A., Akond, Z., Ahmed, F.F., Islam, M.M., Moni, M.A., and Mollah, M.N.H. (2020). In silico identification and characterization of AGO, DCL and RDR gene families and their associated regulatory elements in sweet orange (Citrus sinensis L.). PLoS ONE, 15.","DOI":"10.1371\/journal.pone.0228233"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1389","DOI":"10.1038\/s41477-021-01000-1","article-title":"Structural basis of microRNA processing by Dicer-like 1","volume":"7","author":"Wei","year":"2021","journal-title":"Nat. Plants"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Nakasugi, K., Crowhurst, R.N., Bally, J., Wood, C.C., Hellens, R.P., and Waterhouse, P.M. (2013). De novo transcriptome sequence assembly and analysis of RNA silencing genes of Nicotiana benthamiana. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0059534"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1111\/tpj.12770","article-title":"Differential contributions of plant Dicer-like proteins to antiviral defences against potato virus X in leaves and roots","volume":"81","author":"Andika","year":"2015","journal-title":"Plant J."},{"key":"ref_22","first-page":"001656","article-title":"Genetic evidence for the involvement of Dicer-like 2 and 4 as well as Argonaute 2 in the Nicotiana benthamiana response against Pelargonium line pattern virus","volume":"102","author":"Hevia","year":"2021","journal-title":"J. Gen. Virol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1393","DOI":"10.1016\/j.chom.2021.07.003","article-title":"A calmodulin-binding transcription factor links calcium signaling to antiviral RNAi defense in plants","volume":"29","author":"Wang","year":"2021","journal-title":"Cell Host Microbe"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1016\/j.ijbiomac.2022.09.178","article-title":"Host-induced gene silencing of PcCesA3 and PcOSBP1 confers resistance to Phytophthora capsici in Nicotiana benthamiana through NbDCL3 and NbDCL4 processed small interfering RNAs","volume":"222","author":"Wang","year":"2022","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"6233","DOI":"10.1093\/nar\/gkl886","article-title":"Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing","volume":"34","author":"Blevins","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"3347","DOI":"10.1038\/sj.emboj.7601217","article-title":"An antagonistic function for Arabidopsis DCL2 in development and a new function for DCL4 in generating viral siRNAs","volume":"25","author":"Lauressergues","year":"2006","journal-title":"EMBO J."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1094\/MPMI-07-17-0164-R","article-title":"Revisiting the roles of Tobamovirus replicase complex proteins in viral replication and silencing suppression","volume":"31","author":"Rajeswaran","year":"2018","journal-title":"Mol. Plant Microbe Interact."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1093\/nar\/gkj447","article-title":"Molecular characterization of geminivirus-derived small RNAs in different plant species","volume":"34","author":"Akbergenov","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"2611","DOI":"10.1128\/JVI.02305-13","article-title":"Arabidopsis double-stranded RNA binding protein DRB3 participates in methylation-mediated defense against geminiviruses","volume":"88","author":"Raja","year":"2014","journal-title":"J. Virol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1186\/s12985-020-01414-x","article-title":"RNA silencing-related genes contribute to tolerance of infection with potato virus X and Y in a susceptible tomato plant","volume":"17","author":"Kwon","year":"2020","journal-title":"Virol. J."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1038\/s41556-020-00606-5","article-title":"Phase separation of SERRATE drives dicing body assembly and promotes miRNA processing in Arabidopsis","volume":"23","author":"Xie","year":"2021","journal-title":"Nat. Cell Biol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1038\/s41438-018-0073-7","article-title":"Tomato DCL2b is required for the biosynthesis of 22-nt small RNAs, the resulting secondary siRNAs, and the host defense against ToMV","volume":"5","author":"Wang","year":"2018","journal-title":"Hortic. Res."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1016\/j.plantsci.2014.02.007","article-title":"Generation and characterization of a tomato DCL3-silencing mutant","volume":"221\u2013222","author":"Kravchik","year":"2014","journal-title":"Plant Sci."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1093\/jxb\/ert428","article-title":"Global and local perturbation of the tomato microRNA pathway by a trans-activated DICER-LIKE 1 mutant","volume":"65","author":"Kravchik","year":"2014","journal-title":"J. Exp. Bot."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.1101\/gad.313601.118","article-title":"A novel DCL2-dependent miRNA pathway in tomato affects susceptibility to RNA viruses","volume":"32","author":"Wang","year":"2018","journal-title":"Genes Dev."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"3575","DOI":"10.1105\/tpc.112.100222","article-title":"Failure of the tomato trans-acting short interfering RNA program to regulate AUXIN RESPONSE FACTOR3 and ARF4 underlies the wiry leaf syndrome","volume":"24","author":"Yifhar","year":"2012","journal-title":"Plant Cell"},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Shamandi, N., Zytnicki, M., Charbonnel, C., Elvira-Matelot, E., Bochnakian, A., Comella, P., Mallory, A.C., Lep\u00e8re, G., S\u00e1ez-V\u00e1squez, J., and Vaucheret, H. (2015). Plants encode a general siRNA suppressor that is induced and suppressed by viruses. PLoS Biol., 13.","DOI":"10.1371\/journal.pbio.1002326"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1016\/j.molcel.2015.11.015","article-title":"A Dicer-independent route for biogenesis of siRNAs that direct DNA methylation in Arabidopsis","volume":"61","author":"Ye","year":"2016","journal-title":"Mol. Cell"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"5003","DOI":"10.1093\/nar\/gkr119","article-title":"Massive production of small RNAs from a non-coding region of Cauliflower mosaic virus in plant defense and viral counter-defense","volume":"39","author":"Blevins","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"581","DOI":"10.15252\/embj.201489453","article-title":"Specific but interdependent functions for Arabidopsis AGO4 and AGO6 in RNA-directed DNA methylation","volume":"34","author":"Duan","year":"2015","journal-title":"EMBO J."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"866","DOI":"10.1111\/nph.16397","article-title":"Natural variation in the Arabidopsis AGO2 gene is associated with susceptibility to potato virus X","volume":"226","author":"Brosseau","year":"2020","journal-title":"New Phytol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1104\/pp.16.00015","article-title":"Abscisic acid induces resistance against Bamboo Mosaic Virus through Argonaute2 and 3","volume":"174","author":"Alazem","year":"2017","journal-title":"Plant Physiol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1016\/j.coviro.2018.08.003","article-title":"Dissection of RNAi-based antiviral immunity in plants","volume":"32","author":"Yang","year":"2018","journal-title":"Curr. Opin. Virol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1016\/S0092-8674(00)80863-6","article-title":"Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance","volume":"101","author":"Mourrain","year":"2000","journal-title":"Cell"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"15209","DOI":"10.1128\/JVI.79.24.15209-15217.2005","article-title":"RDR6 has a broad-spectrum but temperature-dependent antiviral defense role in Nicotiana benthamiana","volume":"79","author":"Qu","year":"2005","journal-title":"J. Virol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"6297","DOI":"10.1073\/pnas.0304346101","article-title":"A natural variant of a host RNA-dependent RNA polymerase is associated with increased susceptibility to viruses by Nicotiana benthamiana","volume":"101","author":"Yang","year":"2004","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Li, F., Huang, C., Li, Z., and Zhou, X. (2014). Suppression of RNA silencing by a plant DNA virus satellite requires a host calmodulin-like protein to repress RDR6 expression. PLoS Pathog., 10.","DOI":"10.1371\/journal.ppat.1003921"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"11324","DOI":"10.1038\/srep11324","article-title":"OsRDR6 plays role in host defense against double-stranded RNA virus, Rice Dwarf Phytoreovirus","volume":"5","author":"Hong","year":"2015","journal-title":"Sci. Rep."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1016\/j.virusres.2011.11.016","article-title":"RNA-dependent RNA polymerase 6 of rice (Oryza sativa) plays role in host defense against negative-strand RNA virus, Rice stripe virus","volume":"163","author":"Jiang","year":"2012","journal-title":"Virus Res."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"14613","DOI":"10.1073\/pnas.1407131111","article-title":"Virus infection triggers widespread silencing of host genes by a distinct class of endogenous siRNAs in Arabidopsis","volume":"111","author":"Cao","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1382","DOI":"10.1111\/nph.17657","article-title":"Nuclear exportin 1 facilitates turnip mosaic virus infection by exporting the sumoylated viral replicase and by repressing plant immunity","volume":"232","author":"Zhang","year":"2021","journal-title":"New Phytol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"e2302069120","DOI":"10.1073\/pnas.2302069120","article-title":"Salicylic acid and RNA interference mediate antiviral immunity of plant stem cells","volume":"120","author":"Incarbone","year":"2023","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"101490","DOI":"10.1016\/j.xplc.2025.101490","article-title":"Antiviral RNA interference in plants: Increasing complexity and integration with other biological processes","volume":"6","author":"Li","year":"2025","journal-title":"Plant Commun."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Verlaan, M.G., Hutton, S.F., Ibrahem, R.M., Kormelink, R., Visser, R.G., Scott, J.W., Edwards, J.D., and Bai, Y. (2013). The Tomato Yellow Leaf Curl Virus resistance genes Ty-1 and Ty-3 are allelic and code for DFDGD-class RNA-dependent RNA polymerases. PLoS Genet., 9.","DOI":"10.1371\/journal.pgen.1003399"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"12942","DOI":"10.1073\/pnas.1400894111","article-title":"Tomato yellow leaf curl virus resistance by Ty-1 involves increased cytosine methylation of viral genomes and is compromised by cucumber mosaic virus infection","volume":"111","author":"Butterbach","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1111\/mpp.12885","article-title":"Ty-1, a universal resistance gene against geminiviruses that is compromised by co-replication of a betasatellite","volume":"21","author":"Voorburg","year":"2020","journal-title":"Mol. Plant Pathol."},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Li, X., Zhou, X., and Li, F. (2025). Pelota: A double-edged sword in virus infection. PLoS Pathog., 21.","DOI":"10.1371\/journal.ppat.1013328"},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Voorburg, C.M., Bai, Y., and Kormelink, R. (2021). Small RNA profiling of susceptible and resistant Ty-1 encoding tomato plants upon tomato yellow leaf curl virus infection. Front. Plant Sci., 12.","DOI":"10.3389\/fpls.2021.757165"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"2368","DOI":"10.1101\/gad.1231804","article-title":"SGS3 and SGS2\/SDE1\/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis","volume":"18","author":"Peragine","year":"2004","journal-title":"Genes. Dev."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1038\/emboj.2009.2","article-title":"dsRNA with 5\u2032 overhangs contributes to endogenous and antiviral RNA silencing pathways in plants","volume":"28","author":"Fukunaga","year":"2009","journal-title":"EMBO J."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1016\/S0092-8674(00)80864-8","article-title":"An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus","volume":"101","author":"Dalmay","year":"2000","journal-title":"Cell"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"e2102885118","DOI":"10.1073\/pnas.2102885118","article-title":"Cooperative recruitment of RDR6 by SGS3 and SDE5 during small interfering RNA amplification in Arabidopsis","volume":"118","author":"Yoshikawa","year":"2021","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"4117","DOI":"10.1073\/pnas.1217050110","article-title":"3\u2032 fragment of miR173-programmed RISC-cleaved RNA is protected from degradation in a complex with RISC and SGS3","volume":"110","author":"Yoshikawa","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1111\/j.1742-4658.2008.06828.x","article-title":"A neomorphic sgs3 allele stabilizing miRNA cleavage products reveals that SGS3 acts as a homodimer","volume":"276","author":"Elmayan","year":"2009","journal-title":"FEBS J."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"1004","DOI":"10.1111\/j.1365-313X.2004.02103.x","article-title":"Geminivirus VIGS of endogenous genes requires SGS2\/SDE1 and SGS3 and defines a new branch in the genetic pathway for silencing in plants","volume":"38","author":"Muangsan","year":"2004","journal-title":"Plant J."},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Li, F., Wang, Y., and Zhou, X. (2017). SGS3 cooperates with RDR6 in triggering geminivirus-induced gene silencing and in suppressing geminivirus infection in Nicotiana benthamiana. Viruses, 9.","DOI":"10.3390\/v9090247"},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"Li, F., Zhao, N., Li, Z., Xu, X., Wang, Y., Yang, X., Liu, S.S., Wang, A., and Zhou, X. (2017). A calmodulin-like protein suppresses RNA silencing and promotes geminivirus infection by degrading SGS3 via the autophagy pathway in Nicotiana benthamiana. PLoS Pathog., 13.","DOI":"10.1371\/journal.ppat.1006213"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1016\/j.tim.2022.07.009","article-title":"Antiviral RNAi drives host adaptation to viral infection","volume":"30","author":"Li","year":"2022","journal-title":"Trends Microbiol."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"4169","DOI":"10.3390\/v7082815","article-title":"BnSGS3 has differential effects on the accumulation of CMV, ORMV and TuMV in Oilseed Rape","volume":"7","author":"Chen","year":"2015","journal-title":"Viruses"},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"Qi, X., Bao, F.S., and Xie, Z. (2009). Small RNA deep sequencing reveals role for Arabidopsis thaliana RNA-dependent RNA polymerases in viral siRNA biogenesis. PLoS ONE, 4.","DOI":"10.1371\/annotation\/8d1a816e-b366-4833-b558-724ec28d1b87"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"1195","DOI":"10.1111\/mpp.13104","article-title":"RNA-dependent RNA polymerase 1 delays the accumulation of viroids in infected plants","volume":"22","author":"Li","year":"2021","journal-title":"Mol. Plant Pathol."},{"key":"ref_72","doi-asserted-by":"crossref","unstructured":"Adkar-Purushothama, C.R., and Perreault, J.P. (2019). Suppression of RNA-dependent RNA polymerase 6 favors the accumulation of potato spindle tuber viroid in Nicotiana benthamiana. Viruses, 11.","DOI":"10.3390\/v11040345"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"1199","DOI":"10.1094\/MPMI-04-14-0109-R","article-title":"Silencing suppressor protein VPg of a potyvirus interacts with the plant silencing-related protein SGS3","volume":"27","author":"Streng","year":"2014","journal-title":"Mol. Plant Microbe Interact."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1111\/mpp.13192","article-title":"The nonstructural protein NSs encoded by tomato zonate spot virus suppresses RNA silencing by interacting with NbSGS3","volume":"23","author":"Chen","year":"2022","journal-title":"Mol. Plant Pathol."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1016\/j.molp.2024.03.012","article-title":"Chloroplast immunity: A cornerstone of plant defense","volume":"17","author":"Liu","year":"2024","journal-title":"Mol. Plant"},{"key":"ref_76","first-page":"e8","article-title":"Targeting of viral RNAs by nonsense-mediated decay is compromised by virus-plant interactions","volume":"1","author":"Chen","year":"2024","journal-title":"New Plant Prot."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1146\/annurev-virology-091919-064218","article-title":"The role of viruses in identifying and analyzing RNA silencing","volume":"9","author":"Baulcombe","year":"2022","journal-title":"Annu. Rev. Virol."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1038\/s41580-022-00496-5","article-title":"Roles of RNA silencing in viral and non-viral plant immunity and in the crosstalk between disease resistance systems","volume":"23","author":"Baulcombe","year":"2022","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"e0003522","DOI":"10.1128\/mmbr.00035-22","article-title":"Infection defects of RNA and DNA viruses induced by antiviral RNA interference","volume":"87","author":"Liu","year":"2023","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"1691","DOI":"10.1016\/j.chom.2024.08.009","article-title":"Antiviral RNA interference inhibits virus vertical transmission in plants","volume":"32","author":"Liu","year":"2024","journal-title":"Cell Host Microbe"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"2994","DOI":"10.1038\/s41467-022-30771-0","article-title":"Identification of positive and negative regulators of antiviral RNA interference in Arabidopsis thaliana","volume":"13","author":"Liu","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1038\/s41577-018-0071-x","article-title":"Small RNA-based antimicrobial immunity","volume":"19","author":"Guo","year":"2019","journal-title":"Nat. Rev. Immunol."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"1539","DOI":"10.1007\/s11427-019-1565-1","article-title":"Pivoting plant immunity from theory to the field","volume":"62","author":"Li","year":"2019","journal-title":"Sci. China Life Sci."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"792","DOI":"10.1016\/j.tim.2019.05.007","article-title":"RNA-targeted antiviral immunity: More than just RNA silencing","volume":"27","author":"Li","year":"2019","journal-title":"Trends Microbiol."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"3256","DOI":"10.1105\/tpc.20.00249","article-title":"DNA geminivirus infection induces an imprinted E3 ligase gene to epigenetically activate viral gene transcription","volume":"32","author":"Chen","year":"2020","journal-title":"Plant Cell"},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1007\/s11427-020-1829-4","article-title":"Hijack to escape: A geminivirus seizes a host imprinted E3 ligase to escape epigenetic repression","volume":"64","author":"Zhou","year":"2021","journal-title":"Sci. China Life Sci."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"1388","DOI":"10.1073\/pnas.1715556115","article-title":"A virus-targeted plant receptor-like kinase promotes cell-to-cell spread of RNAi","volume":"115","author":"Zhang","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"e2022547118","DOI":"10.1073\/pnas.2022547118","article-title":"The receptor-like kinases BAM1 and BAM2 are required for root xylem patterning","volume":"118","author":"Fan","year":"2021","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"4278","DOI":"10.1038\/s41467-021-24617-4","article-title":"Geminiviruses encode additional small proteins with specific subcellular localizations and virulence function","volume":"12","author":"Gong","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"1794","DOI":"10.1016\/j.molp.2023.09.020","article-title":"Plant and animal positive-sense single-stranded RNA viruses encode small proteins important for viral infection in their negative-sense strand","volume":"16","author":"Gong","year":"2023","journal-title":"Mol. Plant"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1007\/s44154-022-00044-3","article-title":"The novel C5 protein from tomato yellow leaf curl virus is a virulence factor and suppressor of gene silencing","volume":"2","author":"Zhao","year":"2022","journal-title":"Stress Biol."},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1093\/plphys\/kiad338","article-title":"Geminivirus C5 proteins mediate formation of virus complexes at plasmodesmata for viral intercellular movement","volume":"193","author":"Zhao","year":"2023","journal-title":"Plant Physiol."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"1046","DOI":"10.1007\/s11427-021-2063-4","article-title":"Tomato yellow leaf curl virus V3 protein traffics along microfilaments to plasmodesmata to promote virus cell-to-cell movement","volume":"65","author":"Gong","year":"2022","journal-title":"Sci. China Life Sci."},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"17094","DOI":"10.1038\/nplants.2017.94","article-title":"Neutralization of mobile antiviral small RNA through peroxisomal import","volume":"3","author":"Incarbone","year":"2017","journal-title":"Nat. Plants"},{"key":"ref_95","doi-asserted-by":"crossref","unstructured":"Zhang, K., Gu, T., Xu, X., Gan, H., Qin, L., Feng, C., and He, Z. (2023). Sugarcane streak mosaic virus P1 protein inhibits unfolded protein response through direct suppression of bZIP60U splicing. PLoS Pathog., 19.","DOI":"10.1371\/journal.ppat.1011738"},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"197640","DOI":"10.1016\/j.virusres.2019.197640","article-title":"RNA silencing suppression mechanisms of Triticum mosaic virus P1: dsRNA binding property and mapping functional motifs","volume":"269","author":"Gupta","year":"2019","journal-title":"Virus Res."},{"key":"ref_97","doi-asserted-by":"crossref","unstructured":"Flobinus, A., Chevigny, N., Charley, P.A., Seissler, T., Klein, E., Bleykasten-Grosshans, C., Ratti, C., Bouzoubaa, S., Wilusz, J., and Gilmer, D. (2018). Beet necrotic yellow vein virus noncoding RNA production depends on a 5\u2032 \u2192 3\u2032 Xrn exoribonuclease activity. Viruses, 10.","DOI":"10.3390\/v10030137"},{"key":"ref_98","doi-asserted-by":"crossref","unstructured":"Flobinus, A., Hleibieh, K., Klein, E., Ratti, C., Bouzoubaa, S., and Gilmer, D. (2016). A viral noncoding RNA complements a weakened viral RNA silencing suppressor and promotes efficient systemic host infection. Viruses, 8.","DOI":"10.3390\/v8100272"},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"10162","DOI":"10.1128\/JVI.01027-08","article-title":"A viral noncoding RNA generated by cis-element-mediated protection against 5\u2032 -> 3\u2032 RNA decay represses both cap-independent and cap-dependent translation","volume":"82","author":"Iwakawa","year":"2008","journal-title":"J. Virol."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"9329","DOI":"10.1093\/nar\/gkz668","article-title":"A 212-nt long RNA structure in the Tobacco necrosis virus-D RNA genome is resistant to Xrn degradation","volume":"47","author":"Gunawardene","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1094\/MPMI-10-15-0226-FI","article-title":"Noncoding RNAs of plant viruses and viroids: Sponges of host translation and RNA interference machinery","volume":"29","author":"Miller","year":"2016","journal-title":"Mol. Plant Microbe Interact."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"15987","DOI":"10.1038\/s41598-023-43001-4","article-title":"Xrn1-resistant RNA motifs are disseminated throughout the RNA virome and are able to block scanning ribosomes","volume":"13","author":"Dilweg","year":"2023","journal-title":"Sci. Rep."},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"838","DOI":"10.1080\/15476286.2019.1592070","article-title":"Structural features of an Xrn1-resistant plant virus RNA","volume":"16","author":"Dilweg","year":"2019","journal-title":"RNA Biol."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"13486","DOI":"10.1128\/JVI.01104-12","article-title":"Noncoding flavivirus RNA displays RNA interference suppressor activity in insect and Mammalian cells","volume":"86","author":"Schnettler","year":"2012","journal-title":"J. Virol."},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.virol.2021.11.002","article-title":"A plant-infecting subviral RNA associated with poleroviruses produces a subgenomic RNA which resists exonuclease XRN1 in vitro","volume":"566","author":"Campbell","year":"2022","journal-title":"Virology"},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"e70073","DOI":"10.1111\/mpp.70073","article-title":"Potato type I protease inhibitor mediates host defence against Potato Virus X infection by interacting with a viral RNA silencing suppressor","volume":"26","author":"Shen","year":"2025","journal-title":"Mol. Plant Pathol."},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"e70061","DOI":"10.1111\/mpp.70061","article-title":"FaNDUFB9 attenuates strawberry mottle virus infection by inhibiting the activity of the viral gene silencing suppressor, Pro2Glu","volume":"26","author":"Xu","year":"2025","journal-title":"Mol. Plant Pathol."},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.1111\/tpj.17037","article-title":"A novel RAV transcription factor from pear interacts with viral RNA-silencing suppressors to inhibit viral infection","volume":"120","author":"Xie","year":"2024","journal-title":"Plant J."},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1126\/science.290.5489.142","article-title":"A calmodulin-related protein that suppresses posttranscriptional gene silencing in plants","volume":"290","author":"Anandalakshmi","year":"2000","journal-title":"Science"},{"key":"ref_110","first-page":"108","article-title":"Geminivirus AL2 protein induces expression of, and interacts with, a calmodulin-like gene, an endogenous regulator of gene silencing","volume":"460\u2013461","author":"Lacatus","year":"2014","journal-title":"Virology"},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"10113","DOI":"10.1073\/pnas.1201628109","article-title":"Tobacco calmodulin-like protein provides secondary defense by binding to and directing degradation of virus RNA silencing suppressors","volume":"109","author":"Nakahara","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"9652","DOI":"10.1038\/s41598-020-66670-x","article-title":"Expression patterns of NbrgsCaM family genes in Nicotiana benthamiana and their potential roles in development and stress responses","volume":"10","author":"Liu","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"3369","DOI":"10.1007\/s11033-020-05409-3","article-title":"Virus-induced CRISPR-Cas9 system improved resistance against tomato yellow leaf curl virus","volume":"47","author":"Farsi","year":"2020","journal-title":"Mol. Biol. Rep."},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"3353","DOI":"10.1093\/jxb\/erw155","article-title":"A petunia ethylene-responsive element binding factor, PhERF2, plays an important role in antiviral RNA silencing","volume":"67","author":"Sun","year":"2016","journal-title":"J. Exp. Bot."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"4930","DOI":"10.1111\/pbi.70254","article-title":"Comparative genomics-driven design of virus-delivered short RNA inserts triggering robust gene silencing","volume":"23","author":"Gioiosa","year":"2025","journal-title":"Plant Biotechnol. J."},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"16207","DOI":"10.1038\/nplants.2016.207","article-title":"Clay nanosheets for topical delivery of RNAi for sustained protection against plant viruses","volume":"3","author":"Mitter","year":"2017","journal-title":"Nat. Plants"},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"1008","DOI":"10.1111\/nph.13944","article-title":"Double-stranded RNAs induce a pattern-triggered immune signaling pathway in plants","volume":"211","author":"Niehl","year":"2016","journal-title":"New Phytol."},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"e70008","DOI":"10.1111\/mpp.70008","article-title":"Comparative analysis of RNA interference and pattern-triggered immunity induced by dsRNA reveals different efficiencies in the antiviral response to potato virus X","volume":"25","author":"Necira","year":"2024","journal-title":"Mol. Plant Pathol."},{"key":"ref_119","doi-asserted-by":"crossref","unstructured":"Tabein, S., Jansen, M., Noris, E., Vaira, A.M., Marian, D., Behjatnia, S.A.A., Accotto, G.P., and Miozzi, L. (2020). The induction of an effective dsRNA-mediated resistance against tomato spotted wilt virus by exogenous application of double-stranded RNA largely depends on the selection of the viral RNA target region. Front. Plant Sci., 11.","DOI":"10.3389\/fpls.2020.533338"},{"key":"ref_120","doi-asserted-by":"crossref","unstructured":"Delgado-Mart\u00edn, J., Ruiz, L., Janssen, D., and Velasco, L. (2022). Exogenous application of dsRNA for the control of viruses in Cucurbits. Front. Plant Sci., 13.","DOI":"10.3389\/fpls.2022.895953"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/2\/184\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,29]],"date-time":"2026-01-29T16:10:56Z","timestamp":1769703056000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/2\/184"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,29]]},"references-count":120,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2026,2]]}},"alternative-id":["v18020184"],"URL":"https:\/\/doi.org\/10.3390\/v18020184","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,29]]}}}