Ding SW, Voinnet O. Antiviral immunity directed by small RNAs. Cell. 2007;130:413426.
Calarco JP, Martienssen RA. Genome reprogramming and small interfering RNA in the Arabidopsis germline. Curr Opin Genet Dev. 2011;21:134–9.
Chen X. Small RNAs—secrets and surprises of the genome. Plant J. 2010;61:941–58.
Cogoni C, Macino G. Gene silencing in Neurospora crassa requires a protein homologous to RNA-dependent RNA polymerase. Nature. 1999;399:166–9.
Dalmay T, Hamilton A, Rudd S, Angell S, Baulcombe DC. An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell. 2000;101:543–53.
Wang XB, Wu Q, Ito T, Cillo F, Li WX, Chen X, Yu JL, Ding SW. RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana. Proc Natl Acad Sci USA. 2010;107:484–9.
Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol 2004;2:e104.
Bouché N, Lauressergues D, Gasciolli V, Vaucheret H. An antagonistic function for Arabidopsis DCL2 in development and a new function for DCL4 in generating viral siRNAs. EMBO J. 2006;25:3347–56.
Andika IB, Maruyama K, Sun L, Kondo H, Tamada T, Suzuki N. Differential contributions of plant Dicer-like proteins to antiviral defences against Potato virus X in leaves and roots. Plant J. 2015a;81:781–93.
Brosseau C, Moffett P. Functional and genetic analysis identify a role for Arabidopsis ARGONAUTE5 in antiviral RNA silencing. Plant Cell. 2015a;27:1742–54.
Deleris A, Gallego-Bartolome J, Bao J, Kasschau KD, Carrington JC, Voinnet O. Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense. Science. 2006;313:68–71.
Diaz-Pendon JA, Li F, Li WX, Ding SW. Suppression of antiviral silencing by Cucumber mosaic virus 2b protein in Arabidopsis is associated with drastically reduced accumulation of three classes of viral small interfering RNAs. Plant Cell. 2007;19:2053–63.
Dunoyer P, Himber C, Ruiz-Ferrer V, Alioua A, Voinnet O. Intra- and intercellular RNA interference in Arabidopsis thaliana requires components of the microRNA and heterochromatic silencing pathways. Nat Genet. 2007;39:848–56.
Garcia-Ruiz H, Carbonell A, Hoyer JS, Fahlgren N, Gilbert KB, Takeda A, Giampetruzzi A, Garcia Ruiz MT, McGinn MG, Lowery N, Martinez Baladejo MT, Carrington JC. Roles and programming of Arabidopsis ARGONAUTE proteins during turnip mosaic virus infection. PLoS Pathog. 2015;11:e1004755.
Qu F, Ye X, Morris TJ. Arabidopsis DRB4, AGO1, AGO7, and RDR6 participate in a DCL4-initiated antiviral RNA silencing pathway negatively regulated by DCL1. Proc Natl Acad Sci USA. 2008;105:14732–7.
Zhang C, Wu Z, Li Y, Wu J. Biogenesis, function, and applications of virus-derived small RNAs in plants. Front Microbiol. 2015a;6:1237.
Minoia S, Carbonell A, Di Serio F, Gisel A, Carrington JC, Navarro B, Flores R. Specific argonautes selectively bind small RNAs derived from Potato Spindle Tuber Viroid and Attenuate Viroid accumulation in vivo. J Virol. 2014;88:11933–45.
Schuck J, Gursinsky T, Pantaleo V, Burgyán J, Behrens SE. AGO/RISC-mediated antiviral RNA silencing in a plant in vitro system. Nucleic Acids Res. 2013;41:5090–103.
Takeda A, Iwasaki S, Watanabe T, Utsumi M, Watanabe Y. The mechanism selecting the guide strand from small RNA duplexes is different among Argonaute proteins. Plant Cell Physiol. 2008;49:493–500.
Wang XB, Jovel J, Udomporn P, Wang Y, Wu Q, Li WX, Gasciolli V, Vaucheret H, Ding SW. The 21-nucleotide, but not 22-nucleotide, viral secondary small interfering RNAs direct potent antiviral defense by two cooperative Argonautes in Arabidopsis thaliana. Plant Cell. 2011;23:1625–38.
Carbonell A, Carrington JC. Antiviral roles of plant ARGONAUTES. Curr Opin Plant Biol. 2015;27:111–7.
Harvey JJ, Lewsey MG, Patel K, Westwood J, Heimstädt S, Carr JP, Baulcombe DC. An antiviral defense role of AGO2 in plants. PLoS ONE. 2011;6:e14639.
Jaubert M, Bhattacharjee S, Mello AF, Perry KL, Moffett P. ARGONAUTE2 mediates RNA-silencing antiviral defenses against Potato virus X in arabidopsis. Plant Physiol. 2011;156:1556–64.
Ma X, Nicole MC, Meteignier LV, Hong N, Wang G, Moffett P. Different roles for RNA silencing and RNA processing components in virus recovery and virus-induced gene silencing in plants. J Exp Bot. 2015;66:919–32.
Odokonyero D, Mendoza MR, Alvarado VY, Zhang J, Wang X, Scholthof HB. Transgenic down-regulation of ARGONAUTE2 expression in Nicotiana benthamiana interferes with several layers of antiviral defenses. Virology. 2015;486:209–18.
Fernández-Calvino L, Martínez-Priego L, Szabo EZ, Guzmán-Benito I, González I, Canto T, Lakatos L, Llave C. Tobacco rattle virus 16K silencing suppressor binds ARGONAUTE 4 and inhibits formation of RNA silencing complexes. J Gen Virol. 2016;97:246–57.
Scholthof HB, Alvarado VY, Vega-Arreguin JC, Ciomperlik J, Odokonyero D, Brosseau C, Jaubert M, Zamora A, Moffett P. Identification of an ARGONAUTE for antiviral RNA silencing in Nicotiana benthamiana. Plant Physiol. 2015;156:1548–55.
Zhang C, Wu Z, Li Y, Wu J. Biogenesis, function, and applications of virus-derived small RNAs in plants. Front Microbiol. 2015b;6:1237.
Andika IB, Maruyama K, Sun L, Kondo H, Tamada T, Suzuki N. Different Dicer-like protein components required for intracellular and systemic antiviral silencing in Arabidopsis thaliana. Plant Signal Behav. 2015b;10:e1039214.
Brosseau C, Moffett P. Functional and genetic analysis identify a role for Arabidopsis ARGONAUTE5 in antiviral RNA silencing. Plant Cell. 2015b;27:1742–54.
Plisson C, Drucker M, Blanc S, German-Retana S, Le Gall O, Thomas D, Bron P. Structural characterization of HC-Pro, a plant virus multifunctional protein. J Biol Chem. 2003;278:23753–61.
Karasev AV, Gray SM. Continuous and emerging challenges of potato virus Y in potato. Annu Rev Phytopathol. 2013;51:571–86.
Riechmann JL, Laín S, García JA. Highlights and prospects of potyvirus molecular biology. J Gen Virol. 1992;73:1–16.
Chung BYW, Miller WA, Atkins JF, Firth AE. An overlapping essential gene in the Potyviridae. Proc Natl Acad Sci USA. 2008;105:5897–902.
Olspert A, Chung BYW, Atkins JF, Carr JP, Firth AE. Transcriptional slippage in the positive-sense RNA virus family Potyviridae. EMBO Rep. 2015;16:995–1004.
Wylie SJ, Adams M, Chalam C, Kreuze J, López-Moya JJ, Ohshima K, Zerbini FM. ICTV virus taxonomy profile: Potyviridae. J Gen Virol. 2017;98:352.
Komoda YH, Choi SH, Sato M, Atsumi G, Abe J, Fukuda J, Honjo MN, Nagano AJ, Komoda K, Nakahara KS, Uyeda I. Truncated yet functional viral protein produced via RNA polymerase slippage implies underestimated coding capacity of RNA viruses. Sci Rep UK. 2016;6:21411.
Bergougnoux V. The history of tomato: from domestication to biopharming. Biotechnol Adv. 2014;32:170–89.
Bai M, Yang GS, Chen WT, Mao ZC, Kang HX, Chen GH, Yang YH, Xie BY. 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. Gene. 2012;501:52–62.
Kravchik M, Sunkar R, Damodharan S, Stav R, Zohar M, Isaacson T, Arazi T. Global and local perturbation of the tomato microRNA pathway by a trans-activated DICER-LIKE 1 mutant. J Exp Bot. 2014;65:725–39.
Kravchik M, Damodharan S, Stav R, Arazi T. Characterization of a tomato DCL3-silencing mutant. Plant Sci. 2014;221:81–9.
Yifhar T, Pekker I, Peled D, Friedlander G, Pistunov A, Sabban M, Eshed Y. Failure of the tomato trans-acting short interfering RNA program to regulate AUXIN RESPONSE FACTOR3 and ARF4 underlies the wiry leaf syndrome. Plant Cell. 2012;24:3575–89.
Wang Z, Hardcastle TJ, Pastor AC, Yip WH, Tang S, Baulcombe DC. A novel DCL2-dependent miRNA pathway in tomato affects susceptibility to RNA viruses. Gene Dev. 2018;32:1155–60.
Wang T, Deng Z, Zhang X, Wang H, Wang Y, Liu X, Liu S, Xu F, Li T, Fu D, Shu B, Luo Y, Zhu H. Tomato DCL2b is required for the biosynthesis of 22-nt small RNAs, the resulting secondary siRNAs, and the host defense against ToMV. Hortic Res. 2018;5:1–14.
Suzuki T, Ikeda S, Kasai A, Taneda A, Fujibayashi M, Sugawara K, Sano T. RNAi-mediated down-regulation of Dicer-like 2 and 4 changes the response of ‘Moneymaker’ tomato to potato spindle tuber viroid infection from tolerance to lethal systemic necrosis, accompanied by up-regulation of miR398, 398a–3p and production of excessive amount of reactive oxygen species. Viruses. 2019;11:344.
Naoi T, Kitabayashi S, Kasai A, Sugawara K, Adkar-Purushothama CR, Senda M, Hataya T, Sano T. Suppression of RNA-dependent RNA polymerase 6 in tomatoes allows potato spindle tuber viroid to invade basal part but not apical part including pluripotent stem cells of shoot apical meristem. PLoS ONE. 2020;15:e0236481.
Chapman S, Kavanagh T, Baulcombe DC. Potato virus X as a vector for gene expression in plants. Plant J. 1992;2:549–57.
Ohki T, Sano M, Asano K, Nakayama T, Maoka T. Effect of temperature on resistance to Potato virus Y in potato cultivars carrying the resistance gene Rychc. Plant Pathol. 2018;67:1629–35.
Masuta C, Nishimura M, Morishita H, Hataya T. A single amino acid change in viral genome-associated protein of potato virus Y correlates with resistance breaking in ‘Virgin A Mutant’ tobacco. Phytopathology. 1999;89:118–23.
Jeon EJ, Tadamura K, Murakami T, Inaba JI, Kim BM, Sato M, Nakahara KS. rgs-CaM detects and counteracts viral RNA silencing suppressors in plant immune priming. J Virol. 2017;91:e00761-e817.
Nakahara KS, Masuta C, Yamada S, Shimura H, Kashihara Y, Wada TS, Sekiguchi T. Tobacco calmodulin-like protein provides secondary defense by binding to and directing degradation of virus RNA silencing suppressors. Proc Natl Acad Sci USA. 2012;109:10113–8.
Silva TF, Romanel EA, Andrade RR, Farinelli L, Østerås M, Deluen C, Vaslin MF. Profile of small interfering RNAs from cotton plants infected with the polerovirus Cotton leafroll dwarf virus. BMC Mol Biol. 2011;12:40.
Campos L, Granell P, Tárraga S, López-Gresa P, Conejero V, Bellés JM, Lisón P. Salicylic acid and gentisic acid induce RNA silencing-related genes and plant resistance to RNA pathogens. Plant Physiol Biochem. 2014;77:35–43.
Cordero T, Cerdán L, Carbonell A, Katsarou K, Kalantidis K, Daròs JA. Dicer-Like 4 Is involved in restricting the systemic movement of Zucchini yellow mosaic virus in Nicotiana benthamiana. Mol Plant Microbe Interact. 2017;30:63–71.
Vazquez F. Arabidopsis endogenous small RNAs: highways and byways. Trends Plant Sci. 2006;11:460–8.
Garcia-Ruiz H, Takeda A, Chapman EJ, Sullivan CM, Fahlgren N, Brempelis KJ, Carrington JC. Arabidopsis RNA-dependent RNA polymerases and Dicer-like proteins in antiviral defense and small interfering RNA biogenesis during turnip mosaic virus infection. Plant Cell. 2010;22:481–96.
Senshu H, Ozeki J, Komatsu K, Hashimoto M, Hatada K, Aoyama M, Namba S. Variability in the level of RNA silencing suppression caused by triple gene block protein 1 (TGBp1) from various potexviruses during infection. J Gen Virol. 2009;90:1014–24.
Van Wezel R, Hong Y. Virus survival of RNA silencing without deploying protein-mediated suppression in Nicotiana benthamiana. FEBS Lett. 2004;562:65–70.
Csorba T, Pantaleo V, Burgyán J. RNA silencing: an antiviral mechanism. Adv Virus Res. 2009;75:35–71.
Ludman M, Burgyán J, Fátyol K. Crispr/Cas9 mediated inactivation of argonaute 2 reveals its differential involvement in antiviral responses. Sci Rep UK. 2017;7:1–12.
Verchot-Lubicz J, Ye CM, Bamunusinghe D. Molecular biology of potexviruses: recent advances. J Gen Virol. 2007;88:1643–55.
Voinnet O, Lederer C, Baulcombe DC. A viral movement protein prevents spread of the gene silencing signal in Nicotiana benthamiana. Cell. 2000;103:157–67.
Cho SK, Ryu MY, Shah P, Poulsen CP, Yang SW. Post-translational regulation of miRNA pathway components, AGO1 and HYL1, in plants. Mol Cells. 2016;39:581.
Malcuit I, Marano MR, Kavanagh TA, De Jong W, Forsyth A, Baulcombe DC. The 25-kDa movement protein of PVX elicits nb-mediated hypersensitive cell death in potato. Mol Plant Microbe Interact. 1999;12:536–43.
Ye C, Dickman MB, Whitham SA, Payton M, Verchot J. The Unfolded protein response is triggered by a plant viral movement protein. Plant Physiol. 2011;156:741–55.
Lu Y, Yin M, Wang X, Chen B, Yang X, Peng J, MacFarlane S. The unfolded protein response and programmed cell death are induced by expression of Garlic virus X p11 in Nicotiana benthamiana. J Gen Virol. 2016;97:1462–8.
Ozeki J, Takahashi S, Komatsu K, Kagiwada S, Yamashita K, Mori T, Namba S. A single amino acid in the RNA-dependent RNA polymerase of Plantago asiatica mosaic virus contributes to systemic necrosis. Arch Virol. 2006;151:2067–75.
Kagiwada S, Yamaji Y, Komatsu K, Takahashi S, Mori T, Hirata H, Suzuki M, Ugaki M, Namba S. A single amino acid residue of RNA-dependent RNA polymerase in the potato virus X genome determines the symptoms in Nicotiana plants. Virus Res. 2005;110:177–82.
Pacheco R, García-Marcos A, Barajas D, Martiáñez J, Tenllado F. PVX—potyvirus synergistic infections differentially alter microRNA accumulation in Nicotiana benthamiana. Virus Res. 2012;165:231–5.
García-Marcos A, Pacheco R, Manzano A, Aguilar E, Tenllado F. Oxylipin biosynthesis genes positively regulate programmed cell death during compatible infections with the synergistic pair Potato virus X-Potato virus Y and Tomato spotted wilt virus. J Virol. 2013;87:5769–73.
Montillet JL, Chamnongpol S, Rusterucci C, Dat J, van de Cotte B, Agnel JP, Battesti C, Inze D, Van Breusegem F, Triantaphylides C. Fatty acid hydroperoxides and H2O2 in the execution of hypersensitive cell death in tobacco leaves. Plant Physiol. 2005;138:1516–26.
Fátyol K, Fekete KA, Ludman M. Double-stranded-RNA-binding protein 2 participates in antiviral defense. J Virol. 2020;94:11.