Samson R, Legendre JB, Christen R, Fischer-Le Saux M, Achouak W, et al. Transfer of Pectobacterium chrysanthemi and Brenneria paradisiaca to the genus Dickeya gen. Nov. as Dickeya chrysanthemi comb. nov. and Dickeya paradisiaca comb. nov. and delineation of four novel species, Dickeya dadantii sp. nov., Dickeya dianthicola sp. nov., Dickeya dieffenbachiae sp. nov. and Dickeya zeae sp. nov. Int J Syst Evol Microbiol. 2005;55:1415–27.
Toth IK, Bell KS, Holeva MC, Birch PR. Soft rot erwiniae: from genes to genomes. Mol Plant Pathol. 2003;4:17–30.
Yan X, Ye W, Li Y, Jiang J, Cao Y, et al. Isolation, identification and pahtogenicity analysis of soft rot pathogen from Oncidium 'Gower Ramsey'. Subtropical Plant Sci. 2017;46:201–8.
Fu SF, Tsai TM, Chen YR, Liu CP, Haiso LJ, et al. Characterization of the early response of the orchid, Phalaenopsis amabilis, to Erwinia chrysanthemi infection using expression profiling. Physiol Plant. 2012;145:406–25.
Sherameti I, Shahollari B, Venus Y, Altschmied L, Varma A, et al. The endophytic fungus Piriformospora indica stimulates the expression of nitrate reductase and the starch-degrading enzyme glucan-water dikinase in tobacco and Arabidopsis roots through a homeodomain transcription factor that binds to a conserved motif in their promoters. J Biol Chem. 2005;280:26241–7.
Yadav V, Kumar M, Deep DK, Kumar H, Sharma R, et al. A phosphate transporter from the root endophytic fungus Piriformospora indica plays a role in phosphate transport to the host plant. J Biol Chem. 2010;285:26532–44.
Peśkan-Berghöfer T, Shahollari B, Giong PH, Hehl S, Markert C, et al. Association of Piriformospora indica with Arabidopsis thaliana roots represents a novel system to study beneficial plant-microbe interactions and involves early plant protein modifications in the endoplasmic reticulum and at the plasma membrane. Physiol Plant. 2004;122:465–77.
Shahollari B, Varma A, Oelmüller R. Expression of a receptor kinase in Arabidopsis roots is stimulated by the basidiomycete Piriformospora indica and the protein accumulates in triton X-100 insoluble plasma membrane microdomains. J Plant Physiol. 2005;162:945–58.
Lee Y-C, Johnson JM, Chien C-T, Yeh K-W. Growth promotion of Chinese cabbage and Arabidopsis by Piriformospora indica is not stimulated by mycelium-synthesized Auxin. MPMI. 2011;20:421–31.
Dolatabadi HK, Goltapeh EM, Jaimand K, Rohani N, Varma A. Effects of Piriformospora indica and Sebacina vermifera on growth and yield of essential oil in fennel (Foeniculum vulgare) under greenhouse conditions. J Basic Microbiol. 2011;51:33–9.
Hua MD, Senthil Kumar R, Shyur LF, Cheng YB, Tian Z, et al. Metabolomic compounds identified in Piriformospora indica-colonized Chinese cabbage roots delineate symbiotic functions of the interaction. Sci Rep. 2017;7:9291.
Varma A, Savita V. Sudha, Sahay N, Butehorn B, et al. Piriformospora indica, a cultivable plant-growth-promoting root endophyte. Appl Environ Microbiol. 1999;65:2741–4.
Waller F, Achatz B, Baltruschat H, Fodor J, Becker K, et al. The endophytic fungus Piriformospora indica reprograms barley to salt-stress tolerance, disease resistance, and higher yield. Proc Natl Acad Sci U S A. 2005;102:13386–91.
Sun C, Shao Y, Vahabi K, Lu J, Bhattacharya S, Dong S, Yeh K-W, Sherameti I, Lou B, Baldwin IT, et al. The beneficial fungus Piriformospora indica protects Arabidopsis from Verticillium dahliaeinfection by downregulation plant defense responses. BMC Plant Biol. 2014;14(1):268.
Matsuo M, Johnson JM, Hieno A, Tokizawa M, Nomoto M, et al. High REDOX RESPONSIVE TRANSCRIPTION FACTOR1 levels result in accumulation of reactive oxygen species in Arabidopsis thaliana shoots and roots. Mol Plant. 2015;8:1253–73.
Johnson JM, Thürich J, Petutschnig EK, Altschmied L, Meichsner D, et al. A poly(a) ribonuclease controls the cellotriose-based interaction between Piriformospora indica and its host Arabidopsis. Plant Physiol. 2018;176:2496–514.
Meyers BC, Kozik A, Griego A, Kuang H, Michelmore RW. Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell. 2003;15:809–34.
Zhou T, Wang Y, Chen JQ, Araki H, Jing Z, et al. Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes. Mol Gen Genomics. 2004;271:402–15.
EAvd B, JDG J. The NB-ARC domain:a novel signalling motif shared by plant resistance gene products and regulators of cell death in animals. Curr Biol. 1998;8:226–8.
Pan Q, Wendel J, Fluhr R. Divergent evolution of plant NBS-LRR resistance gene homologues in dicot and cereal genomes. J Mol Evol. 2000;50:203–13.
Baulcombe D. RNA silencing in plants. Nature. 2004;431:356–63.
Hajdarpasic A, Ruggenthaler P. Analysis of miRNA expression under stress in Arabidopsis thaliana. Bosn J Basic Med Sci. 2012;12:169–76.
Li Y, Zhang Q, Zhang J, Wu L, Qi Y, et al. Identification of microRNAs involved in pathogen-associated molecular pattern-triggered plant innate immunity. Plant Physiol. 2010;152:2222–31.
Navarro L, Dunoyer P, Jay F, Arnold B, Dharmasiri N, et al. A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science. 2006;312:436–9.
Navarro L, Jay F, Nomura K, He SY, Voinnet O. Suppression of the microRNA pathway by bacterial effector proteins. Science. 2008;321:964–7.
Li H, Deng Y, Wu T, Subramanian S, Yu O. Misexpression of miR482, miR1512, and miR1515 increases soybean nodulation. Plant Physiol. 2010;153:1759–70.
Jue D, Sang X, Liu L, Shu B, Wang Y, et al. Identification of WRKY gene family from Dimocarpus longan and its expression analysis during flower induction and abiotic stress responses. Int J Mol Sci. 2018;19(8):E2169.
Yang L, Mu X, Liu C, Cai J, Shi K, et al. Overexpression of potato miR482e enhanced plant sensitivity to Verticillium dahliae infection. J Integr Plant Biol. 2015;57:1078–88.
Devers EA, Branscheid A, May P, Krajinski F. Stars and symbiosis: microRNA- and microRNA*-mediated transcript cleavage involved in arbuscular mycorrhizal symbiosis. Plant Physiol. 2011;156:1990–2010.
Ye W, Shen C-H, Lin Y, Chen P-J, Xu X, et al. Growth promotion-related miRNAs in oncidium orchid roots colonized by the endophytic fungus Piriformospora indica. PLoS One. 2014;9:e84920.
Meyers BC, Dickerman AW, Michelmore RW, Sivaramakrishnan S, Sobral BW, et al. Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. Plant J. 1999;20:317–32.
Chini A, Grant JJ, Seki M, Shinozaki K, Loake GJ. Drought tolerance established by enhanced expression of the CC-NBS-LRR gene, ADR1, requires salicylic acid, EDS1 and ABI1. Plant J. 2004;38:810–22.
Cai J, Liu X, Vanneste K, Proost S, Tsai W-C, et al. The genome sequence of the orchid Phalaenopsis equestris. Nat Genet. 2015;47:65–72.
Yan L, Wang X, Liu H, Tian Y, Lian J, et al. The genome of Dendrobium officinale illuminates the biology of the important traditional Chinese orchid herb. Mol Plant. 2015;8:922–34.
Arya P, Kumar G, Acharya V, Singh AK. Genome-wide identification and expression analysis of NBS-encoding genes in Malus x domestica and expansion of NBS genes family in Rosaceae. PLoS One. 2014;9:e107987.
Kohler A, Rinaldi C, Duplessis S, Baucher M, Geelen D, et al. Genome-wide identification of NBS resistance genes in Populus trichocarpa. Plant Mol Biol. 2008;66:619–36.
Kang YJ, Kim KH, Shim S, Yoon MY, Sun S, et al. Genome-wide mapping of NBS-LRR genes and their association with disease resistance in soybean. BMC Plant Biol. 2012;12:139.
Lozano R, Ponce O, Ramirez M, Mostajo N, Orjeda G. Genome-wide identification and mapping of NBS-encoding resistance genes in Solanum tuberosum group phureja. PLoS One. 2012;7:e34775.
Song H, Wang PF, Li TT, Xia H, Zhao SZ, et al. Genome-wide identification and evolutionary analysis of nucleotide-binding site-encoding resistance genes in Lotus japonicus (Fabaceae). Genet Mol Res. 2015;14:16024–40.
Zhu Q, Fan L, Liu Y, Xu H, Llewellyn D, et al. miR482 Regulation of NBS-LRR Defense Genes during Fungal Pathogen Infection in Cotton. PLoS One. 2013;8:e84390.
Zhai J, Jeong DH, De Paoli E, Park S, Rosen BD, et al. MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. Genes Dev. 2011;25:2540–53.
Shivaprasad PV, Chen HM, Patel K, Bond DM, Santos BA, et al. A microRNA superfamily regulates nucleotide binding site-leucine-rich repeats and other mRNAs. Plant Cell. 2012;24:859–74.
Stein E, Molitor A, Kogel KH, Waller F. Systemic resistance in Arabidopsis conferred by the mycorrhizal fungus Piriformospora indica requires jasmonic acid signaling and the cytoplasmic function of NPR1. Plant Cell Physiol. 2008;49:1747–51.
Fu ZQ, Dong X. Systemic acquired resistance: turning local infection into global defense. Annu Rev Plant Biol. 2013;64:839–63.
Choudhary DK, Johri BN. Interactions of Bacillus spp. and plants -with special reference to induced systemic resistance (ISR). Microbiol Res. 2009;164:493–513.
Waller F, Mukherjee K, Deshmukh SD, Achatz B, Sharma M, et al. Systemic and local modulation of plant responses by Piriformospora indica and related Sebacinales species. J Plant Physiol. 2008;165:60–70.
Schäfer P, Khatabi B, Kogel KH. Root cell death and systemic effects of Piriformospora indica: a study on mutualism. FEMS Microbiol Lett. 2007;275:1–7.
Schäfer P, Pfiffi S, Voll LM, Zajic D, Chandler PM, et al. Manipulation of plant innate immunity and gibberellin as factor of compatibility in the mutualistic association of barley roots with Piriformospora indica. Plant J. 2009;59:461–74.
Yang S, Perna NT, Cooksey DA, Okinaka Y, Lindow SE, Ibekwe AM, Keen NT, Yang C-H. Genome-wide identification of plant-Upregulated genes of Erwinia chrysanthemi 3937 using a GFP-based IVET leaf Array. Mol Plant-Microb Interact. 2004;17:999–1008.
Expert D. Withholding and exchanging iron: interactions between Erwinia spp. and their plant hosts. Annu. Rev. Phytopathol. 1999;37:307–34.
Franza T, Expert D. The virulence-associated chrysobactin iron uptake system of Erwinia chrysanthemi 3937 involves an operon encoding transport and biosynthetic functions. J Bacteriol. 1991;173:6874–81.
Franza T, Sauvage C, Expert D. Iron regulation and pathogenicity in Erwinia chrysanthemi 3937: role of the Fur repressor protein. Mol Plant-Microbe Interact. 1999;12:119–28.
Hassouni ME, Chambost JP, Expert D, Van Gijsegem F, Barras F. The minimal gene set member msrA, encoding peptide methionine sulfoxide reductase, is a virulence determinant of the plant pathogen Erwinia chrysanthemi. Proc Natl Acad Sci U S A. 1999;96:887–92.
López-Solanilla E, Llama-Palacios A, Collmer A, García-Olmedo F, Rodríguez-Palenzuela P. Relative effects on virulence of mutations in the sap, pel, and hrp loci of Erwinia chrysanthemi. Mol Plant-Microbe Interact. 2001;14:386–93.
Tardy F, Nasser W, Robert-Baudouy J, Hugouvieux-Cotte-Pattat N. Comparative analysis of the five major Erwinia chrysanthemi pectate lyases: enzyme characteristics and potential inhibitors. J Bacteriol. 1997;179:2503–11.
Chatterjee AK, Dumenyo CK, Liu Y, Chatterjee A. Erwinia: Genetics of pathogenicity factors. In: Lederberg J, editor. Encyclopedia of Microbiology, vol. 2. 2nd ed. New York: Academic Press; 2000. p. 236–59.
Collmer A. Keen NT the role of pectic enzymes in plant pathogenesis. Annu Rev Phytopathol. 1986;24:383–409.
Hugouvieux-Cotte-Pattat N, Condemine G, Nasser W, Reverchon S. Regulation of pectinolysis in Erwinia. Annu Rev Microbiol. 1996;50:213–57.
Perombelon MCM, Kelman A. Ecology of the soft rot erwinias. Annu. Rev. Phytopathol. 1980;18:361–87.49.
Croston TL, Lemons AR, Beezhold DH, Green BJ. MicroRNA regulation of host immune responses following fungal exposure. Front Immunol. 2018;9:170.
Islas-Flores T, Rahman A, Ullah H, Villanueva MA. The receptor for activated C kinase in plant signaling: tale of a promiscuous little molecule. Front Plant Sci. 2015;6:1090.
Claycomb JM. Ancient endo-siRNA pathways reveal new tricks. Curr Biol. 2014;24:R703–15.
Seo JK, Wu J, Lii Y, Li Y, Jin H. Contribution of small RNA pathway components in plant immunity. Mol Plant-Microbe Interact. 2013;26:617–25.
Staiger D, Korneli C, Lummer M, Navarro L. Emerging role for RNA-based regulation in plant immunity. New Phytol. 2013;197:394–404.
Naqvi AR, Sarwat M, Hasan S, Roychodhury N. Biogenesis, functions and fate of plant microRNAs. J Cell Physiol. 2012;227:3163–8.
Hohn T, Vazquez F. RNA silencing pathways of plants: silencing and its suppression by plant DNA viruses. Biochim Biophys Acta. 1809;2011:588–600.
Li Z, Rana TM. Molecular mechanisms of RNA-triggered gene silencing machineries. Acc Chem Res. 2012;45:1122–31.
Lu S, Sun YH, Amerson H, Chiang VL. MicroRNAs in loblolly pine (Pinus taeda L.) and their association with fusiform rust gall development. Plant J. 2007;51:1077–98.
Bazin J, Bustos-Sanmamed P, Hartmann C, Lelandais-Briere C, Crespi M. Complexity of miRNA-dependent regulation in root symbiosis. Philos Trans R Soc B Biol Sci. 2012;367:1570–9.
Li F, Pignatta D, Bendix C, Brunkard JO, Cohn MM, Tung J, Sun H, Kumar P, Baker B. MicroRNA regulation of plant innate immune receptors. Proc Natl Acad Sci U S A. 2012;109(5):1790–5.
Hu Z, Jiang Q, Ni Z, Chen R, Xu S, Zhang H. Analyses of a Glycine max degradome library identify microRNA targets and microRNAs that trigger secondary siRNA biogenesis. J Integr Plant Biol. 2013;55(2):160–76.
Shen D, Suhrkamp I, Wang Y, Liu S, Menkhaus J, Verreet JA, Fan L, Cai D. Identification and characterization of microRNAs in oilseed rape (Brassica napus) responsive to infection with the pathogenic fungus Verticillium longisporum using Brassica AA (Brassica rapa) and CC (Brassica oleracea) as reference genomes. New Phytol. 2014;204(3):577–94.
Molitor A, Kogel KH. Induced resistance triggered by Piriformospora indica. Plant Signal Behav. 2009;4:215–6.
Staswick PE, Tiryaki I. The oxylipin signal jasmonic acid is activated by an enzyme that conjugates it to isoleucine in Arabidopsis. Plant Cell. 2004;16:2117–27.
Lorenzo O, Chico JM, Sánchez-Serrano JJ, Solano R. JASMONATE-INSENSITIVE1 encodes a MYC transcription factor essential to discriminate between different jasmonate-regulated defense responses in Arabidopsis. Plant Cell. 2004;16:1938–50.
Cao H, Bowling SA, Gordon AS, Dong X. Characterization of an Arabidopsis mutant that is nonresponsive to inducers of systemic acquired resistance. Plant Cell. 1994;6:1583–92.
Lawton K, Weymann K, Friedrich L, Vernooij B, Uknes S, Ryals J. Systemic acquired resistance in Arabidopsis requires salicylic acid but not ethylene. Mol Plant-Microbe Interact. 1995;8:863–70.
Pieterse CM, Van Wees SC, Van Pelt JA, Knoester M, Laan R, Gerrits H, et al. A novel signaling pathway controlling induced systemic resistance in Arabidopsis. Plant Cell. 1998;10:1571–80.
Knoester M, Pieterse CMJ, Bol JF, Van Loon LC. Systemic resistance in Arabidopsis induced by rhizobacteria requires ethylene-dependent signaling at the site of application. Mol Plant-Microbe Interact. 1999;12:720–7.
Nie P, Li X, Wang S, Guo J, Zhao H, et al. Induced systemic resistance against Botrytis cinerea by Bacillus cereus AR156 through a JA/ET- and NPR1-dependent signaling pathway activates PAMP-triggered immunity in Arabidopsis. Front Plant Sci. 2017;8:238.
Iavicoli A, Boutet E, Buchala A, Metraux JP. Induced systemic resistance in Arabidopsis thaliana in response to root inoculation with Pseudomonas fluorescens CHA0. Mol Plant-Microbe Interact. 2003;16:851–8.
Alonso JM, Hirayama T, Roman G, Nourizadeh S, Ecker JR. EIN2, a bifunctional transducer of ethylene and stress responses in Arabidopsis. Science. 1999;284:2148–52.
Bleecker AB, Estelle MA, Somerville C, Kende H. Insensitivity to ethylene conferred by a dominant mutation in Arabidopsis thaliana. Science. 1988;241:1086–9.
Jacobs S, Zechmann B, Molitor A, Trujillo M, Petutschnig E, et al. Broad-spectrum suppression of innate immunity is required for colonization of Arabidopsis roots by the fungus Piriformospora indica. Plant Physiol. 2011;156:726–40.
Molitor A, Zajic D, Voll LM, Pons-K Hnemann J, Samans B, Kogel KH, Waller F. Barley leaf transcriptome and metabolite analysis reveals new aspects of compatibility and Piriformospora indica-mediated systemic induced resistance to powdery mildew. Mol Plant-Microbe Interact. 2011;24:1427–39.
Vahabi K, Camehl I, Sherameti I, Oelmüller R. Growth of Arabidopsis seedlings on high fungal doses of Piriformospora indica has little effect on plant performance, stress, and defense gene expression in spite of elevated jasmonic acid and jasmonic acid-isoleucine levels in the roots. Plant Signal Behav. 2013;8:e26301.
Vahabi K, Dorcheh SK, Monajembashi S, Westermann M, Reichelt M, et al. Stress promotes Arabidopsis - Piriformospora indica interaction. Plant Signal Behav. 2016;11:e1136763.
Xu L, Wu C, Oelmüller R, Zhang W. Role of Phytohormones in Piriformospora indica-induced growth promotion and stress tolerance in plants: more questions than answers. Front Microbiol. 2018;9:1646.
Glaeser SP, Imani J, Alabid I, Guo H, Kumar N, Kämpfer P, Hardt M, Blom J, Goesmann A, Rothballer M, Hartmann A, Kogel KH. Non-pathogenic rhizobium radiobacter F4 deploys plant beneficial activity independent of its host Piriformospora indica. ISME J. 2016;10:871–84.
Pedrotti L, Mueller MJ, Waller F. Piriformospora indica root colonization triggers local and systemic root responses and inhibits secondary colonization of distal roots. PLoS One. 2013;8:e69352.
Wang YQ, Ohara Y, Nakayashiki H, Tosa Y, Mayama S. Microarray analysis of the gene expression profile induced by the endophytic plant growth-promoting rhizobacteria Pseudomonas fluorescens FPT9601-T5 in Arbidopsis. Mol Plant-Microbe Interact. 2005;18:385–96.
Verhagen BWM, Glazebrook J, Zhu T, Chang HS, Van Loon LC, Pieterse CMJ. The transcriptome of rhizobacteria induced systemic resistance in Arabidopsis. Mol Plant-Microbe Interact. 2004;17:895–908.
Van Wees SCM, Luijendijk M, Smoorenburg I, Van Loon LC, Pieterse CMJ. Rhizobacteria-mediated induced systemic resistance (ISR) in Arabidopsis is not associated with a direct effect of expression of known defense-related genes but stimulates the expression of the jasmonate-inducible gene Atvsp upon challenge. Plant Mol Biol. 1999;41:537–49.
Lucas SJ, Baştaş K, Budak H. Exploring the interaction between small RNAs and R genes during Brachypodium response to Fusarium culmorum infection. Gene. 2014;536:254–64.
Felle HH, Waller F, Molitor A, Kogel KH. The mycorrhiza fungus Piriformospora indica induces fast root-surface pH signaling and primes systemic alkalinization of the leaf apoplast upon powdery mildew infection. Mol Plant-Microbe Interact. 2009;22:1179–85.
Gilroy S, Białasek M, Suzuki N, Górecka M, Devireddy AR, Karpiński S, Mittler R. ROS, calcium, and electric signals: key mediators of rapid systemic signaling in plants. Plant Physiol. 2016;171:1606–15.
Bauer DW, Bogdanove AJ, Beer SV, Collmer A. Erwinia chrysanthemi hrp genes and their involvement in soft rot pathogenesis and elicitation of the hypersensitive response. Mol Plant-Microbe Interact. 1994;7:573–81.
Rojas CM, Ham JH, Schechter LM, Kim JF, Beer SV, et al. The Erwinia chrysanthemi EC16 hrp/hrc gene cluster encodes an active Hrp type III secretion system that is flanked by virulence genes functionally unrelated to the Hrp system. Mol Plant-Microbe Interact. 2004;17:644–53.
Fagard M, Dellagi A, Roux C, Perino C, Rigault M, et al. Arabidopsis thaliana expresses multiple lines of defense to counterattack Erwinia chrysanthemi. Mol Plant-Microbe Interact. 2007;20:794–805.
Kraepiel Y, Pedron J, Patrit O, Simond-Cote E, Hermand V, et al. Analysis of the plant bos1 mutant highlights necrosis as an efficient defence mechanism during D. dadantii/Arabidospis thaliana interaction. PLoS One. 2011;6:e18991.
Perez-Bueno ML, Granum E, Pineda M, Flors V, Rodriguez-Palenzuela P, et al. Temporal and spatial resolution of activated plant defense responses in leaves of Nicotiana benthamiana infected with Dickeya dadantii. Front Plant Sci. 2015;6:1209.
Li Y, Ye W, Jiang J. Observation on biological characteristics of 24 germplasm resources of Oncidium. Fujian Agric Sci Technol. 2013;Z1:99–101.
Chen SP, Lin IW, Chen X, Huang YH, Chang SC, et al. Sweet potato NAC transcription factor, IbNAC1, upregulates sporamin gene expression by binding the SWRE motif against mechanical wounding and herbivore attack. Plant J. 2016;86:234–48.
Senthilkumar S, Krishnamurthy KV, Britto SJ, Arockiasamy DI. Visualization of orchid mycorrhizal fungal structures with fluorescence dye using epifluorescence microscopy. Curr Sci. 2000;79:1527–8.
Lozano R, Hamblin MT, Prochnik S, Jannink JL. Identification and distribution of the NBS-LRR gene family in the cassava genome. BMC Genomics. 2015;16:360.
An FM, Hsiao SR, Chan MT. Sequencing-based approaches reveal low ambient temperature-responsive and tissue-specific microRNAs in Phalaenopsis orchid. PLoS One. 2011;6:e18937.