1. DanglJL, JonesJD (2001) Plant pathogens and integrated defense responses to infection. Nature 411: 826–833.
2. NavarroL, ZipfelC, RowlandO, KellerI, RobatzekS, et al. (2004) The transcriptional innate immune response to flg22. Interplay and overlap with Avr gene-dependent defense responses and bacterial pathogenesis. Plant Physiol 135: 1113–1128.
3. ZipfelC, RobatzekS, NavarroL, OakeleyEJ, JonesJD, et al. (2004) Bacterial disease resistance in Arabidopsis through flagellin perception. Nature 428: 764–767.
4. MelottoM, UnderwoodW, KoczanJ, NomuraK, HeSY (2006) Plant stomata function in innate immunity against bacterial invasion. Cell 126: 969–980.
5. SchwessingerB, ZipfelC (2008) News from the frontline: recent insights into PAMP-triggered immunity in plants. Curr Opin Plant Biol 11: 389–395.
6. GöhreV, RobatzekS (2008) Breaking the barriers: microbial effector molecules subvert plant immunity. Annu Rev Phytopathol 46: 189–215.
7. LindebergM, CunnacS, CollmerA (2009) The evolution of Pseudomonas syringae host specificity and type III effector repertoires. Mol Plant Pathol 10: 767–75.
8. KuferTA, SansonettiPJ (2011) NLR functions beyond pathogen recognition. Nat Immunol 12: 121–8.
9. MeyersBC, KozikA, GriegoA, KuangH, MichelmoreRW (2003) Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell 15: 809–34.
10. JonesJD, DanglJL (2006) The plant immune system. Nature 444: 323–329.
11. OldroydGE, StaskawiczBJ (1998) Genetically engineered broad-spectrum disease resistance in tomato. Proc Natl Acad Sci USA 95: 10300–10305.
12. BendahmaneA, Kanyuka1K, BaulcombeDC (1999) The Rx Gene from Potato Controls Separate Virus Resistance and Cell Death Responses. Plant Cell 11: 781–792.
13. TaoY, YuanF, LeisterRT, AusubelFM, KatagiriF (2000) Mutational analysis of the Arabidopsis nucleotide binding site-leucine-rich repeat resistance gene RPS2. Plant Cell 12: 2541–2554.
14. ZhangY, GoritschnigS, DongX, LiX (2003) A gain-of-function mutation in a plant disease resistance gene leads to constitutive activation of downstream signal transduction pathways in suppressor of npr1-1, constitutive 1. Plant Cell 15: 2636–46.
15. ZhangY, DoreyS, SwiderskiM, JonesJD (2004) Expression of RPS4 in tobacco induces an AvrRps4-independent HR that requires EDS1, SGT1 and HSP90. Plant J 40: 213–24.
16. ZhouF, MosherS, TianM, SassiG, ParkerJ, KlessigDF (2008) The Arabidopsis gain-of-function mutant ssi4 requires RAR1 and SGT1b differentially for defense activation and morphological alterations. Mol Plant Microbe Interact 21: 40–9.
17. JohnsonKCM, DongOX, HuangY, LiX (2012) A Rolling Stone Gathers No Moss, but Resistant Plants Must Gather Their MOSes. Cold Spring Harb Symp Quant Biol 77: 259–68.
18. YiH, RichardsEJ (2007) A cluster of disease resistance genes in Arabidopsis is coordinately regulated by transcriptional activation and RNA silencing. Plant Cell 19: 2929–2939.
19. Ruiz-FerrerV, VoinnetO (2009) Roles of plant small RNAs in biotic stress responses. Annu Rev Plant Biol 60: 485–510.
20. ZhaiJ, JeongDH, De PaoliE, ParkS, RosenBD, et al. (2011) MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased trans-acting siRNAs. Genes Dev 25: 2540–2553.
21. ShivaprasadPV, ChenHM, PatelK, BondDM, SantosBA, BaulcombeDC (2012) A MicroRNA Superfamily Regulates Nucleotide Binding Site-Leucine-Rich Repeats and other mRNAs. Plant Cell 24: 859–874.
22. LiF, PignattaD, BendixC, BrunkardJO, CohnMM, et al. (2012) MicroRNA regulation of plant innate immune receptors. Proc Natl Acad Sci USA 109: 1790–1795.
23. DowenRH, PelizzolaM, SchmitzRJ, ListerR, DowenJM, et al. (2012) Widespread dynamic DNA methylation in response to biotic stress. Proc Natl Acad Sci USA 109: E2183–91.
24. YuA, LepèreG, JayF, WangJY, BapaumeL, et al. (2013) Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense. Proc Natl Acad Sci USA 110: 2389–94.
25. VaucheretH (2006) Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev 20: 759–71.
26. BrodersenP, VoinnetO (2006) The diversity of RNA silencing pathways in plants. Trends Genet 22: 268–80.
27. BaulcombeD (2004) RNA silencing in plants. Nature 2431: 356–63.
28. MourrainP, BéclinC, ElmayanT, FeuerbachF, GodonC, et al. (2000) Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell 101: 533–42.
29. DalmayT, HamiltonA, RuddS, AngellS, BaulcombeDC (2000) An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell 101: 543–53.
30. QuF, YeX, HouG, SatoS, ClementeTE, MorrisTJ (2005) RDR6 has a broad-spectrum but temperature-dependent antiviral defense role in Nicotiana benthamiana. J Virol 79: 15209–15217.
31. SchwachF, VaistijFE, JonesL, BaulcombeDC (2005) An RNA-dependent RNA polymerase prevents meristem invasion by potato virus X and is required for the activity but not the production of a systemic silencing signal. Plant Physiol 138: 1842–1852.
32. Katiyar-AgarwalS, JinH (2010) Role of small RNAs in host-microbe interactions. Annu Rev Phytopathol 48: 225–46.
33. VazquezF, VaucheretH, RajagopalanR, LepersC, GasciolliV, et al. (2004) Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell 16: 69–79.
34. YoshikawaM, PeragineA, ParkMY, PoethigRS (2005) A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev 19: 2164–75.
35. CuperusJT, CarbonellA, FahlgrenN, Garcia-RuizH, BurkeRT, et al. (2010) Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis. Nat Struct Mol Biol 17: 997–1003.
36. ManavellaPA, KoenigD, WeigelD (2012) Plant secondary siRNA production determined by microRNA-duplex structure. Proc Natl Acad Sci USA 109: 2461–6.
37. NavarroL, JayF, NomuraK, HeSY, VoinnetO (2008) Suppression of the MicroRNA Pathway by Bacterial Effector Proteins. Science 321: 964–967.
38. LiY, ZhangQ, ZhangJ, WuL, QiY, et al. (2010) Identification of microRNAs involved in pathogen-associated molecular pattern-triggered plant innate immunity. Plant Physiol 152: 2222–2231.
39. PeragineA, YoshikawaM, WuG, AlbrechtHL, PoethigRS (2004) SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev 18: 2368–79.
40. TorresMA, JonesJD, DanglJL (2006) Reactive oxygen species signaling in response to pathogens. Plant Physiol 141: 373–8.
41. AsaiT, TenaG, PlotnikovaJ, WillmannMR, ChiuWL, et al. (2002) MAP kinase signalling cascade in Arabidopsis innate immunity. Nature 415: 977–983.
42. HauckP, ThilmonyR, HeSY (2003) A Pseudomonas syringae type III effector suppresses cell wall-based extracellular defense in susceptible Arabidopsis plants. Proc Natl Acad Sci USA 100: 8577–8582.
43. DebRoyS, ThilmonyR, KwackYB, NomuraK, HeSY (2004) A family of conserved bacterial effectors inhibits salicylic acid-mediated basal immunity and promotes disease necrosis in plants. Proc Natl Acad Sci USA 101: 9927–9932.
44. ZengW, HeSY (2010) A prominent role of the flagellin receptor FLAGELLIN-SENSING2 in mediating stomatal response to Pseudomonas syringae pv tomato DC3000 in Arabidopsis. Plant Physiol 153: 1188–98.
45. MalloryAC, VaucheretH (2009) ARGONAUTE 1 homeostasis invokes the coordinate action of the microRNA and siRNA pathways. EMBO Rep 10: 521–526.
46. LuC, KulkarniK, SouretFF, MuthuValliappanR, TejSS, et al. (2006) MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. Genome Res 16: 1276–88.
47. SimonichMT, InnesRW (1995) A disease resistance gene in Arabidopsis with specificity for the avrPph3 gene of Pseudomonas syringae pv. phaseolicola. Mol Plant Microbe Interact 8: 637–640.
48. HuangX, LiJ, BaoF, ZhangX, YangS (2010) A gain-of-function mutation in the Arabidopsis disease resistance gene RPP4 confers sensitivity to low temperature. Plant Physiol 154: 796–809.
49. LlaveC, XieZ, KasschauKD, CarringtonJC (2002) Cleavage of Scarecrow-like mRNA Targets Directed by a Class of Arabidopsis miRNA. Science 297: 2053–2056.
50. ZhangZ, WuY, GaoM, ZhangJ, KongQ, et al. (2012) Disruption of PAMP-induced MAP kinase cascade by a Pseudomonas syringae effector activates plant immunity mediated by the NB-LRR protein SUMM2. Cell Host Microbe 11: 253–63.
51. PieterseCM, Leon-ReyesA, Van der EntS, Van WeesSC (2009) Networking by small-molecule hormones in plant immunity. Nat Chem Biol 5: 308–316.
52. ShapiroAD, ZhangC (2001) The Role of NDR1 in Avirulence Gene-Directed Signaling and Control of Programmed Cell Death in Arabidopsis. Plant Physiol 127: 1089–1101.
53. WildermuthMC, DewdneyJ, WuG, AusubelF (2001) Isochorismate synthase is required to synthetize salicylic acid for plant defense. Nature 414: 562–565.
54. CaoH, GlazebrookJ, ClarkeJD, VolkoS, DongX (1997) The Arabidopsis NPR1 gene that controls systemic acquired resistance encodes a novel protein containing ankyrin repeats. Cell 88: 57–63.
55. ShirasuK, LahayeT, TanMW, ZhouF, AzevedoC, Schulze-LefertP (1999) A novel class of eukaryotic zinc-binding proteins is required for disease resistance signaling in barley and development in C. elegans. Cell 99: 355–366.
56. WarrenRF, MerrittPM, HolubE, InnesRW (1999) Identification of three putative signal transduction genes involved in R gene-specified disease resistance in Arabidopsis. Genetics 152: 401–12.
57. AustinMJ, MuskettPJ, KahnK, FeysBJ, JonesJDG, et al. (2002) Regulatory role of SGT1 in early R-mediated plant defenses. Science 295: 2077–2080.
58. MuskettPR, KahnK, AustinMJ, MoisanLJ, SadanandomA, et al. (2002) Arabidopsis RAR1 exerts rate-limiting control of R gene-mediated defenses against multiple pathogens. Plant Cell 14: 979–992.
59. TorneroP, MerrittP, SadanandomA, ShirasuK, InnesRW, et al. (2002) RAR1 and NDR1 contribute quantitatively to disease resistance in Arabidopsis and their relative contributions are dependent on the R gene assayed. Plant Cell 14: 1005–1015.
60. AzevedoC, SadanandomA, KitigawaK, FreialdenhovenA, ShirasuK, et al. (2002) The RAR1 interactor SGT1 is an essential component of R-gene triggered disease resistance. Science 295: 2073–2076.
61. TörM, GordonP, CuzickA, EulgemT, SinapidouE, et al. (2002) Arabidopsis SGT1b is required for defense signaling conferred by several downy mildew (Peronospora parasitica) resistance genes. Plant Cell 14: 993–1003.
62. TakahashiA, CasaisC, IchimuraK, ShirasuK (2003) HSP90 interacts with RAR1 and SGT1 and is essential for RPS2-mediated disease resistance in Arabidopsis. Proc Natl Acad Sci USA 100: 11777–11782.
63. HubertDA, TorneroP, BelkhadirY, KrishnaP, TakahashiA, et al. (2003) Cytosolic HSP90 associates with and modulates the Arabidopsis RPM1 disease resistance protein. EMBO J 22: 5679–5689.
64. HoltBF, BelkhadirY, DanglJL (2005) Antagonistic control of disease resistance protein stability in the plant immune system. Science 309: 929–932.
65. VenugopalSC, JeongRD, MandalMK, ZhuS, Chandra-ShekaraAC, et al. (2009) Enhanced disease susceptibility 1 and salicylic acid act redundantly to regulate resistance gene-mediated signaling. PLoS Genet 5: e1000545.
66. BoyesDC, NamJ, DanglJL (1998) The Arabidopsis thaliana RPM1 disease resistance gene product is a peripheral plasma membrane protein that is degraded coincident with the hypersensitive response. Proc Natl Acad Sci USA 95: 15849–15854.
67. AxtellMJ, StaskawiczBJ (2003) Initiation of RPS2-specified disease resistance in Arabidopsis is coupled to the AvrRpt2-directed elimination of RIN4. Cell 112: 369–377.
68. BelkhadirY, NimchukZ, HubertDA, MackeyD, DanglJL (2004) Arabidopsis RIN4 negatively regulates disease resistance mediated by RPS2 and RPM1 downstream or independent of the NDR1 signal modulator, and is not required for the virulence functions of bacterial type III effectors AvrRpt2 or AvrRpm1. Plant Cell 16: 2822–2835.
69. VaistijFE, JonesL (2009) Compromised virus-induced gene silencing in RDR6-deficient plants. Plant Physiol 149: 1399–1407.
70. Di SerioF, Martínez de AlbaAE, NavarroB, GiselA, FloresR (2010) RNA-dependent RNA polymerase 6 delays accumulation and precludes meristem invasion of a viroid that replicates in the nucleus. J Virol 84: 2477–89.
71. NicaiseV, RouxM, ZipfelC (2009) Recent Advances in PAMP-Triggered Immunity against Bacteria: Pattern Recognition Receptors Watch over and Raise the Alarm. Plant Physiol 150: 1638–1647.
72. NavarroL, DunoyerP, JayF, ArnoldB, DharmasiriN, et al. (2006) A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science 312: 436–439.
73. ConrathU (2011) Molecular aspects of defense priming. Trends Plant Sci 16: 524–531.
74. ShenQH, SaijoY, MauchS, BiskupC, BieriS, et al. (2007) Nuclear activity of MLA immune receptors links isolate-specific and basal disease-resistance responses. Science 315: 1098–1103.
75. TrujilloM, IchimuraK, CasaisC, ShirasuK (2008) Negative regulation of PAMP-triggered immunity by E3 ubitquitin ligase triplet in Arabidopsis. Curr Biol 18: 1396–1401.
76. LuD, LinW, GaoX, WuS, ChengC, et al. (2011) Direct ubiquitination of pattern recognition receptor FLS2 attenuates plant innate immunity. Science 332: 1439–42.
77. BombliesK, LempeJ, EppleP, WarthmannN, LanzC, et al. (2007) Autoimmune Response as a Mechanism for a Dobzhansky-Muller-Type Incompatibility Syndrome in Plants. PLoS Biol 5: e236.
78. TsudaK, KatagiriF (2010) Comparing signaling mechanisms engaged in pattern-triggered and effector-triggered immunity. Curr Opin Plant Biol 13: 459–65.
79. BonardiV, TangS, StallmannA, RobertsM, CherkisK, et al. (2011) Expanded functions for a family of plant intracellular immune receptors beyond specific recognition of pathogen effectors. Proc Natl Acad Sci U S A 108: 16463–8.
80. ZhangZ, WuY, GaoM, QiY, TsudaK, et al. (2011) Physical association of pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) immune receptors in Arabidopsis. Mol Plant Pathol 12: 702–8.
81. TsudaK, SatoM, StoddardT, GlazebrookJ, KatagiriF (2009) Network properties of robust immunity in plants. PLoS Genet 5: e1000772.
82. ThommaBP, NürnbergerT, JoostenMH (2011) Of PAMPs and effectors: the blurred PTI-ETI dichotomy. Plant Cell 23: 4–15.
83. RossAF (1961) Systemic acquired resistance induced by localized virus infections in plants. Virology 14: 340–358.
84. DurrantWE, DongX (2004) Systemic acquired resistance. Annu Rev Phytopathol 42: 185–209.
85. MishinaTE, ZeierJ (2007) Pathogen-associated molecular pattern recognition rather than development of tissue necrosis contributes to bacterial induction of systemic acquired resistance in Arabidopsis. Plant J 50: 500–513.
86. SpoelSH, DongX (2012) How do plants achieve immunity? Defence without specialized immune cells. Nat Rev Immunol 12: 89–100.
87. XieZ, JohansenLK, GustafsonAM, KasschauKD, LellisAD, et al. (2004) Genetic and functional diversification of small RNA pathways in plants. PLoS Biol 2: e104.
88. SchwackeR, HagerA (1992) Fungal elicitors induce a transient release of active oxygen species from cultured spruce cells that is dependent on Ca2+ and protein-kinase activity. Planta 187: 136–141.
89. ShiptonWA, BrownJF (1962) A whole-leaf clearing and staining technique to demonstrate host-pathogen relationships of wheat stem rust. Phytopathology 52: 1313–1318.
90. AdamL, SomervilleSC (1996) Genetic characterization of five powdery mildew disease resistance loci in Arabidopsis thaliana. Plant J 9: 341–356.
91. ShiR, ChiangVL (2005) Facile means for quantifying microRNA expression by real-time PCR. BioTechniques 39: 519–525.
92. HardcastleTJ, KellyKA (2010) baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 11: 422.
93. KurtzS, PhillippyA, DelcherAL, SmootM, ShumwayM, et al. (2004) Versatile and open software for comparing large genomes. Genome Biology 5: R12.
94. TarazonaS, García-AlcaldeF, DopazoJ, FerrerA, ConesaA (2011) Differential expression in RNA-seq: a matter of depth. Genome Res 21: 2213–23.
95. Griffiths-JonesS (2004) The miRNA Registry. Nucleic Acids Res 32: D109–D111.
96. Griffiths-JonesS, GrocockRJ, van DongenS, BatemanA, EnrightAJ (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34: D140–D144.
97. Griffiths-JonesS, SainiHK, van DongenS, EnrightAJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36: D154–D158.
98. KozomaraA, Griffiths-JonesS (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 2011 39: D152–D157.