Huffaker A, Pearce G, Ryan CA. An endogenous peptide signal in Arabidopsis activates components of the innate immune response. Proc Natl Acad Sci U S A. 2006;103(26):10098–103. https://doi.org/10.1073/pnas.0603727103.
Bartels S, Lori M, Mbengue M, Van Verk M, Klauser D, Hander T, et al. The family of peps and their precursors in arabidopsis: differential expression and localization but similar induction of pattern-triggered immune responses. J Exp Bot. 2013;64(17):5309–21. https://doi.org/10.1093/jxb/ert330.
Lori M, Van Verk MC, Hander T, Schatowitz H, Klauser D, Flury P, et al. Evolutionary divergence of the plant elicitor peptides (peps) and their receptors: interfamily incompatibility of perception but compatibility of downstream signalling. J Exp Bot. 2015;66(17):5315–25. https://doi.org/10.1093/jxb/erv236.
Tang J, Han Z, Sun Y, Zhang H, Gong X, Chai J. Structural basis for recognition of an endogenous peptide by the plant receptor kinase PEPR1. Cell Res. 2015;25(1):110–20. https://doi.org/10.1038/cr.2014.161.
Albert M. Peptides as triggers of plant defence. J Exp Bot. 2013;64(17):5269–79. https://doi.org/10.1093/jxb/ert275.
Article
CAS
PubMed
Google Scholar
Yamaguchi Y, Huffaker A. Endogenous peptide elicitors in higher plants. Curr Opin Plant Biol. 2011;14(4):351–7. https://doi.org/10.1016/j.pbi.2011.05.001.
Article
CAS
PubMed
Google Scholar
Huffaker A, Pearce G, Veyrat N, Erb M, Turlings TCJ, Sartor R, et al. Plant elicitor peptides are conserved signals regulating direct and indirect antiherbivore defense. Proc Natl Acad Sci U S A. 2013;110(14):5707–12. https://doi.org/10.1073/pnas.1214668110.
Trivilin AP, Hartke S, Moraes MG. Components of different signalling pathways regulated by a new orthologue of AtPROPEP1 in tomato following infection by pathogens. Plant Pathol. 2014;63(5):1110–8. https://doi.org/10.1111/ppa.12190.
Article
CAS
Google Scholar
Ruiz C, Nadal A, Montesinos E, Pla M. Novel Rosaceae plant elicitor peptides as sustainable tools to control Xanthomonas arboricola pv. Pruni in Prunus spp. Mol Plant Pathol. 2017;19(2):418–31. https://doi.org/10.1111/mpp.12534.
Ruiz C, Nadal A, Foix L, Montesinos L, Montesinos E, Pla M. Diversity of plant defense elicitor peptides within the Rosaceae. BMC Genet. 2018;19:1–12.
Article
Google Scholar
Yamaguchi Y, Pearce G, Ryan CA. The cell surface leucine-rich repeat receptor for AtPep1, an endogenous peptide elicitor in Arabidopsis, is functional in transgenic tobacco cells. Proc Natl Acad Sci U S A. 2006;103(26):10104–9. https://doi.org/10.1073/pnas.0603729103.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yamaguchi Y, Huffaker A, Bryan AC, Tax FE, Ryan CA. PEPR2 is a second receptor for the Pep1 and Pep2 peptides and contributes to defense responses in Arabidopsis. Plant Cell. 2010;22(2):508–22. https://doi.org/10.1105/tpc.109.068874.
Article
CAS
PubMed
PubMed Central
Google Scholar
Klauser D, Flury P, Boller T, Bartels S. Several MAMPs, including chitin fragments, enhance AtPep-triggered oxidative burst independently of wounding. Plant Signal Behav. 2013;8(9):10–2. https://doi.org/10.4161/psb.25346.
Article
Google Scholar
Krol E, Mentzel T, Chinchilla D, Boller T, Felix G, Kemmerling B, et al. Perception of the Arabidopsis danger signal peptide 1 involves the pattern recognition receptor AtPEPR1 and its close homologue AtPEPR2. J Biol Chem. 2010;285(18):13471–9. https://doi.org/10.1074/jbc.M109.097394.
Lu D, Wu S, Gao X, Zhang Y, Shan L, He P. A receptor-like cytoplasmic kinase, BIK1, associates with a flagellin receptor complex to initiate plant innate immunity. Proc Natl Acad Sci U S A. 2010;107(1):496–501. https://doi.org/10.1073/pnas.0909705107.
Article
PubMed
Google Scholar
Hander T, Fernández-Fernández ÁD, Kumpf RP, Willems P, Schatowitz H, Rombaut D, et al. Damage on plants activates Ca 2+ −dependent metacaspases for release of immunomodulatory peptides. Science. 2019;363:6433.
Article
Google Scholar
Ortiz-Morea FA, Savatin DV, Dejonghe W, Kumar R, Luo Y, Adamowski M, et al. Danger-associated peptide signaling in Arabidopsis requires clathrin. Proc Natl Acad Sci. 2016;113(39):11028–33. https://doi.org/10.1073/pnas.1605588113.
Qi Z, Verma R, Gehring C, Yamaguchi Y, Zhao Y, Ryan CA, et al. Ca2+ signaling by plant Arabidopsis thaliana Pep peptides depends on AtPepR1, a receptor with guanylyl cyclase activity, and cGMP-activated Ca2+ channels. Proc Natl Acad Sci U S A. 2010;107:21193–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bigeard J, Colcombet J, Hirt H. Signaling mechanisms in pattern-triggered immunity (PTI). Mol Plant. 2015;8(4):521–39. https://doi.org/10.1016/j.molp.2014.12.022.
Article
CAS
PubMed
Google Scholar
Cui F, Sun W, Kong X. RLCKs bridge plant immune receptors and MAPK cascades. Trends Plant Sci. 2018;23(12):1039–41. https://doi.org/10.1016/j.tplants.2018.10.002.
Article
CAS
PubMed
Google Scholar
Ryan CA, Huffaker A, Yamaguchi Y. New insights into innate immunity in Arabidopsis. Cell Microbiol. 2007;9(8):1902–8. https://doi.org/10.1111/j.1462-5822.2007.00991.x.
Article
CAS
PubMed
Google Scholar
Ross A, Yamada K, Hiruma K, Yamashita-Yamada M, Lu X, Takano Y, et al. The Arabidopsis PEPR pathway couples local and systemic plant immunity. EMBO J. 2014;33(1):62–75. https://doi.org/10.1002/embj.201284303.
Boller T, Felix G. A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors. Annu Rev Plant Biol. 2009;60(1):379–406. https://doi.org/10.1146/annurev.arplant.57.032905.105346.
Article
CAS
PubMed
Google Scholar
Segonzac C, Zipfel C. Activation of plant pattern-recognition receptors by bacteria. Curr Opin Microbiol. 2011;14(1):54–61. https://doi.org/10.1016/j.mib.2010.12.005.
Article
CAS
PubMed
Google Scholar
Safaeizadeh M, Boller T. Differential and tissue-specific activation pattern of the AtPROPEP and AtPEPR genes in response to biotic and abiotic stress in Arabidopsis thaliana. Plant Signal Behav. 2019;14(5):1–17. https://doi.org/10.1080/15592324.2019.1590094.
Article
CAS
Google Scholar
Bartels S, Boller T. Quo vadis, pep? Plant elicitor peptides at the crossroads of immunity, stress, and development. J Exp Bot. 2015;66(17):5183–93. https://doi.org/10.1093/jxb/erv180.
Article
CAS
PubMed
Google Scholar
Gully K, Hander T, Boller T, Bartels S. Perception of Arabidopsis AtPep peptides, but not bacterial elicitors, accelerates starvation-induced senescence. Front Plant Sci. 2015:1–10. https://doi.org/10.3389/fpls.2015.00014.
FAOSTAT. http://www.fao.org/faostat/en/#data/QC. Accessed 21 Sept 2020.
Esteve-Codina A. RNA-Seq Data Analysis, Applications and Challenges. 1st ed: Elsevier B.V.; 2018. https://doi.org/10.1016/bs.coac.2018.06.001.
Reimand J, Isserlin R, Voisin V, Kucera M, Tannus-Lopes C, Rostamianfar A, Wadi L, Meyer M, Wong J, Xu C, Merico D, Bader GD Pathway enrichment analysis and visualization of omics data using g:profiler, GSEA, Cytoscape and EnrichmentMap. Nat Protoc 2019;14:482–517. https://doi.org/10.1038/s41596-018-0103-9.
Ramšak Ž, Coll A, Stare T, Tzfadia O, Baebler Š, Van de Peer Y, et al. Network modeling unravels mechanisms of crosstalk between ethylene and salicylate signaling in potato. Plant Physiol. 2018;178:488–99.
Preston GM. Pseudomonas syringae pv. Tomato: the right pathogen, of the right plant, at the right time. Mol Plant Pathol. 2000;1(5):263–75. https://doi.org/10.1046/j.1364-3703.2000.00036.x.
Article
CAS
PubMed
Google Scholar
Klauser D, Desurmont GA, Glauser G, Vallat A, Flury P, Boller T, et al. The Arabidopsis pep-PEPR system is induced by herbivore feeding and contributes to JA-mediated plant defence against herbivory. J Exp Bot. 2015;66(17):5327–36. https://doi.org/10.1093/jxb/erv250.
Liu Z, Wu Y, Yang F, Zhang Y, Chen S, Xie Q, et al. BIK1 interacts with PEPRs to mediate ethylene-induced immunity. Proc Natl Acad Sci U S A. 2013;110(15):6205–10. https://doi.org/10.1073/pnas.1215543110.
Veronese P, Nakagami H, Bluhm B, AbuQamar S, Chen X, Salmeron J, et al. The membrane-anchored BOTRYTIS-INDUCED KINASE1 plays distinct roles in Arabidopsis resistance to necrotrophic and biotrophic pathogens. Plant Cell. 2006;18(1):257–73. https://doi.org/10.1105/tpc.105.035576.
Zhang J, Li W, Xiang T, Liu Z, Laluk K, Ding X, et al. Receptor-like cytoplasmic kinases integrate signaling from multiple plant immune receptors and are targeted by a Pseudomonas syringae effector. Cell Host Microbe. 2010;7(4):290–301. https://doi.org/10.1016/j.chom.2010.03.007.
Li L, Li M, Yu L, Zhou Z, Liang X, Liu Z, et al. The FLS2-associated kinase BIK1 directly phosphorylates the NADPH oxidase RbohD to control plant immunity. Cell Host Microbe. 2014;15(3):329–38. https://doi.org/10.1016/j.chom.2014.02.009.
Orosa B, Yates G, Verma V, Srivastava AK, Srivastava M, Campanaro A, et al. SUMO conjugation to the pattern recognition receptor FLS2 triggers intracellular signalling in plant innate immunity. Nat Commun. 2018;9(1):1–12. https://doi.org/10.1038/s41467-018-07696-8.
Garner CM, Kim SH, Spears BJ, Gassmann W. Express yourself: transcriptional regulation of plant innate immunity. Semin Cell Dev Biol. 2016;56:150–62. https://doi.org/10.1016/j.semcdb.2016.05.002.
Logemann E, Birkenbihl RP, Rawat V, Schneeberger K, Schmelzer E, Somssich IE. Functional dissection of the PROPEP2 and PROPEP3 promoters reveals the importance of WRKY factors in mediating microbe-associated molecular pattern-induced expression. New Phytol. 2013;198(4):1165–77. https://doi.org/10.1111/nph.12233.
Mishina TE, Zeier J. Pathogen-associated molecular pattern recognition rather than development of tissue necrosis contributes to bacterial induction of systemic acquired resistance in Arabidopsis. Plant J. 2007;50(3):500–13. https://doi.org/10.1111/j.1365-313X.2007.03067.x.
Article
CAS
PubMed
Google Scholar
Liu Y, Zhang S. Phosphorylation of 1-aminocyclopropane-1-carboxylic acid synthase by MPK6, a stress-responsive mitogen-activated protein kinase, induces ethylene biosynthesis in arabidopsis. Plant Cell. 2004;16(12):3386–99. https://doi.org/10.1105/tpc.104.026609.
Article
CAS
PubMed
PubMed Central
Google Scholar
Qin YM, Hu CY, Pang Y, Kastaniotis AJ, Hiltunen JK, Zhu YX. Saturated very-long-chain fatty acids promote cotton fiber and Arabidopsis cell elongation by activating ethylene biosynthesis. Plant Cell. 2007;19:3692–704.
Huang PY, Catinot J, Zimmerli L. Ethylene response factors in Arabidopsis immunity. J Exp Bot. 2016;67(5):1231–41. https://doi.org/10.1093/jxb/erv518.
Article
CAS
PubMed
Google Scholar
Xin XF, Nomura K, Ding X, Chen X, Wang K, Aung K, et al. Pseudomonas syringae effector avirulence protein E localizes to the host plasma membrane and down-regulates the expression of the NONRACE-SPECIFIC DISEASE RESISTANCE1/HARPIN-INDUCED1-LIKE13 gene required for antibacterial immunity in Arabidopsis. Plant Physiol. 2015;169(1):793–802. https://doi.org/10.1104/pp.15.00547.
Wu Y, Zhang D, Chu JY, Boyle P, Wang Y, Brindle ID, et al. The Arabidopsis NPR1 protein is a receptor for the plant defense hormone salicylic acid. Cell Rep. 2012;1(6):639–47. https://doi.org/10.1016/j.celrep.2012.05.008.
Mauch-Mani B, Mauch F. The role of abscisic acid in plant-pathogen interactions. Curr Opin Plant Biol. 2005;8(4):409–14. https://doi.org/10.1016/j.pbi.2005.05.015.
Article
CAS
PubMed
Google Scholar
Zhang Y, Li X. Salicylic acid: biosynthesis, perception, and contributions to plant immunity. Curr Opin Plant Biol. 2019;50:29–36. https://doi.org/10.1016/j.pbi.2019.02.004.
Article
CAS
PubMed
Google Scholar
Choi WG, Miller G, Wallace I, Harper J, Mittler R, Gilroy S. Orchestrating rapid long-distance signaling in plants with Ca2+, ROS and electrical signals. Plant J. 2017;90(4):698–707. https://doi.org/10.1111/tpj.13492.
Article
CAS
PubMed
PubMed Central
Google Scholar
Toyota M, Spencer D, Sawai-toyota S, Jiaqi W, Zhang T. Glutamate triggers long-distance, calcium-based plant defense signaling. Science. 2018;361:1112–5.
Article
CAS
PubMed
Google Scholar
Qiu XM, Sun YY, Ye XY, Li ZG. Signaling Role of Glutamate in Plants. Front Plant Sci. 2020;10:1–11.
Article
Google Scholar
Lewis JD, Wu R, Guttman DS, Desveaux D. Allele-specific virulence attenuation of the Pseudomonas syringae HopZ1a type III effector via the Arabidopsis ZAR1 resistance protein. PLoS Genet. 2010;6(4):e1000894. https://doi.org/10.1371/journal.pgen.1000894.
Article
CAS
PubMed
PubMed Central
Google Scholar
Park CJ, Ronald PC. Cleavage and nuclear localization of the rice XA21 immune receptor. Nat Commun. 2012;3(1):920. https://doi.org/10.1038/ncomms1932.
Article
CAS
PubMed
Google Scholar
Narusaka Y, Narusaka M, Park P, Kubo Y, Hirayama T, Seki M, et al. RCH1, a locus in Arabidopsis that confers resistance to the hemibiotrophic fungal pathogen Colletotrichum higginsianum. Mol Plant-Microbe Interact. 2004;17(7):749–62. https://doi.org/10.1094/MPMI.2004.17.7.749.
Liu W, Frick M, Huel R, Nykiforuk CL, Wang X, Gaudet DA, et al. The stripe rust resistance gene Yr10 encodes an evolutionary-conserved and unique CC-NBS-LRR sequence in wheat. Mol Plant. 2014;7(12):1740–55. https://doi.org/10.1093/mp/ssu112.
Gervasi F, Ferrante P, Dettori MT, Scortichini M, Verde I. Transcriptome reprogramming of resistant and susceptible peach genotypes during Xanthomonas arboricola pv. Pruni early leaf infection. PLoS One. 2018;13:1–21.
Boudon S, Manceau C, Nottéghem J-L. Structure and origin of Xanthomonas arboricola pv. Pruni populations causing bacterial spot of stone fruit trees in Western Europe. Phytopathology. 2005;95(9):1081–8. https://doi.org/10.1094/PHYTO-95-1081.
Article
PubMed
Google Scholar
Bardsley SJ, Ngugi HK. Reliability and accuracy of visual methods to quantify severity of foliar bacterial spot symptoms on peach and nectarine. Plant Pathol. 2013;62(2):460–74. https://doi.org/10.1111/j.1365-3059.2012.02651.x.
Article
Google Scholar
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: Ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15–21.
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. https://doi.org/10.1186/s13059-014-0550-8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jung S, Lee T, Cheng CH, Buble K, Zheng P, Yu J, et al. 15 years of GDR: new data and functionality in the genome database for Rosaceae. Nucleic Acids Res. 2019;47(D1):D1137–45. https://doi.org/10.1093/nar/gky1000.
Hulsen T, de Vlieg J, Alkema W. BioVenn - A web application for the comparison and visualization of biological lists using area-proportional Venn diagrams. BMC Genomics. 2008;9:1–6.
Article
Google Scholar
R Core Team. R: a Language and Environment for Statistical Computing. Vienna: R Found Stat Comput; 2019. http://www.r-project.org.
Google Scholar
Murtagh F, Legendre P. Ward’s hierarchical agglomerative clustering method: which algorithms implement Ward’s criterion? J Classif. 2014;31:274–95.
Article
Google Scholar
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102(43):15545–50. https://doi.org/10.1073/pnas.0506580102.
Zagorščak M, Blejec A, Ramšak Ž, Petek M, Stare T, Gruden K. DiNAR: revealing hidden patterns of plant signalling dynamics using differential network analysis in R. Plant Methods. 2018;14(1):1–9. https://doi.org/10.1186/s13007-018-0345-0.
Van Bel M, Diels T, Vancaester E, Kreft L, Botzki A, Van De Peer Y, et al. PLAZA 4.0: An integrative resource for functional, evolutionary and comparative plant genomics. Nucleic Acids Res. 2018;46:D1190–6.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: A software Environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498–504.
Thimm O, Bläsing O, Gibon Y, Nagel A, Meyer S, Krüger P, et al. MAPMAN: A user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 2004;37:914–39.
Article
CAS
PubMed
Google Scholar
Ramšak Ž, Baebler Š, Rotter A, Korbar M, Mozetič I, Usadel B, et al. GoMapMan: Integration, consolidation and visualization of plant gene annotations within the MapMan ontology. Nucleic Acids Res. 2014;42:D1167–75.
Article
PubMed
Google Scholar
Tong Z, Gao Z, Wang F, Zhou J, Zhang Z. Selection of reliable reference genes for gene expression studies in peach using real-time PCR. BMC Mol Biol. 2009;10:1–3.
Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, et al. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002;3:1–2.
Ligges U, Mächler M. Scatterplot3d - An R package for visualizing multivariate data. J Stat Softw. 2003;8(11). https://doi.org/10.18637/jss.v008.i11.
Lewis LA, Polanski K, de Torres-Zabala M, Jayaraman S, Bowden L, Moore J, et al. Transcriptional dynamics driving MAMP-triggered immunity and pathogen effector-mediated immunosuppression in Arabidopsis leaves following infection with Pseudomonas syringae pv tomato DC3000. Plant Cell. 2015;27(11):3038–64. https://doi.org/10.1105/tpc.15.00471.