Thomma BP, Van Esse HP, Crous PW, De Wit PJ. Cladosporium fulvum, (syn. Passalora fulva), a highly specialized plant pathogen as a model for functional studies on plant pathogenic mycosphaerellaceae. Mol Plant Pathol. 2010;6:379–93.
Joosten M, De WP. The tomato-Cladosporium fulvum interaction: a versatile experimental system to study plant-pathogen interactions. Annu Rev Phytopathol. 1999;37:335–67.
Rivas S, Thomas CM. Molecular interactions between tomato and the leaf mold pathogen Cladosporium fulvum. Annu Rev Phytopathol. 2005;43:395–436.
Jones JD, Dangl JL. The plant immune system. Nature. 2006;444:323–9.
De Wit PJGM, Mehrabi R, Van Den Burg HA, Stergiopoulos I. Fungal effector proteins: past, present and future. Mol Plant Pathol. 2009;10:735–47.
Rajamuthiah R, Mylonakis E. Effector triggered immunity: activation of innate immunity in metazoans by bacterial effectors. Virulence. 2014;5:697–702.
Hammondkosack KE, Jones JDG. Incomplete dominance of tomato Cf genes for resistance to Cladosporium fulvum. Mol Plant Microbe In. 1994;7:58–70.
Balint-Kurti PJ, Dixon MS, Jones DA, Norcott KA, Jones JDG. RFLP linkage analysis of the Cf-4 and Cf-9 genes for resistance to Cladosporium fulvum in tomato. Theor Appl Genet. 1994;88:691–700.
Kreuger J, Thomas CM, Golstein C, Dixon MS, Smoker M. A tomato cysteine protease required for Cf-2-dependent disease resistance and suppression of autonecrosis. Science. 2002;296:744–7.
Koomangersmann M, Honee G, Bonnema G, De Wit P. A high-affinity binding site for the Avr9 peptide elicitor of Cladosporium fulvum is present on plasma membranes of tomato and other solanaceous plants. Plant Cell. 1996;8:929–38.
Hong W, Xu YP, Zheng Z, Cao JS, Cai XZ. Comparative transcript profiling by cDNA-AFLP reveals similar patterns of Avr4/Cf-4- and Avr9/Cf-9-dependent defence gene expression. Mol Plant Pathol. 2010;8:515–27.
Cai X, Takken FLW, Joosten MH, Wit PJ. Specific recognition of Avr4 and Avr9 results in distinct patterns of hypersensitive cell death in tomato, but similar patterns of defence-related gene expression. Mol Plant Pathol. 2001;2:77–86.
Xue D, Chen X, Zhang H, Chai X, Jiang J. Transcriptome analysis of the Cf-12-mediated resistance response to Cladosporium fulvum in tomato. Front Plant Sci. 2017;7:2012.
Liu G, Liu J, Zhang C, You X, Zhao T. Physiological and RNA-seq analyses provide insights into the response mechanism of the Cf-10-mediated resistance to Cladosporium fulvum infection in tomato. Plant Mol Biol. 2018;19:15.
JAL VK, GFJM VDA, De Wit PJ. Cloning and characterization of cDNA of avirulence gene Avr9 of the fungal pathogen Cladosporium fulvum, causal agent of tomato leaf mold. Mol Plant Microbe In. 1991;4:52–9.
Van Den Ackerveken GF, JAL VK, Joosten MH, Muisers JM, Verbakel HM, De Wit PJ. Characterization of two putative pathogenicity genes of the fungal tomato pathogen Cladosporium fulvum. Mol Plant Microbe In. 1993;6:210–5.
Joosten MH, Cozijnsen TJ, De Wit PJ. Host resistance to a fungal tomato pathogen lost by a single base-pair change in an avirulence gene. Nature. 1994;367:384–6.
Dixon MS, Jones DA, Hatzixanthis K, Ganal MW, Tanksley SD, Jones JD. High-resolution mapping of the physical location of the tomato Cf-2 gene. Mol Plant Microbe In. 1995;8:200–6.
Dixon MS, Jones DA, Keddie JS, Thomas CM, Harrison K, Jones JDG. The tomato Cf-2 disease resistance locus comp rises two functional genes encoding leucine-rich repeat proteins. Cell. 1996;84:451–9.
Dixon MS, Hatzixanthis K, Jones DA, Harrison K, Jones JDG. The tomato Cf-5 disease resistance gene and six homologs show pronounced allelic variation in leucine-rich repeat copy number. Plant Cell. 1998;11:1915–25.
Thomas CM, Jones DA, Parniske M, Harrison K, Balint-Kurti PJ, Hatzixanthis K, Jones JDG. Characterization of the tomato Cf-4 gene for resistance to Cladosporium fulvum identifies sequences that determine recognitional specificity in Cf-4 and Cf-9. Plant Cell. 1997;9:2209–24.
Laugé R, Joosten MH, Haanstra JPW, Goodwin PH, Lindhout P, De Wit PJ. Successful search for a resistance gene in tomato targeted against a virulence factor of a fungal pathogen. Proc Natl Acad Sci U S A. 1998;95:9014–8.
Li S, Zhao TT, Li HJ, Xu XY, Li JF. First report of races 2.5 and 2.4.5 of Cladosporium fulvum (syn. Passalora fulva), causal fungus of tomato leaf mold disease in China. J Gen Plant Pathol. 2015;81(2):162–5.
Bakker EG, Toomajian C, Kreitman M, Bergelson J. A genome wide survey of R gene polymorphisms in A rabidopsis. Plant Cell. 2006;18:1803–18.
Laugé R, Joosten MH, Van Den Ackerveken GF, Van Den Broek HW, De Wit PJ. The in planta-produced extra cellular p roteins Ecp1 and Ecp2 of Cladosporium fulvum are virulence factors. Mol Plant Microbe In. 1997;10:725–34.
Laugé R, Goodwin PH, De Wit PJ, Joosten MH. Specific HR-associated recognition of secreted p roteins from Cladosporium fulvum occurs in both host and non-host plants. Plant J. 2000;23(6):735–45.
Zhao T, Jiang J, Liu G, He S, Zhang H. Mapping and candidate gene screening of tomato Cladosporium fulvum-resistant gene Cf-19, based on high-throughput sequencing technology. BMC Plant Biol. 2016;16:51.
Zhao T, Liu G, Li S, Li J, Jiang J. Differentially expressed gene transcripts related to the Cf-19-mediated resistance response to Cladosporium fulvum, infection in tomato. Physiol Mol Plant P. 2015;89:8–15.
Yang H, Zhao T, Jiang J, Chen X, Zhang H. Transcriptome analysis of the Sm-mediated hypersensitive response to Stemphylium lycopersici in tomato. Front Plant Sci. 2017;8:1257.
Xing M, Lv H, Ma J, Xu D, Li H. Transcriptome profiling of resistance to Fusarium oxysporum f. sp. conglutinans in cabbage (Brassica oleracea) roots. PLoS One. 2016;11:e0148048.
Chini A, Fonseca S, Fernández G, Adie B, Chico JM. The JAZ family of repressors is the missing link in jasmonate signalling. Nature. 2007;448:666–71.
Adie BAT, Perez-Perez J, Perez-Perez MM, Godoy M, Sanchez-Serrano JJ. ABA is an essential signal for plant resistance to pathogens affecting ja biosynthesis and the activation of defenses in Arabidopsis. Plant Cell Online. 2007;19:1665–81.
Robert-Seilaniantz A, Navarro L, Bari R, Jones JD. Pathological hormone imbalances. Curr Opin Plant Biol. 2007;10:372–9.
Cheval C, Aldon D, Galaud JP, Ranty B. Calcium/Calmodulin-mediated regulation of plant immunity. BBA-Mol Cell Res. 1833;2013:1766–71.
Downie AJ. Calcium signals in plant immunity: a spiky issue. New Phytol. 2015;204:733–5.
Morieri G, Martinez EA, Jarynowski A, Driguez H, Morris R. Host-specific nod-factors associated with\r, Medicago truncatula\r, nodule infection differentially induce calcium influx and calcium spiking in root hairs. New Phytol. 2013;200:656–62.
Abramovitch RB, Anderson JC, Martin GB. Bacterial elicitation and evasion of plant innate immunity. Nat Rev Mol Cell Biol. 2006;7:601–11.
Heese A, Hann DR, Gimenez-Ibanez S, Jones AME, Rathjen JP. The receptor-like kinase SERK3/BAK1 is a central regulator of innate immunity in plants. P Nati Acad Sci. 2007;104:12217–22.
Gimenez-Ibanez S, Hann DR, Ntoukakis V, Petutschnig E, Lipka V. AvrPtoB targets the LysM receptor kinase CERK1 to promote bacterial virulence on plants. Curr Biol. 2009;19:423–9.
Wan J, Zhang X, Neece D, Ramonell KM, Clough SA. LysM receptor-like kinase plays a critical role in chitin signaling and fungal resistance in Arabidopsis. Plant Cell. 2008;20:471–81.
Wang X, Kota U, He K, Blackburn K, Li J. Sequential transphosphorylation of the BRI1/BAK1 receptor kinase complex impacts early events in brassinosteroid signaling. Dev Cell. 2008;15:0–235.
Menke FLH, Kang HG, Chen Z, Park JM, Kumar D. Tobacco transcription factor WRKY1 is phosphorylated by the MAP kinase SIPK and mediates HR-like cell death in tobacco. Mol Plant Microbe In. 2005;18:1027–34.
Andreasson E, Jenkins T, Brodersen P, Thorgrimsen S, Petersen NHT. The MAP kinase substrate MKS1 is a regulator of plant defense responses. EMBO J. 2005;24:2579–89.
Hsu FC, Chou MY, Chou SJ, Li YR, Peng HP, Shih MC. Submergence confers immunity mediated by the WRKY22 transcription factor in Arabidopsis. Plant Cell. 2013;25:2699–713.
Lippok B, Birkenbihl RP, Rivory G, Brümmer J, Somssic IE. Expression of AtWRKY33 encoding a pathogen-or PAMP-responsive WRKY transcription factor is regulated by a composite DNA motif containing W box elements. Mol Plant Microbe In. 2007;20:420–9.
Cui H, Wang Y, Xue L, Chu J, Yan C. Pseudomonas syringae effector protein AvrB perturbs Arabidopsis hormone signaling by activating MAP kinase 4. Cell Host Microbe. 2010;7:164–75.
Bigeard J, Colcombet J, Heribert H. Signaling mechanisms in pattern-triggered immunity (PTI). Mol Plant. 2015;8:521–39.
Zhang W, Song W, Zhang ZQ, Wang HD, Yang MM, Guo RJ, Li ML. Transcriptome analysis of Dastarcus helophoroides (Coleoptera: Bothrideridae) using Illumina HiSeq sequencing. PLoS One. 2014;9:e100673.
Trapnell C, Williams BA, Pertea G, Mortazavi A, Pachter L. Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28:511–5.
Dewey CN, Bo L. RSEM: accurate transcript quantification from RNA-seq data with or without a reference genome. BMC Bioinformatics. 2011;12:323.
Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015;12:357–60.
Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11:106.
Tarazona S, Furió-Tarí P, Turrà D. Data quality aware analysis of differential expression in RNA-seq with NOISeq r/Bioc package. Nucleic Acids Res. 2015;43(21):e140 gkv711.
Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B. 1995;57:289–300.
Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT. Stringtie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015;33:290–5.
Chen ZZ, Xue CH, Zhu S, Zhou FF, Ling XB, Liu GP, Chen LB. Go pipe: streamlined gene ontology annotation for batch anonymous sequences with statistics. Prog Biochem Biophys. 2005;32:187–91.
Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 2010;38:355–60.
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods. 2001;25:402–8.
Rotenberg D, Thompson TS, German TL, Willis DK. Methods for effective real-time RT-PCR analysis of virus-induced gene silencing. J Virol Methods. 2006;138:49–59.
Llugany M, Martin SR, Barceló J, Poschenrieder C. Endogenous jasmonic and salicylic acids levels in the cd-hyperaccumulator Noccaea (Thlaspi) praecox exposed to fungal infection and/or mechanical stress. Plant Cell Rep. 2013;32:1243–9.