TY - JOUR AU - Abramovitch, R. B. AU - Anderson, J. C. AU - Martin, G. B. PY - 2006 DA - 2006// TI - Bacterial elicitation and evasion of plant innate immunity JO - Nat Rev Mol Cell Biol VL - 7 UR - https://doi.org/10.1038/nrm1984 DO - 10.1038/nrm1984 ID - Abramovitch2006 ER - TY - JOUR AU - Agarwal, P. AU - Agarwal, P. K. AU - Joshi, A. J. AU - Sopory, S. K. AU - Reddy, M. K. PY - 2010 DA - 2010// TI - Overexpression of PgDREB2A transcription factor enhances abiotic stress tolerance and activates downstream stress-responsive genes JO - Mol Biol Rep VL - 37 UR - https://doi.org/10.1007/s11033-009-9885-8 DO - 10.1007/s11033-009-9885-8 ID - Agarwal2010 ER - TY - JOUR AU - Agrawal, G. K. AU - Jwa, N. -. S. AU - Rakwal, R. PY - 2000 DA - 2000// TI - A novel rice (Oryza sativa L.) acidic PR1 gene highly responsive to cut, phytohormones, and protein phosphatase inhibitors JO - Biochem Biophys Res Commun VL - 274 UR - https://doi.org/10.1006/bbrc.2000.3114 DO - 10.1006/bbrc.2000.3114 ID - Agrawal2000 ER - TY - JOUR AU - Ambawat, S. AU - Sharma, P. AU - Yadav, N. R. AU - Yadav, R. C. PY - 2013 DA - 2013// TI - MYB transcription factor genes as regulators for plant responses: an overview JO - Physiol Mol Biol Plants VL - 19 UR - https://doi.org/10.1007/s12298-013-0179-1 DO - 10.1007/s12298-013-0179-1 ID - Ambawat2013 ER - TY - JOUR AU - Amorim, A. AU - Lidiane, L. AU - Fonseca dos Santos, R. AU - Pacifico Bezerra Neto, J. AU - Guida-Santos, M. AU - Crovella, S. AU - Maria Benko-Iseppon, A. PY - 2017 DA - 2017// TI - Transcription factors involved in plant resistance to pathogens JO - Curr Protein Pept Sci VL - 18 UR - https://doi.org/10.2174/1389203717666160619185308 DO - 10.2174/1389203717666160619185308 ID - Amorim2017 ER - TY - JOUR AU - Anders, S. AU - Huber, W. PY - 2010 DA - 2010// TI - Differential expression analysis for sequence count data JO - Genome Biol VL - 11 UR - https://doi.org/10.1186/gb-2010-11-10-r106 DO - 10.1186/gb-2010-11-10-r106 ID - Anders2010 ER - TY - JOUR AU - Bacete, L. AU - Mélida, H. AU - Miedes, E. AU - Molina, A. PY - 2018 DA - 2018// TI - Plant cell wall-mediated immunity: cell wall changes trigger disease resistance responses JO - Plant J VL - 93 UR - https://doi.org/10.1111/tpj.13807 DO - 10.1111/tpj.13807 ID - Bacete2018 ER - TY - JOUR AU - Bailey-Serres, J. AU - Mittler, R. PY - 2006 DA - 2006// TI - The roles of reactive oxygen species in plant cells JO - Plant Physiol VL - 141 UR - https://doi.org/10.1104/pp.104.900191 DO - 10.1104/pp.104.900191 ID - Bailey-Serres2006 ER - TY - JOUR AU - Berger, S. AU - Sinha, A. K. AU - Roitsch, T. PY - 2007 DA - 2007// TI - Plant physiology meets phytopathology: plant primary metabolism and plant–pathogen interactions JO - J Exp Bot VL - 58 UR - https://doi.org/10.1093/jxb/erm298 DO - 10.1093/jxb/erm298 ID - Berger2007 ER - TY - JOUR AU - Boch, J. AU - Bonas, U. PY - 2010 DA - 2010// TI - Xanthomonas AvrBs3 family-type III effectors: discovery and function JO - Annu Rev Phytopathol VL - 48 UR - https://doi.org/10.1146/annurev-phyto-080508-081936 DO - 10.1146/annurev-phyto-080508-081936 ID - Boch2010 ER - TY - JOUR AU - Boch, J. PY - 2009 DA - 2009// TI - Breaking the code of DNA binding specificity of TAL-type III effectors JO - Science VL - 326 UR - https://doi.org/10.1126/science.1178811 DO - 10.1126/science.1178811 ID - Boch2009 ER - TY - JOUR AU - Bolger, A. M. AU - Lohse, M. AU - Usadel, B. PY - 2014 DA - 2014// TI - Trimmomatic: a flexible trimmer for Illumina sequence data JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu170 DO - 10.1093/bioinformatics/btu170 ID - Bolger2014 ER - TY - JOUR AU - Bonfig, K. B. AU - Schreiber, U. AU - Gabler, A. AU - Roitsch, T. AU - Berger, S. PY - 2006 DA - 2006// TI - Infection with virulent and avirulent P. syringae strains differentially affects photosynthesis and sink metabolism in Arabidopsis leaves JO - Planta VL - 225 UR - https://doi.org/10.1007/s00425-006-0303-3 DO - 10.1007/s00425-006-0303-3 ID - Bonfig2006 ER - TY - JOUR AU - Chang, C. AU - Yu, D. AU - Jiao, J. AU - Jing, S. AU - Schulze-Lefert, P. AU - Shen, Q. -. H. PY - 2013 DA - 2013// TI - Barley MLA immune receptors directly interfere with antagonistically acting transcription factors to initiate disease resistance signaling JO - Plant Cell VL - 25 UR - https://doi.org/10.1105/tpc.113.109942 DO - 10.1105/tpc.113.109942 ID - Chang2013 ER - TY - JOUR AU - Cheng, X. AU - Etalo, D. W. AU - Mortel, J. E. AU - Dekkers, E. AU - Nguyen, L. AU - Medema, M. H. AU - Raaijmakers, J. M. PY - 2017 DA - 2017// TI - Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens JO - Environ Microbiol VL - 19 UR - https://doi.org/10.1111/1462-2920.13927 DO - 10.1111/1462-2920.13927 ID - Cheng2017 ER - TY - JOUR AU - Delgado-Cerezo, M. PY - 2012 DA - 2012// TI - Arabidopsis heterotrimeric G-protein regulates cell wall defense and resistance to necrotrophic fungi JO - Mol Plant VL - 5 UR - https://doi.org/10.1093/mp/ssr082 DO - 10.1093/mp/ssr082 ID - Delgado-Cerezo2012 ER - TY - JOUR AU - Deng, D. PY - 2012 DA - 2012// TI - Structural basis for sequence-specific recognition of DNA by TAL effectors JO - Science VL - 335 UR - https://doi.org/10.1126/science.1215670 DO - 10.1126/science.1215670 ID - Deng2012 ER - TY - JOUR AU - Du, Z. AU - Zhou, X. AU - Ling, Y. AU - Zhang, Z. AU - Su, Z. PY - 2010 DA - 2010// TI - agriGO: a GO analysis toolkit for the agricultural community JO - Nucleic Acids Res VL - 38 UR - https://doi.org/10.1093/nar/gkq310 DO - 10.1093/nar/gkq310 ID - Du2010 ER - TY - JOUR AU - Gigolashvili, T. AU - Berger, B. AU - Mock, H. P. AU - Müller, C. AU - Weisshaar, B. AU - Flügge, U. I. PY - 2007 DA - 2007// TI - The transcription factor HIG1/MYB51 regulates indolic glucosinolate biosynthesis in Arabidopsis thaliana JO - Plant J VL - 50 UR - https://doi.org/10.1111/j.1365-313X.2007.03099.x DO - 10.1111/j.1365-313X.2007.03099.x ID - Gigolashvili2007 ER - TY - STD TI - Gnanamanickam S, Priyadarisini VB, Narayanan N, Vasudevan P, Kavitha S (1999) An overview of bacterial blight disease of rice and strategies for its management. Curr Sci:1435–1444 ID - ref20 ER - TY - JOUR AU - Helliwell, E. E. AU - Wang, Q. AU - Yang, Y. PY - 2013 DA - 2013// TI - Transgenic rice with inducible ethylene production exhibits broad-spectrum disease resistance to the fungal pathogens M agnaporthe oryzae and R hizoctonia solani JO - Plant Biotechnol J VL - 11 UR - https://doi.org/10.1111/pbi.12004 DO - 10.1111/pbi.12004 ID - Helliwell2013 ER - TY - JOUR AU - Jain, P. PY - 2017 DA - 2017// TI - Understanding host-pathogen interactions with expression profiling of NILs carrying rice-blast resistance Pi9 gene JO - Front Plant Sci VL - 8 UR - https://doi.org/10.3389/fpls.2017.00093 DO - 10.3389/fpls.2017.00093 ID - Jain2017 ER - TY - JOUR AU - Ji, Z. AU - Ji, C. AU - Liu, B. AU - Zou, L. AU - Chen, G. AU - Yang, B. PY - 2016 DA - 2016// TI - Interfering TAL effectors of Xanthomonas oryzae neutralize R-gene-mediated plant disease resistance JO - Nat Commun VL - 7 UR - https://doi.org/10.1038/ncomms13435 DO - 10.1038/ncomms13435 ID - Ji2016 ER - TY - JOUR AU - Jimmy, J. L. AU - Babu, S. PY - 2015 DA - 2015// TI - Role of OsWRKY transcription factors in rice disease resistance JO - Tropical Plant Pathol VL - 40 UR - https://doi.org/10.1007/s40858-015-0058-0 DO - 10.1007/s40858-015-0058-0 ID - Jimmy2015 ER - TY - JOUR AU - Johnson, E. T. AU - Dowd, P. F. PY - 2004 DA - 2004// TI - Differentially enhanced insect resistance, at a cost, in Arabidopsis thaliana constitutively expressing a transcription factor of defensive metabolites JO - J Agric Food Chem VL - 52 UR - https://doi.org/10.1021/jf0308049 DO - 10.1021/jf0308049 ID - Johnson2004 ER - TY - JOUR AU - Journot-Catalino, N. AU - Somssich, I. E. AU - Roby, D. AU - Kroj, T. PY - 2006 DA - 2006// TI - The transcription factors WRKY11 and WRKY17 act as negative regulators of basal resistance in Arabidopsis thaliana JO - Plant Cell VL - 18 UR - https://doi.org/10.1105/tpc.106.044149 DO - 10.1105/tpc.106.044149 ID - Journot-Catalino2006 ER - TY - JOUR AU - Khush, G. S. PY - 1997 DA - 1997// TI - Origin, dispersal, cultivation and variation of rice JO - Plant Mol Biol VL - 35 UR - https://doi.org/10.1023/A:1005810616885 DO - 10.1023/A:1005810616885 ID - Khush1997 ER - TY - JOUR AU - Kim, D. AU - Langmead, B. AU - Salzberg, S. L. PY - 2015 DA - 2015// TI - HISAT: a fast spliced aligner with low memory requirements JO - Nat Methods VL - 12 UR - https://doi.org/10.1038/nmeth.3317 DO - 10.1038/nmeth.3317 ID - Kim2015 ER - TY - JOUR AU - Lin, N. -. C. AU - Martin, G. B. PY - 2007 DA - 2007// TI - Pto-and Prf-mediated recognition of AvrPto and AvrPtoB restricts the ability of diverse Pseudomonas syringae pathovars to infect tomato JO - Mol Plant-Microbe Interact VL - 20 UR - https://doi.org/10.1094/MPMI-20-7-0806 DO - 10.1094/MPMI-20-7-0806 ID - Lin2007 ER - TY - JOUR AU - Liu, D. AU - Chen, X. AU - Liu, J. AU - Ye, J. AU - Guo, Z. PY - 2012 DA - 2012// TI - The rice ERF transcription factor OsERF922 negatively regulates resistance to Magnaporthe oryzae and salt tolerance JO - J Exp Bot VL - 63 UR - https://doi.org/10.1093/jxb/ers079 DO - 10.1093/jxb/ers079 ID - Liu2012 ER - TY - JOUR AU - Livak, K. J. AU - Schmittgen, T. D. PY - 2001 DA - 2001// TI - Analysis of relative gene expression data using real-time quantitative PCR and the 2− ΔΔCT method JO - Methods VL - 25 UR - https://doi.org/10.1006/meth.2001.1262 DO - 10.1006/meth.2001.1262 ID - Livak2001 ER - TY - JOUR AU - Mengiste, T. AU - Chen, X. AU - Salmeron, J. AU - Dietrich, R. PY - 2003 DA - 2003// TI - The BOTRYTIS SUSCEPTIBLE1 gene encodes an R2R3MYB transcription factor protein that is required for biotic and abiotic stress responses in Arabidopsis JO - Plant Cell VL - 15 UR - https://doi.org/10.1105/tpc.014167 DO - 10.1105/tpc.014167 ID - Mengiste2003 ER - TY - JOUR AU - Moffat, C. S. AU - Ingle, R. A. AU - Wathugala, D. L. AU - Saunders, N. J. AU - Knight, H. AU - Knight, M. R. PY - 2012 DA - 2012// TI - ERF5 and ERF6 play redundant roles as positive regulators of JA/et-mediated defense against Botrytis cinerea in Arabidopsis JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0035995 DO - 10.1371/journal.pone.0035995 ID - Moffat2012 ER - TY - JOUR AU - Mohr, P. G. AU - Cahill, D. M. PY - 2007 DA - 2007// TI - Suppression by ABA of salicylic acid and lignin accumulation and the expression of multiple genes, in Arabidopsis infected with Pseudomonas syringae pv. Tomato JO - Funct Integr Genomics VL - 7 UR - https://doi.org/10.1007/s10142-006-0041-4 DO - 10.1007/s10142-006-0041-4 ID - Mohr2007 ER - TY - JOUR AU - Moore, J. W. AU - Loake, G. J. AU - Spoel, S. H. PY - 2011 DA - 2011// TI - Transcription dynamics in plant immunity JO - Plant Cell VL - 23 UR - https://doi.org/10.1105/tpc.111.087346 DO - 10.1105/tpc.111.087346 ID - Moore2011 ER - TY - JOUR AU - Moscou, M. J. AU - Bogdanove, A. J. PY - 2009 DA - 2009// TI - A simple cipher governs DNA recognition by TAL effectors JO - Science. VL - 326 UR - https://doi.org/10.1126/science.1178817 DO - 10.1126/science.1178817 ID - Moscou2009 ER - TY - JOUR AU - Narsai, R. AU - Wang, C. AU - Chen, J. AU - Wu, J. AU - Shou, H. AU - Whelan, J. PY - 2013 DA - 2013// TI - Antagonistic, overlapping and distinct responses to biotic stress in rice (Oryza sativa) and interactions with abiotic stress JO - BMC Genomics VL - 14 UR - https://doi.org/10.1186/1471-2164-14-93 DO - 10.1186/1471-2164-14-93 ID - Narsai2013 ER - TY - JOUR AU - Noda, T. AU - Kaku, H. PY - 1999 DA - 1999// TI - Growth of Xanthomonas oryzae pv. Oryzae in planta and in guttation fluid of rice JO - Jap J Phytopathol VL - 65 UR - https://doi.org/10.3186/jjphytopath.65.9 DO - 10.3186/jjphytopath.65.9 ID - Noda1999 ER - TY - JOUR AU - Nuruzzaman, M. PY - 2015 DA - 2015// TI - NAC transcription factor family genes are differentially expressed in rice during infections with Rice dwarf virus, Rice black-streaked dwarf virus, Rice grassy stunt virus, Rice ragged stunt virus, and Rice transitory yellowing virus JO - Front Plant Sci VL - 6 UR - https://doi.org/10.3389/fpls.2015.00676 DO - 10.3389/fpls.2015.00676 ID - Nuruzzaman2015 ER - TY - JOUR AU - Park, C. Y. PY - 2005 DA - 2005// TI - WRKY group IId transcription factors interact with calmodulin JO - FEBS Lett VL - 579 UR - https://doi.org/10.1016/j.febslet.2005.01.057 DO - 10.1016/j.febslet.2005.01.057 ID - Park2005 ER - TY - JOUR AU - Pertea, M. AU - Pertea, G. M. AU - Antonescu, C. M. AU - Chang, T. -. C. AU - Mendell, J. T. AU - Salzberg, S. L. PY - 2015 DA - 2015// TI - StringTie enables improved reconstruction of a transcriptome from RNA-seq reads JO - Nature Biotechnol VL - 33 UR - https://doi.org/10.1038/nbt.3122 DO - 10.1038/nbt.3122 ID - Pertea2015 ER - TY - STD TI - Pfeilmeier S (2017) Elicitation and evasion of plant innate immunity by beneficial and pathogenic bacteria. https://ueaeprints.uea.ac.uk/66876/. Accessed 08 Feb 2019 UR - https://ueaeprints.uea.ac.uk/66876/ ID - ref42 ER - TY - JOUR AU - Riechmann, J. L. AU - Meyerowitz, E. M. PY - 1998 DA - 1998// TI - The AP2/EREBP family of plant transcription factors JO - Biol Chem VL - 379 ID - Riechmann1998 ER - TY - JOUR AU - Soler, M. PY - 2015 DA - 2015// TI - The Eucalyptus grandis R2R3-MYB transcription factor family: evidence for woody growth-related evolution and function JO - New Phytol VL - 206 UR - https://doi.org/10.1111/nph.13039 DO - 10.1111/nph.13039 ID - Soler2015 ER - TY - JOUR AU - Tao, Z. AU - Liu, H. AU - Qiu, D. AU - Zhou, Y. AU - Li, X. AU - Xu, C. AU - Wang, S. PY - 2009 DA - 2009// TI - A pair of allelic WRKY genes play opposite roles in rice-bacteria interactions JO - Plant Physiol VL - 151 UR - https://doi.org/10.1104/pp.109.145623 DO - 10.1104/pp.109.145623 ID - Tao2009 ER - TY - JOUR AU - Tariq, R. PY - 2018 DA - 2018// TI - Comparative transcriptome profiling of Rice near-isogenic line carrying Xa23 under infection of Xanthomonas oryzae pv. Oryzae JO - Int J Mol Sci VL - 19 UR - https://doi.org/10.3390/ijms19030717 DO - 10.3390/ijms19030717 ID - Tariq2018 ER - TY - JOUR AU - Thilmony, R. AU - Underwood, W. AU - He, S. Y. PY - 2006 DA - 2006// TI - Genome-wide transcriptional analysis of the Arabidopsis thaliana interaction with the plant pathogen Pseudomonas syringae pv. Tomato DC3000 and the human pathogen Escherichia coli O157: H7 JO - Plant J VL - 46 UR - https://doi.org/10.1111/j.1365-313X.2006.02725.x DO - 10.1111/j.1365-313X.2006.02725.x ID - Thilmony2006 ER - TY - JOUR AU - Thimm, O. PY - 2004 DA - 2004// TI - MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes JO - Plant J VL - 37 UR - https://doi.org/10.1111/j.1365-313X.2004.02016.x DO - 10.1111/j.1365-313X.2004.02016.x ID - Thimm2004 ER - TY - JOUR AU - Torres, M. A. AU - Jones, J. D. AU - Dangl, J. L. PY - 2006 DA - 2006// TI - Reactive oxygen species signaling in response to pathogens JO - Plant Physiol VL - 141 UR - https://doi.org/10.1104/pp.106.079467 DO - 10.1104/pp.106.079467 ID - Torres2006 ER - TY - JOUR AU - Tripathy, B. C. AU - Oelmüller, R. PY - 2012 DA - 2012// TI - Reactive oxygen species generation and signaling in plants JO - Plant Signal Behav VL - 7 UR - https://doi.org/10.4161/psb.22455 DO - 10.4161/psb.22455 ID - Tripathy2012 ER - TY - JOUR AU - Wang, X. AU - Liu, Y. AU - Chen, L. AU - Zhao, D. AU - Wang, X. AU - Zhang, Z. PY - 2013 DA - 2013// TI - Wheat resistome in response to barley yellow dwarf virus infection JO - Funct Integr Genomics VL - 13 UR - https://doi.org/10.1007/s10142-013-0309-4 DO - 10.1007/s10142-013-0309-4 ID - Wang2013 ER - TY - JOUR AU - Wang, Z. AU - Gerstein, M. AU - Snyder, M. PY - 2009 DA - 2009// TI - RNA-Seq: a revolutionary tool for transcriptomics JO - Nat Rev Genet VL - 10 UR - https://doi.org/10.1038/nrg2484 DO - 10.1038/nrg2484 ID - Wang2009 ER - TY - JOUR AU - Yu, C. AU - Chen, H. AU - Tian, F. AU - Leach, J. E. AU - He, C. PY - 2014 DA - 2014// TI - Differentially-expressed genes in rice infected by Xanthomonas oryzae pv. Oryzae relative to a flagellin-deficient mutant reveal potential functions of flagellin in host–pathogen interactions JO - Rice VL - 7 UR - https://doi.org/10.1186/s12284-014-0020-7 DO - 10.1186/s12284-014-0020-7 ID - Yu2014 ER - TY - JOUR AU - Zarei, A. AU - Körbes, A. P. AU - Younessi, P. AU - Montiel, G. AU - Champion, A. AU - Memelink, J. PY - 2011 DA - 2011// TI - Two GCC boxes and AP2/ERF-domain transcription factor ORA59 in jasmonate/ethylene-mediated activation of the PDF1. 2 promoter in Arabidopsis JO - Plant Mol Biol VL - 75 UR - https://doi.org/10.1007/s11103-010-9728-y DO - 10.1007/s11103-010-9728-y ID - Zarei2011 ER - TY - JOUR AU - Zhao, Y. AU - Wei, T. AU - Yin, K. Q. AU - Chen, Z. AU - Gu, H. AU - Qu, L. J. AU - Qin, G. PY - 2012 DA - 2012// TI - Arabidopsis RAP2. 2 plays an important role in plant resistance to Botrytis cinerea and ethylene responses JO - New Phytol VL - 195 UR - https://doi.org/10.1111/j.1469-8137.2012.04160.x DO - 10.1111/j.1469-8137.2012.04160.x ID - Zhao2012 ER -