{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T06:28:18Z","timestamp":1790144898737,"version":"4.0.1"},"reference-count":41,"publisher":"Springer Science and Business Media LLC","issue":"3","license":[{"start":{"date-parts":[[2014,12,12]],"date-time":"2014-12-12T00:00:00Z","timestamp":1418342400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Funct Integr Genomics"],"published-print":{"date-parts":[[2015,5]]},"DOI":"10.1007\/s10142-014-0426-8","type":"journal-article","created":{"date-parts":[[2014,12,11]],"date-time":"2014-12-11T09:13:21Z","timestamp":1418289201000},"page":"363-373","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":35,"title":["Upregulation of jasmonate biosynthesis and jasmonate-responsive genes in rice leaves in response to a bacterial pathogen mimic"],"prefix":"10.1007","volume":"15","author":[{"given":"Ashish","family":"Ranjan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jyothilakshmi","family":"Vadassery","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hitendra Kumar","family":"Patel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alok","family":"Pandey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ramesh","family":"Palaparthi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Axel","family":"Mith\u00f6fer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ramesh V.","family":"Sonti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2014,12,12]]},"reference":[{"key":"426_CR1","volume-title":"Technical note: Guide to probe logarithmic intensity error (PLIER) estimation","author":"Affymetrix Inc.","year":"2005","unstructured":"Affymetrix Inc. (2005) Technical note: Guide to probe logarithmic intensity error (PLIER) estimation. Affymetrix, Santa Clara"},{"key":"426_CR2","first-page":"708","volume":"F63","author":"G Aparna","year":"2007","unstructured":"Aparna G, Chatterjee A, Jha G, Sonti RV, Sankaranarayanan R (2007) Crystallization and preliminary crystallographic studies of LipA, a secretory lipase\/esterase from Xanthomonas oryzae pv. oryzae. Acta Crystallogr F63:708\u2013710","journal-title":"Acta Crystallogr"},{"key":"426_CR3","doi-asserted-by":"crossref","first-page":"1860","DOI":"10.1105\/tpc.109.066886","volume":"21","author":"G Aparna","year":"2009","unstructured":"Aparna G, Chatterjee A, Sonti RV, Sankaranarayanan R (2009) A cell wall-degrading esterase of Xanthomonas oryzae requires a unique substrate recognition module for pathogenesis on rice. Plant Cell 21:1860\u20131873","journal-title":"Plant Cell"},{"key":"426_CR4","doi-asserted-by":"crossref","first-page":"1597","DOI":"10.1111\/j.1365-3040.2010.02167.x","volume":"33","author":"DD Bilgin","year":"2010","unstructured":"Bilgin DD, Zavala JA, Zhu J, Clough SJ, Ort DR, DeLucia EH (2010) Biotic stress globally downregulates photosynthesis genes. Plant Cell Environ 33:1597\u20131613","journal-title":"Plant Cell Environ"},{"key":"426_CR5","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1146\/annurev.arplant.043008.092007","volume":"60","author":"J Browse","year":"2009","unstructured":"Browse J (2009) Jasmonate passes muster: a receptor and targets for the defense hormone. Annu Rev Plant Biol 60:183\u2013205","journal-title":"Annu Rev Plant Biol"},{"key":"426_CR6","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1016\/j.febslet.2007.12.039","volume":"582","author":"J Catinot","year":"2008","unstructured":"Catinot J, Buchala A, Abou-Mansour E, M\u00e9traux JP (2008) Salicylic acid production in response to biotic and abiotic stress depends on isochorismate in Nicotiana benthamiana. FEBS Lett 582:473\u2013478","journal-title":"FEBS Lett"},{"key":"426_CR7","doi-asserted-by":"crossref","first-page":"493","DOI":"10.4161\/psb.4.6.8392","volume":"4","author":"Z Chen","year":"2009","unstructured":"Chen Z, Zheng Z, Huang J, Lai Z, Fan B (2009) Biosynthesis of salicylic acid in plants. Plant Signal Behav 4:493\u2013496","journal-title":"Plant Signal Behav"},{"key":"426_CR8","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1111\/j.1365-313X.2009.03852.x","volume":"59","author":"A Chini","year":"2009","unstructured":"Chini A, Fonseca S, Chico JM, Fernandez-Calvo P, Solano R (2009) The ZIM domain mediates homo- and heteromeric interactions between Arabidopsis JAZ proteins. Plant J 59:77\u201387","journal-title":"Plant J"},{"key":"426_CR9","author":"A Dave","year":"2012","unstructured":"Dave A, Graham IA (2012) Oxylipin signaling: a distinct role for the jasmonic acid precursor cis-(+)-12-oxo-phytodienoic acid (cis-OPDA). Front Plant Sci. doi: 10.3389\/fpls.2012.00042. eCollection 2012","journal-title":"Front Plant Sci"},{"key":"426_CR10","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1038\/nrg2812","volume":"11","author":"PN Dodds","year":"2010","unstructured":"Dodds PN, Rathjen JP (2010) Plant immunity: towards an integrated view of plant-pathogen interactions. Nat Rev Genet 11:539\u2013548","journal-title":"Nat Rev Genet"},{"key":"426_CR11","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1038\/nchembio.161","volume":"5","author":"S Fonseca","year":"2009","unstructured":"Fonseca S, Chini A, Hamberg M, Adie B, Porzel A, Kramell R, Miersch O, Wasternack C, Solano R (2009) (+)-7-iso-Jasmonoyl-L-isoleucine is the endogenous bioactive jasmonate. Nat Chem Biol 5:344\u2013350","journal-title":"Nat Chem Biol"},{"key":"426_CR12","doi-asserted-by":"crossref","unstructured":"Grennan AK (2006) Plant response to bacterial pathogens. Overlap between innate and gene-for-gene defense\u00a0response. Plant Physiol 142:809\u2013811","DOI":"10.1104\/pp.106.900207"},{"key":"426_CR13","doi-asserted-by":"crossref","first-page":"6296","DOI":"10.1074\/jbc.M111.316364","volume":"287","author":"T Heitz","year":"2012","unstructured":"Heitz T, Widemann E, Lugan R, Miesch L, Ullmann P, Desaubry L, Holder E, Grausem B, Kandel S, Miesch M, Werck-Reichhart D, Pinot F (2012) Cytochromes P450 CYP94C1 and CYP94B3 catalyze two successive oxidation steps of plant hormone jasmonoyl-isoleucine for catabolic turnover. J Biol Chem 287:6296\u20136306","journal-title":"J Biol Chem"},{"key":"426_CR14","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1111\/j.1574-6968.2007.00638.x","volume":"269","author":"J Hu","year":"2007","unstructured":"Hu J, Qian W, He C (2007) The Xanthomonas oryzae pv. oryzae eglXoB endoglucanase gene is required for virulence to rice. FEMS Microbiol Lett 269:273\u2013279","journal-title":"FEMS Microbiol Lett"},{"key":"426_CR15","doi-asserted-by":"crossref","first-page":"e15","DOI":"10.1093\/nar\/gng015","volume":"31","author":"RA Irizarry","year":"2003","unstructured":"Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP (2003a) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31:e15","journal-title":"Nucleic Acids Res"},{"key":"426_CR16","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1093\/biostatistics\/4.2.249","volume":"4","author":"RA Irizarry","year":"2003","unstructured":"Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP (2003b) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostat 4:249\u2013264","journal-title":"Biostat"},{"key":"426_CR17","doi-asserted-by":"crossref","first-page":"D717","DOI":"10.1093\/nar\/gkj154","volume":"34","author":"P Jaiswal","year":"2006","unstructured":"Jaiswal P, Ni J, Yap I, Ware D, Spooner W, Youens-Clark K, Ren L, Liang C, Zhao W, Ratnapu K, Faga B, Canaran P, Fogleman M, Hebbard C, Avraham S, Schmidt S, Casstevens TM, Buckler ES, Stein L, McCouch S (2006) Gramene: a bird\u2019s eye view of cereal genomes. Nucleic Acids Res 34:D717\u2013D723","journal-title":"Nucleic Acids Res"},{"key":"426_CR18","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1094\/MPMI-18-0891","volume":"18","author":"G Jha","year":"2005","unstructured":"Jha G, Rajeshwari R, Sonti RV (2005) Bacterial type two secretion system secreted proteins: double-edged swords for plant pathogens. Mol Plant-Microbe Interact 18:891\u2013898","journal-title":"Mol Plant-Microbe Interact"},{"key":"426_CR19","doi-asserted-by":"crossref","unstructured":"Jha G, Rajeshwari R, Sonti RV (2007) Functional interplay between two Xanthomonas oryzae pv. oryzae secretion systems in modulating virulence on rice. Mol Plant-Microbe Interact 20:31\u201340","DOI":"10.1094\/MPMI-20-0031"},{"key":"426_CR20","doi-asserted-by":"crossref","unstructured":"Jha G, Patel H, Dasgupta M, Palaparthi R, Sonti RV (2010) Transcriptional profiling of rice leaves undergoing a hypersensitive response like reaction induced by Xanthomonas oryzae pv. oryzae cellulase. Rice 3:1\u201321","DOI":"10.1007\/s12284-009-9033-z"},{"key":"426_CR21","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/1939-8433-6-4","volume":"6","author":"Y Kawahara","year":"2013","unstructured":"Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S, Childs KL, Davidson RM, Lin H, Quesada-Ocampo L, Vaillancourt B, Sakai H, Lee SS, Kim J, Numa H, Itoh T, Buell CR, Matsumoto T (2013) Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice 6:4","journal-title":"Rice"},{"key":"426_CR22","doi-asserted-by":"crossref","first-page":"3807","DOI":"10.1016\/S0031-9422(00)97532-0","volume":"31","author":"O Kodama","year":"1992","unstructured":"Kodama O, Miyakawa J, Akatsuka T, Kiyosawa S (1992) Sakuranetin, a flavanone phytoalexin from ultraviolet-irradiated rice leaves. Phytochem 31:3807\u20133809","journal-title":"Phytochem"},{"key":"426_CR23","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1146\/annurev.pp.32.060181.002543","volume":"32","author":"PE Kolattukudy","year":"1981","unstructured":"Kolattukudy PE (1981) Structure, biosynthesis, and biodegradation of cutin and suberin. Annu Rev Plant Physiol 32:539\u2013567","journal-title":"Annu Rev Plant Physiol"},{"key":"426_CR24","doi-asserted-by":"crossref","first-page":"9298","DOI":"10.1073\/pnas.1103542108","volume":"108","author":"AJK Koo","year":"2011","unstructured":"Koo AJK, Cooke TF, Howe GA (2011) Cytochrome P450 CYP94B3 mediates catabolism and inactivation of the plant hormone jasmonoyl-L-isoleucine. Proc Natl Acad Sci U S A 108:9298\u20139303","journal-title":"Proc Natl Acad Sci U S A"},{"key":"426_CR25","doi-asserted-by":"crossref","first-page":"5791","DOI":"10.1016\/S0040-4020(01)81437-X","volume":"44","author":"R Kramell","year":"1988","unstructured":"Kramell R, Schmidt J, Schneider G, Sembdner G, Schreiber K (1988) Synthesis of n-(jasmonoyl) amino acid conjugates. Tetrahedron 44:5791\u20135807","journal-title":"Tetrahedron"},{"key":"426_CR26","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1146\/annurev.py.33.090195.001423","volume":"33","author":"J Kuc","year":"1995","unstructured":"Kuc J (1995) Phytoalexins, stress metabolism, and disease resistance in plants. Annu Rev Phytopathol 33:275\u2013297","journal-title":"Annu Rev Phytopathol"},{"key":"426_CR27","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1006\/meth.2001.1262","volume":"25","author":"KJ Livak","year":"2001","unstructured":"Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2-\u0394\u0394Ct method. Methods 25:402\u2013408","journal-title":"Methods"},{"key":"426_CR28","doi-asserted-by":"crossref","first-page":"14165","DOI":"10.1073\/pnas.96.24.14165","volume":"96","author":"R Mittler","year":"1999","unstructured":"Mittler R, Herr EH, Orvar BL, van Camp W, Willekens H, Inze D, Ellis BE (1999) Transgenic tobacco plants with reduced capability to detoxify reactive oxygen intermediates are hyperresponsive to pathogen infection. Proc Natl Acad Sci U S A 96:14165\u201314170","journal-title":"Proc Natl Acad Sci U S A"},{"key":"426_CR29","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1007\/s00709-012-0400-z","volume":"250","author":"K Miyamoto","year":"2013","unstructured":"Miyamoto K, Shimizu T, Mochizuki S, Nishizawa Y, Minami E, Nojiri H, Yamane H, Okada K (2013) Stress-induced expression of the transcription factor RERJ1 is tightly regulated in response to jasmonic acid accumulation in rice. Protoplasma 250:241\u2013249","journal-title":"Protoplasma"},{"key":"426_CR30","doi-asserted-by":"crossref","first-page":"3187","DOI":"10.1128\/JB.01558-09","volume":"192","author":"A Pandey","year":"2010","unstructured":"Pandey A, Sonti RV (2010) Role of the FeoB protein and siderophore in promoting virulence of Xanthomonas oryzae pv. oryzae on rice. J Bacteriol 192:3187\u20133203","journal-title":"J Bacteriol"},{"key":"426_CR31","doi-asserted-by":"crossref","first-page":"830","DOI":"10.1094\/MPMI-18-0830","volume":"18","author":"R Rajeshwari","year":"2005","unstructured":"Rajeshwari R, Jha G, Sonti RV (2005) Role of an in planta-expressed xylanase of Xanthomonas oryzae pv. oryzae in promoting virulence on rice. Mol Plant-Microbe Interact 18:830\u2013837","journal-title":"Mol Plant-Microbe Interact"},{"key":"426_CR32","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1094\/MPMI.2000.13.4.394","volume":"13","author":"SK Ray","year":"2000","unstructured":"Ray SK, Rajeshwari R, Sonti RV (2000) Mutants of Xanthomonas oryzae pv. oryzae deficient in general secretory pathway are virulence deficient and unable to secrete xylanase. Mol Plant-Microbe Interact 13:394\u2013401","journal-title":"Mol Plant-Microbe Interact"},{"key":"426_CR33","doi-asserted-by":"crossref","first-page":"2117","DOI":"10.1105\/tpc.104.023549","volume":"16","author":"PE Staswick","year":"2004","unstructured":"Staswick PE, Tiryaki I (2004) The oxylipin signal jasmonic acid is activated by an enzyme that conjugates it to isoleucine in Arabidopsis. Plant Cell 16:2117\u20132127","journal-title":"Plant Cell"},{"key":"426_CR34","doi-asserted-by":"crossref","first-page":"9440","DOI":"10.1073\/pnas.1530509100","volume":"100","author":"JD Storey","year":"2003","unstructured":"Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100:9440\u20139445","journal-title":"Proc Natl Acad Sci U S A"},{"key":"426_CR35","doi-asserted-by":"crossref","first-page":"15107","DOI":"10.1073\/pnas.95.25.15107","volume":"95","author":"BP Thomma","year":"1998","unstructured":"Thomma BP, Eggermont K, Penninckx IA, Mauch-Mani B, Vogelsang R, Cammue BP, Broekaert WF (1998) Separate jasmonate-dependent and salicylate dependent defense-response pathways in Arabidopsis are essential for resistance to distinct microbial pathogens. Proc Natl Acad Sci U S A 95:15107\u201315111","journal-title":"Proc Natl Acad Sci U S A"},{"key":"426_CR36","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1094\/MPMI-20-8-0955","volume":"20","author":"SR Uppalapati","year":"2007","unstructured":"Uppalapati SR, Ishiga Y, Wangdi T, Kunkel BN, Anand A, Mysore KS, Bender CL (2007) The phytotoxin coronatine contributes to pathogen fitness and is required for suppression of salicylic acid accumulation in tomato inoculated with Pseudomonas syringae pv. tomato DC3000. Mol Plant-Microbe Interact 20:955\u2013965","journal-title":"Mol Plant-Microbe Interact"},{"key":"426_CR37","doi-asserted-by":"crossref","first-page":"1159","DOI":"10.1104\/pp.112.198150","volume":"159","author":"J Vadassery","year":"2012","unstructured":"Vadassery J, Reichelt M, Hause B, Gershenzon J, Boland W, Mith\u00f6fer A (2012) CML42 mediated calcium signaling coordinates responses to spodoptera herbivory and abiotic stresses in Arabidopsis. Plant Physiol 159:1159\u20131175","journal-title":"Plant Physiol"},{"key":"426_CR38","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1146\/annurev.phyto.050908.135202","volume":"47","author":"AC Vlot","year":"2009","unstructured":"Vlot AC, Dempsey DMA, Klessig DF (2009) Salicylic acid, a multifaceted hormone to combat disease. Annu Rev Phytopathol 47:177\u2013206","journal-title":"Annu Rev Phytopathol"},{"key":"426_CR39","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1093\/mp\/ssp106","volume":"3","author":"T Vogt","year":"2010","unstructured":"Vogt T (2010) Phenylpropanoid biosynthesis. Mol Plant 3:2\u201320","journal-title":"Mol Plant"},{"key":"426_CR40","doi-asserted-by":"crossref","first-page":"1021","DOI":"10.1093\/aob\/mct067","volume":"111","author":"C Wasternack","year":"2013","unstructured":"Wasternack C, Hause B (2013) Jasmonates: biosynthesis, perception, signal transduction and action in plant stress response, growth and development. An update to the 2007 review in Annals of Botany. Ann Bot 111:1021\u20131058","journal-title":"Ann Bot"},{"key":"426_CR41","doi-asserted-by":"crossref","first-page":"W358","DOI":"10.1093\/nar\/gkn276","volume":"36","author":"Q Zheng","year":"2008","unstructured":"Zheng Q, Wang XJ (2008) GOEAST: a web-based software toolkit for gene ontology enrichment analysis. Nucleic Acids Res 36:W358\u2013W363","journal-title":"Nucleic Acids Res"}],"container-title":["Functional &amp; Integrative Genomics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10142-014-0426-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s10142-014-0426-8\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10142-014-0426-8","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,29]],"date-time":"2019-05-29T10:27:12Z","timestamp":1559125632000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s10142-014-0426-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,12,12]]},"references-count":41,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2015,5]]}},"alternative-id":["426"],"URL":"https:\/\/doi.org\/10.1007\/s10142-014-0426-8","relation":{},"ISSN":["1438-793X","1438-7948"],"issn-type":[{"value":"1438-793X","type":"print"},{"value":"1438-7948","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,12,12]]}}}