{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,30]],"date-time":"2026-10-30T05:33:46Z","timestamp":1793338426174,"version":"4.5.0"},"reference-count":82,"publisher":"Springer Science and Business Media LLC","issue":"1","funder":[{"name":"Putra Grant","award":["GP-IPB\/2013\/9413601"],"award-info":[{"award-number":["GP-IPB\/2013\/9413601"]}]},{"name":"National Science Fellowship","award":["-"],"award-info":[{"award-number":["-"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"published-print":{"date-parts":[[2016,12]]},"DOI":"10.1186\/s12864-016-2368-0","type":"journal-article","created":{"date-parts":[[2016,1,18]],"date-time":"2016-01-18T21:48:27Z","timestamp":1453153707000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":86,"title":["De novo transcriptome analyses of host-fungal interactions in oil palm (Elaeis guineensis Jacq.)"],"prefix":"10.1186","volume":"17","author":[{"given":"Chai-Ling","family":"Ho","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yung-Chie","family":"Tan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keat-Ai","family":"Yeoh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ahmad-Kamal","family":"Ghazali","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wai-Yan","family":"Yee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chee-Choong","family":"Hoh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2016,1,19]]},"reference":[{"key":"2368_CR1","first-page":"421","volume":"67","author":"G Singh","year":"1991","unstructured":"Singh G. Ganoderma \u2013 the scourge of oil palms in the coastal areas. Planter. 1991;67:421\u201344.","journal-title":"Planter"},{"key":"2368_CR2","volume-title":"Oil Palm Diseases and Disorders","author":"P Turner","year":"1981","unstructured":"Turner P. Oil Palm Diseases and Disorders. Kuala Lumpur: Oxford University Press; 1981."},{"key":"2368_CR3","doi-asserted-by":"crossref","first-page":"1369","DOI":"10.1016\/j.cropro.2006.11.009","volume":"26","author":"RRM Paterson","year":"2007","unstructured":"Paterson RRM. Ganoderma disease of oil palm-A white rot perspective necessary for integrated control. Crop Prot. 2007;26:1369\u201376.","journal-title":"Crop Prot"},{"key":"2368_CR4","first-page":"325","volume":"87","author":"GF Chung","year":"2011","unstructured":"Chung GF. Management of Ganoderma diseases in oil palm plantations. Planter. 2011;87:325\u201339.","journal-title":"Planter"},{"key":"2368_CR5","doi-asserted-by":"crossref","first-page":"1438","DOI":"10.1016\/j.cropro.2011.07.004","volume":"30","author":"AW Mohd As\u2019wad","year":"2011","unstructured":"Mohd As\u2019wad AW, Sariah M, Paterson RRM, Zainal Abidin MA, Lima N. Ergosterol analyses of oil palm seedlings and plants infected with Ganoderma. Crop Prot. 2011;30:1438\u201342.","journal-title":"Crop Prot"},{"key":"2368_CR6","doi-asserted-by":"crossref","DOI":"10.1079\/9780851993881.0225","volume-title":"Development of Molecular Diagnostics for the Detection of Ganoderma Isolates Pathogenic to Oil Palm","author":"P Bridge","year":"2000","unstructured":"Bridge P, Ogrady E, Pilotti C, Sanderson F. Development of Molecular Diagnostics for the Detection of Ganoderma Isolates Pathogenic to Oil Palm. Oxfordshire: CABI Publishing; 2000."},{"key":"2368_CR7","unstructured":"Idris A, Yamaoka M, Hayakawa S, Basri M, Noorhasimah I, Ariffin D: PCR technique for detection of Ganoderma. MPOB Inf Ser 2003"},{"key":"2368_CR8","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1046\/j.1439-0434.2000.00478.x","volume":"148","author":"C Utomo","year":"2000","unstructured":"Utomo C, Niepold F. Development of diagnostic methods for detecting Ganoderma-infected oil palms. J Phytopathol. 2000;148:507\u201314.","journal-title":"J Phytopathol"},{"key":"2368_CR9","unstructured":"9 Breton F, Hasan Y, Hariadi S, Lubis Z, de Franqueville H: Characterization of parameters for the development of an early screening test for basal stem rot tolerance in oil palm progenies. J Oil Palm Res 2006, Special is:24\u201336."},{"key":"2368_CR10","doi-asserted-by":"crossref","DOI":"10.1079\/9780851993881.0083","volume-title":"A Control Strategy for Basal Stem Rot (Ganoderma) on Oil Palm","author":"H Soepena","year":"2000","unstructured":"Soepena H, Purba R, Pawirosukarto S. A Control Strategy for Basal Stem Rot (Ganoderma) on Oil Palm. Wallingford: CABI International; 2000."},{"key":"2368_CR11","doi-asserted-by":"crossref","first-page":"101","DOI":"10.17221\/23\/2008-PPS","volume":"44","author":"MZ Nur Ain Izzati","year":"2008","unstructured":"Nur Ain Izzati MZ, Abdullah F. Disease suppression in Ganoderma-infected oil palm seedlings treated with Trichoderma harzianum. Plant Prot Sci. 2008;44:101\u20137.","journal-title":"Plant Prot Sci"},{"key":"2368_CR12","first-page":"970","volume":"7","author":"S Siddiquee","year":"2009","unstructured":"Siddiquee S, Yusuf UK, Hossain K, Jahan S. In vitro studies on the potential Trichoderma harzianum for antagonistic properties against Ganoderma boninense. J Food Agric Env. 2009;7:970\u20136.","journal-title":"J Food Agric Env"},{"key":"2368_CR13","first-page":"470","volume":"20","author":"S Shamala","year":"2008","unstructured":"Shamala S, Faridah A, Zainal A, Umi K. Efficacy of single and mixed treatments of Trichoderma harzianum as biocontrol agents of Ganoderma basal stem rot in oil palm. J Oil Palm Res. 2008;20:470\u201383.","journal-title":"J Oil Palm Res"},{"key":"2368_CR14","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1007\/s11046-004-4429-1","volume":"159","author":"T Durand-Gasselin","year":"2005","unstructured":"Durand-Gasselin T, Asmady H, Flori A, Jacquemard JC, Hayun Z, Breton F, et al. Possible sources of genetic resistance in oil palm (Elaeis guineensis Jacq.) to basal stem rot caused by Ganoderma boninense-prospects for future breeding. Mycopathologia. 2005;159:93\u2013100.","journal-title":"Mycopathologia"},{"key":"2368_CR15","first-page":"12","volume":"16","author":"A Idris","year":"2004","unstructured":"Idris A, Kushairi A, Ismail S, Ariffin D. Selection for partial resistance in oil palm progenies to Ganoderma basal stem rot. J Oil Palm Res. 2004;16:12\u20138.","journal-title":"J Oil Palm Res"},{"key":"2368_CR16","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1016\/j.pmpp.2011.06.006","volume":"76","author":"L Naher","year":"2011","unstructured":"Naher L, Ho CL, Tan SG, Yusuf UK, Abdullah F. Cloning of transcripts encoding chitinases from Elaeis guineensis Jacq. and their expression profiles in response to fungal infections. Physiol Mol Plant Pathol. 2011;76:96\u2013103.","journal-title":"Physiol Mol Plant Pathol"},{"key":"2368_CR17","doi-asserted-by":"crossref","first-page":"1455","DOI":"10.1016\/j.jplph.2013.05.009","volume":"170","author":"YC Tan","year":"2013","unstructured":"Tan YC, Yeoh KA, Wong MY, Ho CL. Expression profiles of putative defence-related proteins in oil palm (Elaeis guineensis) colonized by Ganoderma boninense. J Plant Physiol. 2013;170:1455\u201360.","journal-title":"J Plant Physiol"},{"key":"2368_CR18","doi-asserted-by":"crossref","first-page":"1565","DOI":"10.1016\/j.jplph.2012.07.006","volume":"169","author":"KA Yeoh","year":"2012","unstructured":"Yeoh KA, Othman A, Meon S, Abdullah F, Ho CL. Sequence analysis and gene expression of putative exo- and endo-glucanases from oil palm (Elaeis guineensis) during fungal infection. J Plant Physiol. 2012;169:1565\u201370.","journal-title":"J Plant Physiol"},{"key":"2368_CR19","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1007\/s11033-012-2043-8","volume":"40","author":"KA Yeoh","year":"2013","unstructured":"Yeoh KA, Othman A, Meon S, Abdullah F, Ho CL. Sequence analysis and gene expression of putative oil palm chitinase and chitinase-like proteins in response to colonization of Ganoderma boninense and Trichoderma harzianum. Mol Biol Rep. 2013;40:147\u201358.","journal-title":"Mol Biol Rep"},{"key":"2368_CR20","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1016\/j.jplph.2010.12.007","volume":"168","author":"F Alizadeh","year":"2011","unstructured":"Alizadeh F, Abdullah SNA, Khodavandi A, Abdullah F, Yusuf UK, Chong PP. Differential expression of oil palm pathology genes during interactions with Ganoderma boninense and Trichoderma harzianum. J Plant Physiol. 2011;168:1106\u201313.","journal-title":"J Plant Physiol"},{"key":"2368_CR21","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1007\/s11295-012-0559-7","volume":"9","author":"SS Tee","year":"2013","unstructured":"Tee SS, Tan YC, Abdullah F, Ong-Abdullah M, Ho CL. Transcriptome of oil palm (Elaeis guineensis Jacq.) roots treated with Ganoderma boninense. Tree Genet Genomes. 2013;9:377\u201386.","journal-title":"Tree Genet Genomes"},{"key":"2368_CR22","doi-asserted-by":"crossref","first-page":"e0117571","DOI":"10.1371\/journal.pone.0117571","volume":"10","author":"A Ariani","year":"2015","unstructured":"Ariani A, Di Baccio D, Romeo S, Lombardi L, Andreucci A, Lux A, et al. RNA sequencing of Populus x canadensis roots identifies key molecular mechanisms underlying physiological adaption to excess zinc. PLoS ONE. 2015;10:e0117571.","journal-title":"PLoS ONE"},{"key":"2368_CR23","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1101\/gr.4041005","volume":"15","author":"CV Jongeneel","year":"2005","unstructured":"Jongeneel CV, Delorenzi M, Iseli C, Zhou D, Haudenschild CD, Khrebtukova I, et al. An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Res. 2005;15:1007\u201314.","journal-title":"Genome Res"},{"key":"2368_CR24","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1186\/1471-2164-11-711","volume":"11","author":"W Huang","year":"2010","unstructured":"Huang W, Khatib H. Comparison of transcriptomic landscapes of bovine embryos using RNA-Seq. BMC Genomics. 2010;11:711.","journal-title":"BMC Genomics"},{"key":"2368_CR25","doi-asserted-by":"crossref","first-page":"984","DOI":"10.1186\/1471-2164-15-984","volume":"15","author":"ND Md-Mustafa","year":"2014","unstructured":"Md-Mustafa ND, Khalid N, Gao H, Peng Z, Alimin MF, Bujang N, et al. Transcriptome profiling shows gene regulation patterns in a flavonoid pathway in response to exogenous phenylalanine in Boesenbergia rotunda cell culture. BMC Genomics. 2014;15:984.","journal-title":"BMC Genomics"},{"key":"2368_CR26","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1186\/1471-2164-15-475","volume":"15","author":"M Ye","year":"2014","unstructured":"Ye M, Chen Z, Su X, Ji L, Wang J, Liao W, et al. Study of seed hair growth in Populus tomentosa, an important character of female floral bud development. BMC Genomics. 2014;15:475.","journal-title":"BMC Genomics"},{"key":"2368_CR27","doi-asserted-by":"crossref","first-page":"1787","DOI":"10.1104\/pp.109.149716","volume":"152","author":"S Zenoni","year":"2010","unstructured":"Zenoni S, Ferrarini A, Giacomelli E, Xumerle L, Fasoli M, Malerba G, et al. Characterization of transcriptional complexity during berry development in Vitis vinifera using RNA-Seq. Plant Physiol. 2010;152:1787\u201395.","journal-title":"Plant Physiol"},{"key":"2368_CR28","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1186\/1471-2164-14-279","volume":"14","author":"J Zhang","year":"2013","unstructured":"Zhang J, Wu K, Zeng S, da Silva JAT, Zhao X, Tian C-E, et al. Transcriptome analysis of Cymbidium sinense and its application to the identification of genes associated with floral development. BMC Genomics. 2013;14:279.","journal-title":"BMC Genomics"},{"key":"2368_CR29","doi-asserted-by":"crossref","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","volume":"11","author":"S Anders","year":"2010","unstructured":"Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11:R106.","journal-title":"Genome Biol"},{"key":"2368_CR30","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1111\/j.1365-313X.2008.03590.x","volume":"56","author":"G Doehlemann","year":"2008","unstructured":"Doehlemann G, Wahl R, Horst RJ, Voll LM, Usadel B, Poree F, et al. Reprogramming a maize plant: Transcriptional and metabolic changes induced by the fungal biotroph Ustilago maydis. Plant J. 2008;56:181\u201395.","journal-title":"Plant J"},{"key":"2368_CR31","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1042\/bst0220394","volume":"22","author":"G Lorenzo De","year":"1994","unstructured":"De Lorenzo G, Cervone F, Bellincampi D, Caprari C, Clark A, Desiderio A, et al. Polygalacturonase, PGIP and oligogalacturonides in cell-cell communication. Biochem Soc Trans. 1994;22:394\u20137.","journal-title":"Biochem Soc Trans"},{"key":"2368_CR32","doi-asserted-by":"crossref","first-page":"826","DOI":"10.1038\/35081161","volume":"411","author":"JL Dangl","year":"2001","unstructured":"Dangl JL, Jones JD. Plant pathogens and integrated defence responses to infection. Nature. 2001;411:826\u201333.","journal-title":"Nature"},{"key":"2368_CR33","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1111\/j.1365-313X.2008.03503.x","volume":"55","author":"J Staal","year":"2008","unstructured":"Staal J, Kaliff M, Dewaele E, Persson M, Dixelius C. RLM3, a TIR domain encoding gene involved in broad-range immunity of Arabidopsis to necrotrophic fungal pathogens. Plant J. 2008;55:188\u2013200.","journal-title":"Plant J"},{"key":"2368_CR34","doi-asserted-by":"crossref","first-page":"e1000139","DOI":"10.1371\/journal.pbio.1000139","volume":"7","author":"J Liu","year":"2009","unstructured":"Liu J, Elmore JM, Fuglsang AT, Palmgren MG, Staskawicz BJ, Coaker G. RIN4 functions with plasma membrane H+-ATPases to regulate stomatal apertures during pathogen attack. PLoS Biol. 2009;7:e1000139.","journal-title":"PLoS Biol"},{"key":"2368_CR35","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1007\/s004250100654","volume":"214","author":"AJ De-Jong","year":"2002","unstructured":"De-Jong AJ, Yakimova ET, Kapchina VM, Woltering EJ. A critical role for ethylene in hydrogen peroxide release during programmed cell death in tomato suspension cells. Planta. 2002;214:537\u201345.","journal-title":"Planta"},{"key":"2368_CR36","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1104\/pp.101.1.13","volume":"101","author":"K Croft","year":"1993","unstructured":"Croft K, Juttner F, Slusarenko AJ. Volatile products of the lipoxygenase pathway Evolved from Phaseolus vulgaris (L.) leaves inoculated with Pseudomonas syringae pv phaseolicola. Plant Physiol. 1993;101:13\u201324.","journal-title":"Plant Physiol"},{"key":"2368_CR37","doi-asserted-by":"crossref","first-page":"1919","DOI":"10.1105\/tpc.003368","volume":"14","author":"L Xu","year":"2002","unstructured":"Xu L, Liu F, Lechner E, Genschik P, Crosby WL, Ma H, et al. The SCF(COI1) ubiquitin-ligase complexes are required for jasmonate response in Arabidopsis. Plant Cell. 2002;14:1919\u201335.","journal-title":"Plant Cell"},{"key":"2368_CR38","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1126\/science.280.5366.1091","volume":"280","author":"DX Xie","year":"1998","unstructured":"Xie DX, Feys BF, James S, Nieto-Rostro M, Turner JG. COI1: an Arabidopsis gene required for jasmonate-regulated defense and fertility. Science. 1998;280:1091\u20134.","journal-title":"Science"},{"key":"2368_CR39","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1016\/S0168-9525(00)02107-7","volume":"16","author":"BJ Feys","year":"2000","unstructured":"Feys BJ, Parker JE. Interplay of signaling pathways in plant disease resistance. Trends Genet. 2000;16:449\u201355.","journal-title":"Trends Genet"},{"key":"2368_CR40","doi-asserted-by":"crossref","first-page":"S131","DOI":"10.1105\/tpc.001768","volume":"14","author":"KL Wang","year":"2002","unstructured":"Wang KL, Li H, Ecker JR. Ethylene biosynthesis and signaling networks. Plant Cell. 2002;14:S131\u201351.","journal-title":"Plant Cell"},{"key":"2368_CR41","doi-asserted-by":"crossref","first-page":"558","DOI":"10.1111\/j.1365-313X.2004.02232.x","volume":"40","author":"P Veronese","year":"2004","unstructured":"Veronese P, Chen X, Bluhm B, Salmeron J, Dietrich R, Mengiste T. The BOS loci of Arabidopsis are required for resistance to Botrytis cinerea infection. Plant J. 2004;40:558\u201374.","journal-title":"Plant J"},{"key":"2368_CR42","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1105\/tpc.105.035576","volume":"18","author":"P Veronese","year":"2006","unstructured":"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;18:257\u201373.","journal-title":"Plant Cell"},{"key":"2368_CR43","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1016\/S1360-1385(02)02312-9","volume":"7","author":"R Mittler","year":"2002","unstructured":"Mittler R. Oxidative stress, antioxidants and stress tolerance. Trends Plant Sci. 2002;7:405\u201310.","journal-title":"Trends Plant Sci"},{"key":"2368_CR44","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1186\/1471-2229-10-290","volume":"10","author":"L Zhou","year":"2010","unstructured":"Zhou L, Cheung M-Y, Li M-W, Fu Y, Sun Z, Sun S-M, et al. Rice hypersensitive induced reaction protein 1 (OsHIR1) associates with plasma membrane and triggers hypersensitive cell death. BMC Plant Biol. 2010;10:290.","journal-title":"BMC Plant Biol"},{"key":"2368_CR45","doi-asserted-by":"crossref","first-page":"1773","DOI":"10.1105\/tpc.8.10.1773","volume":"8","author":"KE Hammond-Kosack","year":"1996","unstructured":"Hammond-Kosack KE, Jones JD. Resistance gene-dependent plant defense responses. Plant Cell. 1996;8:1773\u201391.","journal-title":"Plant Cell"},{"key":"2368_CR46","doi-asserted-by":"crossref","first-page":"1871","DOI":"10.1104\/pp.106.090803","volume":"143","author":"V Lionetti","year":"2007","unstructured":"Lionetti V, Raiola A, Camardella L, Giovane A, Obel N, Pauly M, et al. Overexpression of pectin methylesterase inhibitors in Arabidopsis restricts fungal infection by Botrytis cinerea. Plant Physiol. 2007;143:1871\u201380.","journal-title":"Plant Physiol"},{"key":"2368_CR47","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1615\/IntJMedMushr.v10.i1.100","volume":"10","author":"G Songulashvili","year":"2008","unstructured":"Songulashvili G, Elisashvili V, Wasser S, Hadar Y, Nevo E. Effect of the carbon source and inoculum preparation method on laccase and manganese peroxidase production in submerged cultivation by the medicinal mushroom Ganoderma lucidum (W Curt: Fr) P Karst (Aphyllophoromycetideae). Int J Med Mushrooms. 2008;10:79\u201386.","journal-title":"Int J Med Mushrooms"},{"key":"2368_CR48","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1016\/S1016-8478(23)13792-7","volume":"16","author":"ST Kim","year":"2003","unstructured":"Kim ST, Cho KS, Kim SG, Kang SY, Kang KY. A rice isoflavone reductase-like gene, OsIRL, is induced by rice blast fungal elicitor. Mol Cells. 2003;16:224\u201331.","journal-title":"Mol Cells"},{"key":"2368_CR49","doi-asserted-by":"crossref","first-page":"e87846","DOI":"10.1371\/journal.pone.0087846","volume":"9","author":"F Tugizimana","year":"2014","unstructured":"Tugizimana F, Steenkamp PA, Piater LA, Dubery IA. Multi-platform metabolomic analyses of ergosterol-induced dynamic changes in Nicotiana tabacum cells. PLoS One. 2014;9:e87846.","journal-title":"PLoS One"},{"key":"2368_CR50","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1007\/s00438-004-1085-6","volume":"272","author":"B Leuthner","year":"2005","unstructured":"Leuthner B, Aichinger C, Oehmen E, Koopmann E, M\u00fcller O, M\u00fcller P, et al. A H2O2-producing glyoxal oxidase is required for filamentous growth and pathogenicity in Ustilago maydis. Mol Genet Genomics. 2005;272:639\u201350.","journal-title":"Mol Genet Genomics"},{"key":"2368_CR51","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1016\/j.fgb.2014.05.011","volume":"72","author":"P Kersten","year":"2014","unstructured":"Kersten P, Cullen D. Copper radical oxidases and related extracellular oxidoreductases of wood-decay Agaricomycetes. Fungal Genet Biol. 2014;72:124\u201330.","journal-title":"Fungal Genet Biol"},{"key":"2368_CR52","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1007\/s11103-006-9002-5","volume":"62","author":"J Lochman","year":"2006","unstructured":"Lochman J, Mikes V. Ergosterol treatment leads to the expression of a specific set of defence-related genes in tobacco. Plant Mol Biol. 2006;62:43\u201351.","journal-title":"Plant Mol Biol"},{"key":"2368_CR53","doi-asserted-by":"crossref","first-page":"4989","DOI":"10.1128\/AEM.70.8.4989-4995.2004","volume":"70","author":"JY Wang","year":"2004","unstructured":"Wang JY, Cai Y, Gou JY, Mao YB, Xu YH, Jiang WH, et al. VdNEP, an elicitor from Verticillium dahliae, induces cotton plant wilting. Appl Environ Microbiol. 2004;70:4989\u201395.","journal-title":"Appl Environ Microbiol"},{"key":"2368_CR54","doi-asserted-by":"crossref","first-page":"10359","DOI":"10.1073\/pnas.0902362106","volume":"106","author":"C Ottmann","year":"2009","unstructured":"Ottmann C, Luberacki B, K\u00fcfner I, Koch W, Brunner F, Weyand M, et al. A common toxin fold mediates microbial attack and plant defense. Proc Natl Acad Sci U S A. 2009;106:10359\u201364.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2368_CR55","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1038\/nrmicro797","volume":"2","author":"GE Harman","year":"2004","unstructured":"Harman GE, Howell CR, Viterbo A, Chet I, Lorito M. Trichoderma species-opportunistic, avirulent plant symbionts. Nat Rev Microbiol. 2004;2:43\u201356.","journal-title":"Nat Rev Microbiol"},{"key":"2368_CR56","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1128\/AEM.65.3.1061-1070.1999","volume":"65","author":"I Yedidia","year":"1999","unstructured":"Yedidia I, Benhamou N, Chet I. Induction of defense responses in cucumber plants (Cucumis sativus L.) by the biocontrol agent Trichoderma harzianum. Appl Environ Microbiol. 1999;65:1061\u201370.","journal-title":"Appl Environ Microbiol"},{"key":"2368_CR57","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1016\/S0981-9428(00)01198-0","volume":"38","author":"I Yedidia","year":"2000","unstructured":"Yedidia I, Benhamou N, Kapulnik Y, Chet I. Induction and accumulation of PR proteins activity during early stages of root colonization by the mycoparasite Trichoderma harzianum strain T-203. Plant Physiol Biochem. 2000;38:863\u201373.","journal-title":"Plant Physiol Biochem"},{"key":"2368_CR58","first-page":"19","volume":"10","author":"MR Chac\u00f3n","year":"2007","unstructured":"Chac\u00f3n MR, Rodr\u00edguez-Gal\u00e1n O, Ben\u00edtez T, Sousa S, Rey M, Llobell A, et al. Microscopic and transcriptome analyses of early colonization of tomato roots by Trichoderma harzianum. Int Microbiol. 2007;10:19\u201327.","journal-title":"Int Microbiol"},{"key":"2368_CR59","doi-asserted-by":"crossref","first-page":"1554","DOI":"10.4161\/psb.6.10.17443","volume":"6","author":"HA Contreras-Cornejo","year":"2011","unstructured":"Contreras-Cornejo HA, Mac\u00edas-Rodr\u00edguez L, Beltr\u00e1n-Pe\u00f1a E, Herrera-Estrella A, L\u00f3pez-Bucio J. Trichoderma-induced plant immunity likely involves both hormonal- and camalexin-dependent mechanisms in Arabidopsis thaliana and confers resistance against necrotrophic fungi Botrytis cinerea. Plant Signal Behav. 2011;6:1554\u201363.","journal-title":"Plant Signal Behav"},{"key":"2368_CR60","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1007\/s10658-011-9782-6","volume":"131","author":"MA Salas-Marina","year":"2011","unstructured":"Salas-Marina MA, Silva-Flores MA, Uresti-Rivera EE, Castro-Longoria E, Herrera-Estrella A, Casas-Flores S. Colonization of Arabidopsis roots by Trichoderma atroviride promotes growth and enhances systemic disease resistance through jasmonic acid\/ethylene and salicylic acid pathways. Eur J Plant Pathol. 2011;131:15\u201326.","journal-title":"Eur J Plant Pathol"},{"key":"2368_CR61","doi-asserted-by":"crossref","first-page":"206","DOI":"10.3389\/fpls.2013.00206","volume":"4","author":"A Mart\u00ednez-Medina","year":"2013","unstructured":"Mart\u00ednez-Medina A, Fern\u00e1ndez I, S\u00e1nchez-Guzm\u00e1n MJ, Jung SC, Pascual JA, Pozo MJ. Deciphering the hormonal signalling network behind the systemic resistance induced by Trichoderma harzianum in tomato. Front Plant Sci. 2013;4:206.","journal-title":"Front Plant Sci"},{"key":"2368_CR62","doi-asserted-by":"crossref","first-page":"1698","DOI":"10.3390\/molecules17021698","volume":"17","author":"F Tugizimana","year":"2012","unstructured":"Tugizimana F, Steenkamp PA, Piater LA, Dubery IA. Ergosterol-induced sesquiterpenoid synthesis in tobacco cells. Molecules. 2012;17:1698\u2013715.","journal-title":"Molecules"},{"key":"2368_CR63","doi-asserted-by":"crossref","first-page":"4994","DOI":"10.1073\/pnas.94.10.4994","volume":"94","author":"DJ Kelleher","year":"1997","unstructured":"Kelleher DJ, Gilmore R. DAD1, the defender against apoptotic cell death, is a subunit of the mammalian oligosaccharyltransferase. Proc Natl Acad Sci U S A. 1997;94:4994\u20139.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2368_CR64","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1094\/PHYTO.2004.94.2.171","volume":"94","author":"LE Hanson","year":"2004","unstructured":"Hanson LE, Howell CR. Elicitors of plant defense responses from biocontrol strains of Trichoderma viren. Phytopathology. 2004;94:171\u20136.","journal-title":"Phytopathology"},{"key":"2368_CR65","doi-asserted-by":"crossref","first-page":"838","DOI":"10.1094\/MPMI-19-0838","volume":"19","author":"S Djonovi\u0107","year":"2006","unstructured":"Djonovi\u0107 S, Pozo MJ, Dangott LJ, Howell CR, Kenerley CM. Sm1, a proteinaceous elicitor secreted by the biocontrol fungus Trichoderma virens induces plant defense responses and systemic resistance. Mol Plant Microbe Interact. 2006;19:838\u201353.","journal-title":"Mol Plant Microbe Interact"},{"key":"2368_CR66","doi-asserted-by":"crossref","first-page":"875","DOI":"10.1104\/pp.107.103689","volume":"145","author":"S Djonovic","year":"2007","unstructured":"Djonovic S, Vargas WA, Kolomiets MV, Horndeski M, Wiest A, Kenerley CM. A proteinaceous elicitor Sm1 from the beneficial fungus Trichoderma virens is required for induced systemic resistance in maize. Plant Physiol. 2007;145:875\u201389.","journal-title":"Plant Physiol"},{"key":"2368_CR67","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1111\/j.1364-3703.2007.00430.x","volume":"8","author":"A Viterbo","year":"2007","unstructured":"Viterbo A, Wiest A, Brotman Y, Chet I, Kenerley C. The 18mer peptaibols from Trichoderma virens elicit plant defence responses. Mol Plant Pathol. 2007;8:737\u201346.","journal-title":"Mol Plant Pathol"},{"key":"2368_CR68","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.soilbio.2007.07.002","volume":"40","author":"F Vinale","year":"2008","unstructured":"Vinale F, Sivasithamparam K, Ghisalberti EL, Marra R, Woo SL, Lorito M. Trichoderma-plant-pathogen interactions. Soil Biol Biochem. 2008;40:1\u201310.","journal-title":"Soil Biol Biochem"},{"key":"2368_CR69","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1007\/s10529-005-3629-1","volume":"27","author":"T Wang","year":"2005","unstructured":"Wang T, Zhang N, Du L. Isolation of RNA of high quality and yield from Ginkgo biloba leaves. Biotechnol Lett. 2005;27:629\u201333.","journal-title":"Biotechnol Lett"},{"key":"2368_CR70","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1101\/gr.074492.107","volume":"18","author":"DR Zerbino","year":"2008","unstructured":"Zerbino DR, Birney E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821\u20139.","journal-title":"Genome Res"},{"key":"2368_CR71","doi-asserted-by":"crossref","first-page":"1086","DOI":"10.1093\/bioinformatics\/bts094","volume":"28","author":"MH Schulz","year":"2012","unstructured":"Schulz MH, Zerbino DR, Vingron M, Birney E. Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics. 2012;28:1086\u201392.","journal-title":"Bioinformatics"},{"key":"2368_CR72","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1093\/bioinformatics\/btg034","volume":"19","author":"G Pertea","year":"2003","unstructured":"Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, et al. TIGR gene indices clustering tools (TGICL): A software system for fast clustering of large EST datasets. Bioinformatics. 2003;19:651\u20132.","journal-title":"Bioinformatics"},{"key":"2368_CR73","doi-asserted-by":"crossref","first-page":"868","DOI":"10.1101\/gr.9.9.868","volume":"9","author":"X Huang","year":"1999","unstructured":"Huang X, Madan A. CAP3: A DNA sequence assembly program. Genome Res. 1999;9:868\u201377.","journal-title":"Genome Res"},{"key":"2368_CR74","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul SF, Madden TL, Sch\u00e4ffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389\u2013402.","journal-title":"Nucleic Acids Res"},{"key":"2368_CR75","doi-asserted-by":"crossref","first-page":"3674","DOI":"10.1093\/bioinformatics\/bti610","volume":"21","author":"A Conesa","year":"2005","unstructured":"Conesa A, G\u00f6tz S, Garc\u00eda-G\u00f3mez JM, Terol J, Tal\u00f3n M, Robles M. Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005;21:3674\u20136.","journal-title":"Bioinformatics"},{"key":"2368_CR76","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","volume":"25","author":"C Trapnell","year":"2009","unstructured":"Trapnell C, Pachter L, Salzberg SL. TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25:1105\u201311.","journal-title":"Bioinformatics"},{"key":"2368_CR77","doi-asserted-by":"crossref","first-page":"914","DOI":"10.1111\/j.1365-313X.2004.02016.x","volume":"37","author":"O Thimm","year":"2004","unstructured":"Thimm O, Blaesing O, Gibon Y, Nagel A, Meyer S, Kr\u00fcger 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\u201339.","journal-title":"Plant J"},{"key":"2368_CR78","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","volume":"57","author":"Y Benjamini","year":"1995","unstructured":"Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist Soc B. 1995;57:289\u2013300.","journal-title":"J R Statist Soc B"},{"key":"2368_CR79","doi-asserted-by":"crossref","first-page":"e21800","DOI":"10.1371\/journal.pone.0021800","volume":"6","author":"F Supek","year":"2011","unstructured":"Supek F, Bo\u0161njak M, \u0160kunca N, \u0160muc T. Revigo summarizes and visualizes long lists of gene ontology terms. PLoS One. 2011;6:e21800.","journal-title":"PLoS One"},{"key":"2368_CR80","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1101\/gr.092759.109","volume":"19","author":"MI Krzywinski","year":"2009","unstructured":"Krzywinski MI, Schein JE, Birol I, Connors J, Gascoyne R, Horsman D, et al. Circos: An information aesthetic for comparative genomics. Genome Res. 2009;19:1639\u201345.","journal-title":"Genome Res"},{"key":"2368_CR81","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1007\/978-3-642-59524-0_3","volume-title":"Rapid Cycle Real-time PCR Methods Appl","author":"R Rasmussen","year":"2001","unstructured":"Rasmussen R. Quantification on the light cycler. In: Meuer S, Wittwer C, Nakagawara K, editors. Rapid Cycle Real-time PCR Methods Appl. Heidelberg: Springer Press; 2001. p. 21\u201334."},{"key":"2368_CR82","doi-asserted-by":"crossref","first-page":"R19","DOI":"10.1186\/gb-2007-8-2-r19","volume":"8","author":"J Hellemans","year":"2007","unstructured":"Hellemans J, Mortier G, De Paepe A, Speleman F, Vandesompele J. qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol. 2007;8:R19.","journal-title":"Genome Biol"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-016-2368-0","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,13]],"date-time":"2024-06-13T17:28:35Z","timestamp":1718299715000},"score":1,"resource":{"primary":{"URL":"http:\/\/www.biomedcentral.com\/1471-2164\/17\/66"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,1,19]]},"references-count":82,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2016,12]]}},"alternative-id":["2368"],"URL":"https:\/\/doi.org\/10.1186\/s12864-016-2368-0","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,1,19]]},"article-number":"66"}}