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Conversion of MapMan to Allow the Analysis of Transcript Data from Solanaceous Species: Effects of Genetic and Environmental Alterations in Energy Metabolism in the Leaf

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Abstract

The tomato microarray TOM1 offers the possibility to monitor the levels of several thousand transcripts in parallel. The microelements represented on this tomato microarray have been putatively assigned to unigenes, and organised in functional classes using the MapMan ontology (Thimm  et al., 2004. Plant J. 37: 914–939). This ontology was initially developed for use with the Arabidopsis ATH1 array, has a low level of redundancy, and can be combined with the MapMan software to provide a biologically structured overview of changes of transcripts, metabolites and enzyme activities. Use of this application is illustrated using three case studies with published or novel TOM1 array data sets for Solanaceous species. Comparison of previously reported data on transcript levels in potato leaves in the middle of the day and the middle of the night identified coordinated changes in the levels of transcripts of genes involved in various metabolic pathways and cellular events. Comparison with diurnal changes of gene expression in Arabidopsis revealed common features, illustrating how MapMan can be used to compare responses in different organisms. Comparison of transcript levels in new experiments performed on the leaves of the cultivated tomato S. lycopersicum and the wild relative S. pennellii revealed a general decrease of levels of transcripts of genes involved in terpene and, phenylpropanoid metabolism as well as chorismate biosynthesis in the crop compared to the wild relative. This matches the recently reported decrease of the levels of secondary metabolites in the latter. In the third case study, new expression array data for two genotypes deficient in TCA cycle enzymes is analysed to show that these genotypes have elevated levels of transcripts associated with photosynthesis. This in part explains the previously documented enhanced rates of photosynthesis in these genotypes. Since the Solanaceous MapMan is intended to be a community resource it will be regularly updated on improvements in tomato gene annotation and transcript profiling resources.

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Abbreviations

cDNA:

complementary DNA

GO:

gene ontology

EST:

expressedsequence tag

References

  • A. Aharoni A.P. Giri S. Deuerlein F. Griepink W.J. Kogel Particlede F.W.A. Verstappen H.A. Verhoeven M.A. Jongsma W. Schwab H.J. Bouwmeester (2003) ArticleTitleTerpenoid metabolism in wild type and transgenic Arabidopsis plants Plant Cell 15 2866–2884 Occurrence Handle10.1105/tpc.016253 Occurrence Handle1:CAS:528:DC%2BD2cXhtVShsw%3D%3D Occurrence Handle14630967

    Article  CAS  PubMed  Google Scholar 

  • R. Alba Z.J. Fei P. Payton Y. Liu S.L. Moore P. Debbie J. Cohn M. D′Ascenzo J.S. Gordon J.K.C. Rose G. Martin S.D. Tanksley M. Bouzayen M.M. Jahn J. Giovannoni (2004) ArticleTitleESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development Plant J. 39 697–714 Occurrence Handle10.1111/j.1365-313X.2004.02178.x Occurrence Handle1:CAS:528:DC%2BD2cXos1ylt7w%3D Occurrence Handle15315633

    Article  CAS  PubMed  Google Scholar 

  • S.F. Altschul W. Gish W. Miller E.W. Myers D.J. Lipman (1990) ArticleTitleBasic local alignment search tool J. Mol. Biol. 215 403–10 Occurrence Handle10.1006/jmbi.1990.9999 Occurrence Handle1:CAS:528:DyaK3MXitVGmsA%3D%3D Occurrence Handle2231712

    Article  CAS  PubMed  Google Scholar 

  • InstitutionalAuthorNameArabidopsis Genome Initiative (2000) ArticleTitleAnalysis of the genome sequence of the flowering plant Arabidopsis thaliana Nature 408 796–815 Occurrence Handle10.1038/35048692

    Article  Google Scholar 

  • G.E. Bartley B.K. Ishida (2002) ArticleTitleDigital fruit ripening: data mining in the TIGR tomato gene index Plant. Mol. Biol. Rep. 20 115–130 Occurrence Handle1:CAS:528:DC%2BD38Xms1Grs70%3D

    CAS  Google Scholar 

  • C.J. Baxter M. Sabar W.P. Quick L.J. Sweetlove (2005) ArticleTitleComparison of changes in fruit gene expression in tomato introgression lines provides evidence of genome wide transcriptional changes and reveals links to mapped QTLs and described traits J. Exp. Bot. 56 1591–1604 Occurrence Handle10.1093/jxb/eri154 Occurrence Handle1:CAS:528:DC%2BD2MXktl2qtbk%3D Occurrence Handle15851417

    Article  CAS  PubMed  Google Scholar 

  • O.E. Bläsing Y. Gibon M. Günther M. Höhne R. Morcuende O. Thimm B. Usadel W.-R. Scheible M. Stitt (2005) ArticleTitleSugars and Circadian Regulation make Major Contributions to the Global Regulation of Diurnal Gene Expression in Arabidopsis Plant Cell 17 3257–3281 Occurrence Handle10.1105/tpc.105.035261 Occurrence Handle16299223

    Article  PubMed  Google Scholar 

  • F. Carbone D. Pizzichini G. Giuliano C. Rosati G. Perrotta (2005) ArticleTitleComparative profiling of tomato fruits and leaves evidences a complex modulation of global transcript profiles Plant Sci. 169 165–175 Occurrence Handle10.1016/j.plantsci.2005.03.011 Occurrence Handle1:CAS:528:DC%2BD2MXltFegsLk%3D

    Article  CAS  Google Scholar 

  • F. Carrari A. Nunes-Nesi Y. Gibon A. Lytovchenko M. Ehlers-Lourario A.R. Fernie (2003) ArticleTitleReduced expression of aconitase results in an enhanced rate of photosynthesis and marked shifts in carbon partitioning in illuminated leaves of Lycopersicon pennellii Plant Physiol. 133 1322–1335 Occurrence Handle10.1104/pp.103.026716 Occurrence Handle1:CAS:528:DC%2BD3sXptFGitbs%3D Occurrence Handle14551334

    Article  CAS  PubMed  Google Scholar 

  • Z. Chen D.R. Gallie (2004) ArticleTitleThe ascorbic acid redox state controls guard cell signalling and stomatal movement Plant Cell 16 1143–1162 Occurrence Handle10.1105/tpc.021584 Occurrence Handle1:CAS:528:DC%2BD2cXktlOqsLc%3D Occurrence Handle15084716

    Article  CAS  PubMed  Google Scholar 

  • T. Czechowski R.P. Bari M. Stitt W.R. Scheible M.K. Udvardi (2004) ArticleTitleReal-time RT-PCR profiling of over 1,400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot- specific genes Plant J. 38 366–379 Occurrence Handle10.1111/j.1365-313X.2004.02051.x Occurrence Handle1:CAS:528:DC%2BD2cXkt1KksLg%3D Occurrence Handle15078338

    Article  CAS  PubMed  Google Scholar 

  • C.H. Danna C.G. Bartoli F. Sacco L.R. Ingala G.E. Santa-Maria J.J. Guiamet R.A. Ugalde (2003) ArticleTitleThylakoid bound ascorbate peroxidase mutant exhibits impaired electron transport and photosynthetic activity Plant Physiol. 133 2116–2125 Occurrence Handle10.1104/pp.103.021717

    Article  Google Scholar 

  • Cannon, S.B., Mitra, A., Baumgarten, A., Young, N.D. and May, G. 2004. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol. 4: Article no. 10.

  • Y. Eshed D. Zamir (1995) ArticleTitleAn introgression line population of Lycopersicum pennellii in the cultivated tomato enables the identification and fine mapping of yield associated QTL Genetics 141 1147–1162 Occurrence Handle1:CAS:528:DyaK28Xht1CltLw%3D Occurrence Handle8582620

    CAS  PubMed  Google Scholar 

  • Z. Fei X. Tang R.M. Alba J.A. White C.M. Ronning G.B. Martin S.D. Tanksley J.J. Giovannoni (2004) ArticleTitleComprehensive EST analysis of tomato and comparative genomics of fruit ripening Plant J. 40 47–59 Occurrence Handle10.1111/j.1365-313X.2004.02188.x Occurrence Handle15361140

    Article  PubMed  Google Scholar 

  • A.R. Fernie L. Willmitzer (2001) ArticleTitleMolecular and biochemical triggers of potato tuber development Plant Physiol. 127 1459–1465 Occurrence Handle10.1104/pp.127.4.1459 Occurrence Handle1:CAS:528:DC%2BD38XjtVWgsA%3D%3D Occurrence Handle11743089

    Article  CAS  PubMed  Google Scholar 

  • A.R. Fernie F. Carrari L.J. Sweetlove (2004) ArticleTitleRespiratory metabolism: glycolysis, the TCA cycle and mitochondrial electron transport Curr. Opin. Plant Biol. 7 254–261 Occurrence Handle10.1016/j.pbi.2004.03.007 Occurrence Handle1:CAS:528:DC%2BD2cXjvVams7k%3D Occurrence Handle15134745

    Article  CAS  PubMed  Google Scholar 

  • R.G. Fray D. Grierson (1993) ArticleTitleMolecular genetics of tomato fruit ripening Trends in Genetics 9 438–443 Occurrence Handle10.1016/0168-9525(93)90108-T Occurrence Handle1:CAS:528:DyaK2cXntlKitQ%3D%3D Occurrence Handle8122312

    Article  CAS  PubMed  Google Scholar 

  • E. Fridman F. Carrari Y.S. Liu A.R. Fernie D. Zamir (2004) ArticleTitleZooming in on a quantitative trait for tomato yield using introspecific introgressions Science 305 1786–1789 Occurrence Handle10.1126/science.1101666 Occurrence Handle1:CAS:528:DC%2BD2cXnsFajur8%3D Occurrence Handle15375271

    Article  CAS  PubMed  Google Scholar 

  • N. Gass T. Glagotskaia S. Mellema J. Stuurman M. Barone T. Mandel U. Roessner-Tunali C. Kuhlemeier (2005) ArticleTitlePyruvate decarboxylase provides growing pollen tubes with a competetive advantage in petunia Plant Cell 17 2355–2368 Occurrence Handle10.1105/tpc.105.033290 Occurrence Handle1:CAS:528:DC%2BD2MXpsFGjsb4%3D Occurrence Handle15994907

    Article  CAS  PubMed  Google Scholar 

  • P. Geigenberger M. Stitt A.R. Fernie (2004) ArticleTitleMetabolic control analysis and regulation of the conversion of sucrose to starch in growing potato tubers Plant Cell Environ. 27 655–673 Occurrence Handle10.1111/j.1365-3040.2004.01183.x Occurrence Handle1:CAS:528:DC%2BD2cXlsVGgtL0%3D

    Article  CAS  Google Scholar 

  • Gentleman, R.C., Carey, V.J., Bates, D.M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., Hornik, K., Hothorn, T., Huber, W., Iacus, S., Irizarry, R., Leisch, F., Li, C., Maechler, M., Rossini, A.J., Sawitzki, G., Smith, C., Smyth, G., Tierney, L., Yang, J.Y. and Zhang, J. 2004. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5: Article no. 80.

  • C. Hanfrey S. Sommer M.J. Mayer D. Burtin A.J. Michael (2001) ArticleTitleArabidopsis polyamine biosynthesis: absence of ornithine decarboxylase and the mechanism of arginine decarboxylase activity Plant J. 27 551–560 Occurrence Handle10.1046/j.1365-313X.2001.01100.x Occurrence Handle1:CAS:528:DC%2BD3MXos12ktLw%3D Occurrence Handle11576438

    Article  CAS  PubMed  Google Scholar 

  • J. Kopka N. Schauer S. Krueger C. Birkemeyer B. Usadel E. Bergmuller P. Dormann Y. Gibon M. Stitt L. Willmitzer A.R. Fernie D. Steinhauser (2005) ArticleTitleGMD@CSB.DB: The Golm Metabolome Database Bioinformatics 21 1635–1638 Occurrence Handle10.1093/bioinformatics/bti236 Occurrence Handle1:CAS:528:DC%2BD2MXjtlGgsrg%3D Occurrence Handle15613389

    Article  CAS  PubMed  Google Scholar 

  • G. Kiddle G.M. Pastori S. Bernard C. Pignocchi J. Antoniw P.J. Verrier C.H Foyer (2003) ArticleTitleEffects of leaf ascorbate content on defence and photosynthesis gene expression in Arabidopsis thaliana Antioxidant Redox Signal 5 23–32 Occurrence Handle10.1089/152308603321223513 Occurrence Handle1:CAS:528:DC%2BD3sXhslGrsLg%3D

    Article  CAS  Google Scholar 

  • Kothapalli, R., Yoder, S.J., Mane, S. and Loughran, T.P. 2002. Microarray results: how accurate are they? BMC Bioinformatics 3: Article no. 22.

  • M. Lemaire-Chamley J. Petit V. Garcia D. Just P. Baldet V. Germain M. Fagard M. Mouassite C. Cheniclet C. Rothan (2005) ArticleTitleChanges in transcriptional profiles are associated with early fruit tissue specialization in tomato Plant Physiol 139 750–769 Occurrence Handle10.1104/pp.105.063719 Occurrence Handle1:CAS:528:DC%2BD2MXhtFCgsb7N Occurrence Handle16183847

    Article  CAS  PubMed  Google Scholar 

  • A.H. Millar V. Mittova G. Kiddle J.L. Heazelwood C.G. Bartoli F.L. Thedoulou C.H. Foyer (2003) ArticleTitleControl of ascorbate synthesis by respiration and its implications for stress responses Plant Physiol. 133 443–447 Occurrence Handle10.1104/pp.103.028399 Occurrence Handle1:CAS:528:DC%2BD3sXosVaqsbc%3D Occurrence Handle14555771

    Article  CAS  PubMed  Google Scholar 

  • S. Moore P. Payton M. Wright S. Tanksley J Giovannoni (2005) ArticleTitleUtilization of tomato microarrays for comparative gene expression analysis in the Solanaceae J. Exp. Bot. 56 2885–2895 Occurrence Handle10.1093/jxb/eri283 Occurrence Handle1:CAS:528:DC%2BD2MXhtFCjt7jP Occurrence Handle16216847

    Article  CAS  PubMed  Google Scholar 

  • L.A. Mueller T.H. Solow N. Taylor B. Skwarecki R. Buels J. Binns C. Lin M.H. Wright R. Ahrens Y. Wang E.V. Herbst E.R. Keyder N. Menda D. Zamir S.D. Tanksley (2005a) ArticleTitleThe SOL Genomics Network: a comparative resource for Solanaceae biology and beyond Plant Physiol. 138 1310–1317 Occurrence Handle10.1104/pp.105.060707 Occurrence Handle1:CAS:528:DC%2BD2MXmvV2lurY%3D

    Article  CAS  Google Scholar 

  • L.A. Mueller S.D. Tanksley J.J. Giovannini J. Eck Particlevan S. Stack D. Choi B.D. Kim M.S. Chen Z.K. Cheng C.Y. Li H.Q. Ling Y.B. Xue G. Seymour G. Bishop G. Bryan R. Sharma J. Khurana A. Tyagi D. Chattopadhyay N.K. Singh W. Stiekema P. Lindhout T. Jesse R.K. Lankhorst M. Bouzayen D. Shibata S. Tabata A. Granell M.A. Botella G. Giullano L. Frusciante M. Causse D Zamir (2005b) ArticleTitleThe tomato sequencing project, the first cornerstone of the International Solanaceae Project (SOL) Comp Funct Genomics 6 153–158 Occurrence Handle10.1186/1471-2164-6-153 Occurrence Handle1:CAS:528:DC%2BD2MXktFersbc%3D

    Article  CAS  Google Scholar 

  • N.J. Mulder R. Apweiler T.K. Attwood A. Bairoch A. Bateman D. Binns P. Bradley P. Bork P. Bucher L. Cerutti R. Copley E. Courcelle U. Das R. Durbin W. Fleischmann J. Gough D. Haft N. Harte N. Hulo D. Kahn A. Kanapin M. Krestyaninova D. Lonsdale R. Lopez I. Letunic M. Madera J. Maslen J. McDowall A. Mitchell A.N. Nikolskaya S. Orchard M. Pagni C.P. Ponting E. Quevillon J. Selengut C.J. Sigrist V. Silventoinen D.J. Studholme R. Vaughan C.H Wu (2005) ArticleTitleInterPro, progress and status in 2005 Nucleic Acids Res. 33 D201–5 Occurrence Handle10.1093/nar/gki106 Occurrence Handle1:CAS:528:DC%2BD2MXisVGlsg%3D%3D Occurrence Handle15608177

    Article  CAS  PubMed  Google Scholar 

  • T. Murashige F. Skoog (1962) ArticleTitleA revised medium for rapid growth and bioassays with tobacco tissue cultures Physiol. Plant 15 473–497 Occurrence Handle1:CAS:528:DyaF3sXksFKm

    CAS  Google Scholar 

  • K.S. Mysore O.R. Crasta R.P. Tuori O. Folkerts P.B. Swirsky G.B. Martin (2002) ArticleTitleComprehensive transcript profiling of Pto- and Prf-mediated host defense responses to infection by Pseudomonas syringae pv. Tomato Plant J. 32 299–315 Occurrence Handle10.1046/j.1365-313X.2002.01424.x Occurrence Handle1:CAS:528:DC%2BD38Xpt12msrs%3D Occurrence Handle12410809

    Article  CAS  PubMed  Google Scholar 

  • T.S. Nuhse A. Stensballe O.N. Jensen S.C. Peck (2004) ArticleTitlePhosphoproteomics of the Arabidopsis plasma membrane and a new phosphorylation site database Plant Cell 16 2394–2405 Occurrence Handle10.1105/tpc.104.023150 Occurrence Handle15308754

    Article  PubMed  Google Scholar 

  • A. Nunes-Nesi F. Carrari A. Lytovchenko A.M. Smith M.E. Loureiro R.G. Ratcliffe L.J. Sweetlove A.R. Fernie (2005) ArticleTitleEnhanced photosynthetic performance and growth as a consequence of decreasing mitochondrial malate dehydrogenase activity in transgenic tomato plants Plant Physiol. 137 611–622 Occurrence Handle10.1104/pp.104.055566 Occurrence Handle1:CAS:528:DC%2BD2MXhs1Kqsbs%3D Occurrence Handle15665243

    Article  CAS  PubMed  Google Scholar 

  • K.P. O’Brien M. Remm E.L. Sonnhammer (2005) ArticleTitleInparanoid: a comprehensive database of eukaryotic orthologs Nucleic Acids Res. 33 476–480 Occurrence Handle10.1093/nar/gki107

    Article  Google Scholar 

  • A. Patzlaff S. McInnis A. Courtenay C. Surman L.J. Newman C. Smith M.W. Bevan S. Mansfield R.W. Whetten R.R. Sederoff M.M. Campbell (2003) ArticleTitleCharacterization of a pine MYB that regulates lignification Plant J. 36 743–754 Occurrence Handle10.1046/j.1365-313X.2003.01916.x Occurrence Handle1:CAS:528:DC%2BD2cXmtlyrsA%3D%3D Occurrence Handle14675440

    Article  CAS  PubMed  Google Scholar 

  • R Development Core Team. 2005. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria ISBN 3-900051-07-0, http://www.R-project.org. Accessed 1.5.2005.

  • M. Remm C.E. Storm E.L. Sonnhammer (2001) ArticleTitleAutomatic clustering of orthologs and in-paralogs from pairwise species comparisons J. Mol. Biol 314 1041–1052 Occurrence Handle10.1006/jmbi.2000.5197 Occurrence Handle1:CAS:528:DC%2BD3MXptVOlsro%3D Occurrence Handle11743721

    Article  CAS  PubMed  Google Scholar 

  • U. Roessner A. Luedemann D. Brust O. Fiehn T. Linke L. Willmitzer A.R. Fernie (2001a) ArticleTitleMetabolic profiling and phenotyping of genetically and environmentally modified systems Plant Cell 13 131–142 Occurrence Handle10.1105/tpc.13.1.11

    Article  Google Scholar 

  • U. Roessner L. Willmitzer A.R. Fernie (2001b) ArticleTitleHigh-resolution metabolic profiling: identification of phenocopies Plant Physiol. 127 749–764 Occurrence Handle10.1104/pp.127.3.749 Occurrence Handle1:CAS:528:DC%2BD3MXos1Kntb4%3D

    Article  CAS  Google Scholar 

  • U. Roessner-Tunali B. Hegemann A. Lytovchenko F. Carrari C. Bruedigam D. Granot A.R. Fernie (2003) ArticleTitleMetabolic profiling of transgenic tomato plants overexpressing hexokinase reveals that the influence of hexose phosphorylation diminishes during fruit development Plant Physiol. 133 84–99 Occurrence Handle10.1104/pp.103.023572 Occurrence Handle1:CAS:528:DC%2BD3sXntlaitLw%3D Occurrence Handle12970477

    Article  CAS  PubMed  Google Scholar 

  • A.I. Saeed V. Sharov J. White J. Li W. Liang N. Bhagabati J. Braisted M. Klapa T. Currier M. Thiagarajan A. Sturn M. Snuffin A. Rezantsev D. Popov A. Ryltsov E. Kostukovich I. Borisovsky Z. Liu A. Vinsavich V. Trush J. Quackenbush (2003) ArticleTitleTM4: a free, open-source system for microarray data management and analysis Biotechniques 34 374–378 Occurrence Handle1:CAS:528:DC%2BD3sXhtlCiur4%3D Occurrence Handle12613259

    CAS  PubMed  Google Scholar 

  • N. Schauer D. Zamir A.R. Fernie (2005) ArticleTitleMetabolic profiling of leaves and fruit of wild species tomato: a survey of the Solanum lycopersicum complex J. Exp. Bot. 56 297–307 Occurrence Handle10.1093/jxb/eri057 Occurrence Handle1:CAS:528:DC%2BD2MXkt1Wltw%3D%3D Occurrence Handle15596477

    Article  CAS  PubMed  Google Scholar 

  • M. Schneider A. Bairoch C.H. Wu R. Apweiler (2005) ArticleTitlePlant protein annotation in the UniProt Knowledgebase Plant Physiol. 138 59–66 Occurrence Handle10.1104/pp.104.058933 Occurrence Handle1:CAS:528:DC%2BD2MXks12itbo%3D Occurrence Handle15888679

    Article  CAS  PubMed  Google Scholar 

  • N. Smirnoff (2000) ArticleTitleAscorbate biosynthesis and function in photoprotection Phil. Trans. R. Soc. Lond. B Biol. Sci. 355 1455–1464 Occurrence Handle10.1098/rstb.2000.0706 Occurrence Handle1:CAS:528:DC%2BD3cXovFKltrw%3D

    Article  CAS  Google Scholar 

  • N. Smirnoff G.L. Wheeler (2000) ArticleTitleAscorbic acid in plants: biosynthesis and function CRC Crit. Rev. Plant Sci. 19 267–290 Occurrence Handle1:CAS:528:DC%2BD3cXmtVCjs74%3D

    CAS  Google Scholar 

  • Smyth, G.K. and Speed, T.P. 2003. Normalization of cDNA microarray data. In: METHODS: Selecting Candidate Genes from DNA Array Screens: Application to Neuroscience , D. Carter (Ed.). Methods Volume 31: 265–273.

  • Smyth, G.K. 2004. Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments. Statistical Applications in Genetics and Molecular Biology 3, 3.

  • U. Sonnewald (2001) ArticleTitleControl of potato tuber sprouting Trends in Plant Sci. 6 333–335 Occurrence Handle10.1016/S1360-1385(01)02020-9 Occurrence Handle1:CAS:528:DC%2BD3MXmtFCksbk%3D

    Article  CAS  Google Scholar 

  • R. Sorek H.M. Safer (2003) ArticleTitleA novel algorithm for computational identification of contaminated EST libraries Nucl. Acids Res. 31 1067–1074 Occurrence Handle10.1093/nar/gkg170 Occurrence Handle1:CAS:528:DC%2BD3sXit1aqtLY%3D Occurrence Handle12560505

    Article  CAS  PubMed  Google Scholar 

  • M. Stitt A.R. Fernie (2003) ArticleTitleFrom measurements of metabolites to metabolomics; an “on the fly” perspective illustrated by recent studies of carbon-nitrogen interactions Curr. Opin. Biotech. 14 136–144 Occurrence Handle10.1016/S0958-1669(03)00023-5 Occurrence Handle1:CAS:528:DC%2BD3sXjsVGlurg%3D Occurrence Handle12732314

    Article  CAS  PubMed  Google Scholar 

  • Y. Tadmor E. Fridman A. Gur O. Larkov E. Lastochkin U. Ravid D. Zamir E. Lewinsohn (2002) ArticleTitleIdentification of malodorous, a wild species allele affecting tomato aroma that was selected against during domestication J. Agri. Food Chem. 50 2005–2009 Occurrence Handle10.1021/jf011237x Occurrence Handle1:CAS:528:DC%2BD38Xht1ektr4%3D

    Article  CAS  Google Scholar 

  • S.D. Tanksley M. Ganal J.P. Prince M.C. Vincente Particlede M.W. Bonierbale P. Broun T.M. Fulton J.J. Giovannoni S. Grandillo Martin et al. (1992) ArticleTitleHigh-density molecular linkage maps of the tomato and potato genomes Genetics 132 1141–1160 Occurrence Handle1:STN:280:ByyD1Mzktl0%3D Occurrence Handle1360934

    CAS  PubMed  Google Scholar 

  • InstitutionalAuthorNameThe Gene Ontology Consortium (2000) ArticleTitleGene Ontology: tool for the unification of biology Nature Genet 25 25–29 Occurrence Handle10.1038/75556

    Article  Google Scholar 

  • O. Thimm O. Blässing Y. Gibon A. Nagel S. Meyer P. Krüger J. Selbig L.A. Müller S.Y. Rhee M. Stitt (2004) ArticleTitleMAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes Plant J. 37 914–939 Occurrence Handle10.1111/j.1365-313X.2004.02016.x Occurrence Handle1:CAS:528:DC%2BD2cXjtFChu78%3D Occurrence Handle14996223

    Article  CAS  PubMed  Google Scholar 

  • D.V. Tieman M.G. Taylor J.A. Ciardi H.J. Klee (2000) ArticleTitleThe tomato ethylene receptors NR and LeETR4 are negative regulators of ethylene response and exhibit functional compensation within a multigene family Proc. Natl. Acad. Sci. USA 97 5663–5668 Occurrence Handle10.1073/pnas.090550597 Occurrence Handle1:CAS:528:DC%2BD3cXjsVWmsbc%3D Occurrence Handle10792050

    Article  CAS  PubMed  Google Scholar 

  • S.R. Uppalapati P. Ayoubi H. Weng D.A. Palmer R.E. Mitchell W. Jones C.L. Bender (2005) ArticleTitleThe phtotoxin coronatine and methyl jasmonate impact multiple phytohormone pathways in tomato Plant J. 42 201–217 Occurrence Handle10.1111/j.1365-313X.2005.02366.x Occurrence Handle1:CAS:528:DC%2BD2MXjvFSrtrw%3D Occurrence Handle15807783

    Article  CAS  PubMed  Google Scholar 

  • E. Urbanczyk-Wochniak A. Luedemann J. Kopka J. Selbig U. Roessner-Tunali L. Willmitzer A.R. Fernie (2003) ArticleTitleParallel analysis of transcript and metabolic profiles: a new approach in systems biology EMBO Rep 4 989–993 Occurrence Handle10.1038/sj.embor.embor944 Occurrence Handle1:CAS:528:DC%2BD3sXnslaqt7g%3D Occurrence Handle12973302

    Article  CAS  PubMed  Google Scholar 

  • E. Urbanczyk-Wochniak C. Baxter A. Kolbe J. Kopka L.J. Sweetlove A.R. Fernie (2005) ArticleTitleProfiling of diurnal patterns of metabolite and transcript abundance in potato (Solanum tuberosum) leaves Planta 221 891–903 Occurrence Handle10.1007/s00425-005-1483-y Occurrence Handle1:CAS:528:DC%2BD2MXos1emtLw%3D Occurrence Handle15744496

    Article  CAS  PubMed  Google Scholar 

  • B. Usadel A. Nagel O. Thimm H. Redestig O.E. Blaesing N. Palacios-Rojas J. Selbig J. Hannemann P. Conceicao D. Steinhauser W.R. Scheible Y. Gibon R. Morcuede D. Weicht S. Meyer M. Stitt (2005) ArticleTitleExtension of the visualisation tool MapMan to allow statistical analysis of arrays, display of co-responding genes and comparison with known responses Plant Physiol. 138 1185–1194 Occurrence Handle10.1104/pp.105.060459

    Article  Google Scholar 

  • R. Hoeven ParticleVan der C. Ronning J. Giovannoni G. Martin S.D. Tanksley (2002) ArticleTitleDeductions about the number, organization, and evolution of genes in the tomato genome based on analysis of a large expressed sequence tag collection and selective genomic sequencing Plant Cell 14 1441–1456 Occurrence Handle10.1105/tpc.010478 Occurrence Handle12119366

    Article  PubMed  Google Scholar 

  • J.Q. Wilkinson M.B. Lanahan H.C. Yen J.J. Giovannoni H.J. Klee (1995) ArticleTitleAn ethylene inducible component of signal transduction encoded by never ripe Science 270 1807–1809 Occurrence Handle1:CAS:528:DyaK2MXhtVSiurnJ Occurrence Handle8525371

    CAS  PubMed  Google Scholar 

  • Y.H. Yang S. Dudoit P. Luu D.M. Lin V. Peng J. Ngai T.P. Speed (2002) ArticleTitleNormalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation Nucl. Acids Res. 30 e15 Occurrence Handle10.1093/nar/30.4.e15 Occurrence Handle11842121

    Article  PubMed  Google Scholar 

  • B.R. Zeeberg W.M. Feng G. Wang M.D. Wang A.T. Fojo M. Sunshine S. Narasimhan D.W. Kane W.C. Reinhold S. Lababidi K.J. Bussey J. Riss J.C. Barrett J.N. Weinstein (2003) ArticleTitleGoMiner: a resource for biological interpretation of genomic and proteomic data Genome Biol. 4 R28 Occurrence Handle10.1186/gb-2003-4-4-r28 Occurrence Handle12702209

    Article  PubMed  Google Scholar 

  • H. Zegzouti B. Jones P. Frasse C. Marty B. Maitre A. Latche J.C. Pech M. Bouzayen (1999) ArticleTitleEthylene regulated gene expression in tomato fruit: characterization of novel ethylene-responsive and ripening-related genes isolated by differential display Plant J. 18 589–600 Occurrence Handle10.1046/j.1365-313x.1999.00483.x Occurrence Handle1:CAS:528:DyaK1MXlsFGhsb0%3D Occurrence Handle10417710

    Article  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, Golm, 14476, Germany

    Ewa Urbanczyk-Wochniak, Björn Usadel, Oliver Thimm, Adriano Nunes-Nesi, Fernando Carrari, Oliver Bläsing, Daniel Weicht, Anna Polinceusz, Mark Stitt & Alisdair R. Fernie

  2. Hort Research Mt Albert, Private Bag 92 169, Auckland, New Zealand

    Marcus Davy

  3. Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Warsaw Agricultural University, Nowoursynowska 166, Warsaw, 02-787, Poland

    Magdalena Kowalczyk

  4. RZPD German Resource Centre for Genome Research, Heubnerweg 6, Berlin S, D-14059, Germany

    Svenja Meyer

  5. CNAP, Department of Biology (Area 7), University of York, York, YO10 5YW, UK

    Oliver Thimm

  6. Instituto de Biotecnología, CICVyA INTA, Castelar, B1712WAA, Argentina

    Fernando Carrari

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  1. Ewa Urbanczyk-Wochniak
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  2. Björn Usadel
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  3. Oliver Thimm
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  4. Adriano Nunes-Nesi
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  5. Fernando Carrari
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  6. Marcus Davy
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  7. Oliver Bläsing
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  8. Magdalena Kowalczyk
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  9. Daniel Weicht
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  10. Anna Polinceusz
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  11. Svenja Meyer
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  12. Mark Stitt
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  13. Alisdair R. Fernie
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Corresponding authors

Correspondence to Björn Usadel or Alisdair R. Fernie.

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Urbanczyk-Wochniak, E., Usadel, B., Thimm, O. et al. Conversion of MapMan to Allow the Analysis of Transcript Data from Solanaceous Species: Effects of Genetic and Environmental Alterations in Energy Metabolism in the Leaf. Plant Mol Biol 60, 773–792 (2006). https://doi.org/10.1007/s11103-005-5772-4

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  • DOI: https://doi.org/10.1007/s11103-005-5772-4

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