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Pure Appl. Chem., 2007, Vol. 79, No. 4, pp. 811-823

http://dx.doi.org/10.1351/pac200779040811

Phytochemical genomics in Arabidopsis thaliana: A case study for functional identification of flavonoid biosynthesis genes

Takayuki Tohge1, Keiko Yonekura-Sakakibara1, Rie Niida1, Akiko Watanabe-Takahashi1 and Kazuki Saito1,2

1 RIKEN Plant Science Center, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa 230-0045, Japan
2 Graduate School of Pharmaceutical Sciences,Chiba University, Yayoi-cho 1-33, Inage-ku, Chiba-shi, Chiba 263-8522, Japan

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  • Tohge Takayuki, Sousa Leonardo Perez de, Fernie Alisdair R.: Genome-enabled plant metabolomics. Journal of Chromatography B 2014. <http://dx.doi.org/10.1016/j.jchromb.2014.04.003>
  • Yin Ruohe, Han Kerstin, Heller Werner, Albert Andreas, Dobrev Petre I., Zažímalová Eva, Schäffner Anton R.: Kaempferol 3-O -rhamnoside-7-O -rhamnoside is an endogenous flavonol inhibitor of polar auxin transport in Arabidopsis shoots. New Phytol 2014, 201, 466. <http://dx.doi.org/10.1111/nph.12558>
  • Tohge Takayuki, Fernie Alisdair R.: Lignin, mitochondrial family, and photorespiratory transporter classification as case studies in using co-expression, co-response, and protein locations to aid in identifying transport functions. Front. Plant Sci. 2014, 5. <http://dx.doi.org/10.3389/fpls.2014.00075>
  • Buer Charles S., Kordbacheh Farzanah, Truong Thy T., Hocart Charles H., Djordjevic Michael A.: Alteration of flavonoid accumulation patterns in transparent testa mutants disturbs auxin transport, gravity responses, and imparts long-term effects on root and shoot architecture. Planta 2013, 238, 171. <http://dx.doi.org/10.1007/s00425-013-1883-3>
  • Saito Kazuki, Yonekura-Sakakibara Keiko, Nakabayashi Ryo, Higashi Yasuhiro, Yamazaki Mami, Tohge Takayuki, Fernie Alisdair R.: The flavonoid biosynthetic pathway in Arabidopsis: Structural and genetic diversity. Plant Physiology and Biochemistry 2013, 72, 21. <http://dx.doi.org/10.1016/j.plaphy.2013.02.001>
  • Tohge Takayuki, Watanabe Mutsumi, Hoefgen Rainer, Fernie Alisdair R.: The evolution of phenylpropanoid metabolism in the green lineage. Critical Reviews in Biochemistry and Molecular Biology 2013, 48, 123. <http://dx.doi.org/10.3109/10409238.2012.758083>
  • Hooft Justin J. J., Vervoort Jacques, Bino Raoul J., Vos Ric C. H.: Spectral trees as a robust annotation tool in LC–MS based metabolomics. Metabolomics 2011, 8, 691. <http://dx.doi.org/10.1007/s11306-011-0363-7>
  • Obayashi Takeshi, Kinoshita Kengo: Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways. J Plant Res 2010, 123, 311. <http://dx.doi.org/10.1007/s10265-010-0333-6>
  • Umezawa Toshiaki: The cinnamate/monolignol pathway. Phytochem Rev 2010, 9, 1. <http://dx.doi.org/10.1007/s11101-009-9155-3>
  • Nakabayashi Ryo, Yamazaki Mami, Saito Kazuki: A polyhedral approach for understanding flavonoid biosynthesis in Arabidopsis. New Biotechnol 2010, 27, 829. <http://dx.doi.org/10.1016/j.nbt.2010.03.004>
  • Tohge Takayuki, Fernie Alisdair R: Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function. UNKNOWN 2010, 5, 1210. <http://dx.doi.org/10.1038/nprot.2010.82>
  • Stracke Ralf, Jahns Oliver, Keck Matthias, Tohge Takayuki, Niehaus Karsten, Fernie Alisdair R., Weisshaar Bernd: Analysis of PRODUCTION OF FLAVONOL GLYCOSIDES-dependent flavonol glycoside accumulation in Arabidopsis thaliana plants reveals MYB11-, MYB12- and MYB111-independent flavonol glycoside accumulation. New Phytol 2010, 188, 985. <http://dx.doi.org/10.1111/j.1469-8137.2010.03421.x>
  • Saito Kazuki, Matsuda Fumio: Metabolomics for Functional Genomics, Systems Biology, and Biotechnology. Annu. Rev. Plant Biol. 2010, 61, 463. <http://dx.doi.org/10.1146/annurev.arplant.043008.092035>
  • Nakabayashi Ryo, Kusano Miyako, Kobayashi Makoto, Tohge Takayuki, Yonekura-Sakakibara Keiko, Kogure Noriyuki, Yamazaki Mami, Kitajima Mariko, Saito Kazuki, Takayama Hiromitsu: Metabolomics-oriented isolation and structure elucidation of 37 compounds including two anthocyanins from Arabidopsis thaliana. Phytochemisry 2009, 70, 1017. <http://dx.doi.org/10.1016/j.phytochem.2009.03.021>
  • Matsuda Fumio, Yonekura-Sakakibara Keiko, Niida Rie, Kuromori Takashi, Shinozaki Kazuo, Saito Kazuki: MS/MS spectral tag-based annotation of non-targeted profile of plant secondary metabolites. Plant J 2009, 57, 555. <http://dx.doi.org/10.1111/j.1365-313X.2008.03705.x>
  • Saito Kazuki, Hirai Masami Y., Yonekura-Sakakibara Keiko: Decoding genes with coexpression networks and metabolomics – ‘majority report by precogs’. Trends Plant Sci 2008, 13, 36. <http://dx.doi.org/10.1016/j.tplants.2007.10.006>
  • Xie Z., Ma X., Gang D. R.: Modules of co-regulated metabolites in turmeric (Curcuma longa) rhizome suggest the existence of biosynthetic modules in plant specialized metabolism. J Exp Bot 2008, 60, 87. <http://dx.doi.org/10.1093/jxb/ern263>
  • Weckwerth Wolfram: Integration of metabolomics and proteomics in molecular plant physiology - coping with the complexity by data-dimensionality reduction. Physiol Plant 2008, 132, 176. <http://dx.doi.org/10.1111/j.1399-3054.2007.01011.x>