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Sample Set Information

ID TSE1347
Title Phytochemical genomics in Arabidopsis thaliana: A case study for functional identification of flavonoid biosynthesis genes
Description The completion of the whole genome sequence of Arabidopsis thaliana has made it possible to explore the phytochemical genomics in this species by determining gene-tometabolite correlation through the comprehensive analysis of metabolite accumulation and gene expression. In this study, flavonoid profiling of wild-type plants and T-DNA insertion mutants was analyzed using ultra-performance liquid chromatography (UPLC)/photodiode array detection (PDA)/electrospray ionization (ESI)/multiple-stage mass spectrometry (MSn). Detailed analysis of the metabolite changes in the mutants suggested the functions of genes that have been mutated. In silico coexpression analysis of genes involved in flavonoid metabolism in Arabidopsis was performed using a publicly available transcriptome database of DNA microarrays. We inferred a coexpression framework model of the genes involved in the pathways of flavonol, anthocyanin, and proanthocyanidin synthesis, suggesting specific functions and coregulation of the genes of pathway enzymes and transcription factors. The metabolic profiling of the omt1 mutant lacking a methyltransferase gene narrowed down by the coexpression analysis showed that AtOMT1 (At5g54160) is involved not only in the production of lignins and sinapoyl esters but also in the methylation of flavonols forming isorhamnetin. These results suggest that the functional genomics approach by detailed targetmetabolite profiling with transcriptome coexpression analysis provides an efficient way of identifying novel gene functions involved in plant metabolism.
Authors Tohge, T., Yonekura-Sakakibara, K., Niida, R., Watanabe-Takahashi, A. and Saito, K.
Reference Pure and Applied Chemistry, 2007, 79, 811-823

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Data Analysis Details Information

Title Flavonoid profiling
Description These standard flavonol glycosides were used for the identification of the peaks in the plant extracts based on retention times, UV–vis absorption spectra, and mass fragmentation by tandem MS analysis. Other flavonoids were annotated by comparing their UV–vis absorption spectra, elution time, m/z values, and MS2 fragmentation patterns with the reported data.

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