title: Targeted Integration of RNA-Seq and Metabolite Data to Elucidate Curcuminoid Biosynthesis in Four Curcuma Species.
abstract: Curcuminoids, namely curcumin and its analogs, are secondary metabolites that act as the primary active constituents of turmeric (Curcuma longa). The contents of these curcuminoids vary among species in the genus Curcuma. For this reason, we compared two wild strains and two cultivars to understand the differences in the synthesis of curcuminoids. Because the fluxes of metabolic reactions depend on the amounts of their substrate and the activity of the catalysts, we analyzed the metabolite concentrations and gene expression of related enzymes. We developed a method based on RNA sequencing (RNA-Seq) analysis that focuses on a specific set of genes to detect expression differences between species in detail. We developed a 'selection-first' method for RNA-Seq analysis in which short reads are mapped to selected enzymes in the target biosynthetic pathways in order to reduce the effect of mapping errors. Using this method, we found that the difference in the contents of curcuminoids among the species, as measured by gas chromatography-mass spectrometry, could be explained by the changes in the expression of genes encoding diketide-CoA synthase, and curcumin synthase at the branching point of the curcuminoid biosynthesis pathway.
authors: Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan nono@is.naist.jp donghan-l@is.naist.jp.
authors: Donghan
authors: D
authors: Li
authors: Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan nono@is.naist.jp donghan-l@is.naist.jp.
authors: Naoaki
authors: N
authors: Ono
authors: Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan.
authors: Tetsuo
authors: T
authors: Sato
authors: Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan.
authors: Tadao
authors: T
authors: Sugiura
authors: Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan.
authors: Md
authors: M
authors: Altaf-Ul-Amin
authors: Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, 599-8531 Japan.
authors: Daisaku
authors: D
authors: Ohta
authors: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan.
authors: Hideyuki
authors: H
authors: Suzuki
authors: Center for Information Biology, National Institute of Genetics, Mishima, 411-8540 Japan RIKEN Center for Sustainable Resource Science, Kanagawa, 230-0045 Japan.
authors: Masanori
authors: M
authors: Arita
authors: Division of Pharmacognosy, College of Pharmaceutical Science, Ritsumeikan University, Kusatsu, 525-8577 Japan.
authors: Ken
authors: K
authors: Tanaka
authors: School of Computer Science and Information Technology, Northeast Normal University, Changchun, 130117, China.
authors: Zhiqiang
authors: Z
authors: Ma
authors: Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan.
authors: Shigehiko
authors: S
authors: Kanaya
mesh_terms: D053898:Biosynthetic Pathways / Q000235:genetics*; D016000:Cluster Analysis; D030024:Curcuma / Q000235:genetics* / Q000378:metabolism*; D003474:Curcumin / Q000378:metabolism*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053858:Metabolic Networks and Pathways / Q000235:genetics; D055432:Metabolomics / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D013045:Species Specificity; D059467:Transcriptome / Q000235:genetics
chemical_list: D003474:Curcumin
keywords: Curcumin; Gene expression analysis; Genus Curcuma; Metabolite analysis; RNA-Seq