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De novo transcriptome sequencing and digital gene expression analysis predict biosynthetic pathway of rhynchophylline and isorhynchophylline from Uncaria rhynchophylla, a non-model plant with potent anti-alzheimer’s properties

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      Abstract

      Background

      The major medicinal alkaloids isolated from Uncaria rhynchophylla (gouteng in chinese) capsules are rhynchophylline (RIN) and isorhynchophylline (IRN). Extracts containing these terpene indole alkaloids (TIAs) can inhibit the formation and destabilize preformed fibrils of amyloid β protein (a pathological marker of Alzheimer’s disease), and have been shown to improve the cognitive function of mice with Alzheimer-like symptoms. The biosynthetic pathways of RIN and IRN are largely unknown.

      Results

      In this study, RNA-sequencing of pooled Uncaria capsules RNA samples taken at three developmental stages that accumulate different amount of RIN and IRN was performed. More than 50 million high-quality reads from a cDNA library were generated and de novo assembled. Sequences for all of the known enzymes involved in TIAs synthesis were identified. Additionally, 193 cytochrome P450 (CYP450), 280 methyltransferase and 144 isomerase genes were identified, that are potential candidates for enzymes involved in RIN and IRN synthesis. Digital gene expression profile (DGE) analysis was performed on the three capsule developmental stages, and based on genes possessing expression profiles consistent with RIN and IRN levels; four CYP450s, three methyltransferases and three isomerases were identified as the candidates most likely to be involved in the later steps of RIN and IRN biosynthesis.

      Conclusion

      A combination of de novo transcriptome assembly and DGE analysis was shown to be a powerful method for identifying genes encoding enzymes potentially involved in the biosynthesis of important secondary metabolites in a non-model plant. The transcriptome data from this study provides an important resource for understanding the formation of major bioactive constituents in the capsule extract from Uncaria, and provides information that may aid in metabolic engineering to increase yields of these important alkaloids.

      Electronic supplementary material

      The online version of this article (doi:10.1186/1471-2164-15-676) contains supplementary material, which is available to authorized users.

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            Author and article information

            Affiliations
            [ ]College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
            [ ]College of Life Science, Agriculture and Forest, Qiqihar University, Qiqihar, 161006 China
            [ ]Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, 100193 China
            [ ]Yunnan Branch Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Jinghong, 530023 China
            [ ]Guangxi Medicinal Botanical Garden, Nanning, 530023 China
            [ ]State Key Laboratory of Tree Genetics and Breeding, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
            [ ]CSIRO Plant Industry, PO Box 1600, Canberra, ACT 2001 Australia
            [ ]Hunan Agricultural University, Changsha, 410128 China
            Contributors
            gqqneau@gmail.com
            xjma@public.bta.net.cn
            weishugen2@126.com
            qiudy@caf.ac.cn
            Iain.Wilson@csiro.au
            horti.pwu@gmail.com
            tangqi423@sina.com
            liulijun281021@163.com
            dongshoukun@yahoo.com.cn
            zuweilucky@163.com
            Journal
            BMC Genomics
            BMC Genomics
            BMC Genomics
            BioMed Central (London )
            1471-2164
            12 August 2014
            12 August 2014
            2014
            : 15
            : 1
            25112168 4143583 6370 10.1186/1471-2164-15-676
            © Guo et al.; licensee BioMed Central Ltd. 2014

            This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.

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            Research Article
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            © The Author(s) 2014

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