Open Access Highly Accessed Research article

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

Qianqian Guo12, Xiaojun Ma34*, Shugen Wei5, Deyou Qiu6, Iain W Wilson7, Peng Wu2, Qi Tang8, Lijun Liu1, Shoukun Dong1 and Wei Zu1*

Author Affiliations

1 College of Agriculture, Northeast Agricultural University, Harbin 150030, China

2 College of Life Science, Agriculture and Forest, Qiqihar University, Qiqihar 161006, China

3 Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China

4 Yunnan Branch Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Jinghong 530023, China

5 Guangxi Medicinal Botanical Garden, Nanning 530023, China

6 State Key Laboratory of Tree Genetics and Breeding, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China

7 CSIRO Plant Industry, PO Box 1600, Canberra ACT 2001, Australia

8 Hunan Agricultural University, Changsha 410128, China

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BMC Genomics 2014, 15:676  doi:10.1186/1471-2164-15-676

Published: 12 August 2014



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.


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.


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.

Transcriptome; DGE; Uncaria rhynchophylla; Rhynchophylline; Isorhynchophylline; Terpene indole alkaloid biosynthesis