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Identification of cucurbitacins and assembly of a draft genome for Aquilaria agallocha

Chuan-Hung Chen14, Tony Chien-Yen Kuo12, Meng-Han Yang5, Ting-Ying Chien6, Mei-Ju Chu1, Li-Chun Huang1, Chien-Yu Chen27, Hsiao-Feng Lo3, Shih-Tong Jeng4 and Long-Fang O Chen1*

Author Affiliations

1 Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei 11529, Taiwan

2 Department of Bio-industrial Mechatronics Engineering, National Taiwan University, Taipei 106, Taiwan

3 Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei 106, Taiwan

4 Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 106, Taiwan

5 Department of Computer Science and Information Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung 811, Taiwan

6 Department of Computer Science and Information Engineering, National Taiwan University, Kaohsiung 811, Taiwan

7 Center of Systems Biology, National Taiwan University, Taipei 106, Taiwan

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BMC Genomics 2014, 15:578  doi:10.1186/1471-2164-15-578

Published: 9 July 2014



Agarwood is derived from Aquilaria trees, the trade of which has come under strict control with a listing in Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora. Many secondary metabolites of agarwood are known to have medicinal value to humans, including compounds that have been shown to elicit sedative effects and exhibit anti-cancer properties. However, little is known about the genome, transcriptome, and the biosynthetic pathways responsible for producing such secondary metabolites in agarwood.


In this study, we present a draft genome and a putative pathway for cucurbitacin E and I, compounds with known medicinal value, from in vitro Aquilaria agallocha agarwood. DNA and RNA data are utilized to annotate many genes and protein functions in the draft genome. The expression changes for cucurbitacin E and I are shown to be consistent with known responses of A. agallocha to biotic stress and a set of homologous genes in Arabidopsis thaliana related to cucurbitacin bio-synthesis is presented and validated through qRT-PCR.


This study is the first attempt to identify cucurbitacin E and I from in vitro agarwood and the first draft genome for any species of Aquilaria. The results of this study will aid in future investigations of secondary metabolite pathways in Aquilaria and other non-model medicinal plants.

Agarwood; Cucurbitacin; Aquilaria; Genome