title: Identification of cucurbitacins and assembly of a draft genome for Aquilaria agallocha.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.forename: Chuan-Hung
authors.initials: CH
authors.lastname: Chen
authors.forename: Tony Chien-Yen
authors.initials: TC
authors.lastname: Kuo
authors.forename: Meng-Han
authors.initials: MH
authors.lastname: Yang
authors.forename: Ting-Ying
authors.initials: TY
authors.lastname: Chien
authors.forename: Mei-Ju
authors.initials: MJ
authors.lastname: Chu
authors.forename: Li-Chun
authors.initials: LC
authors.lastname: Huang
authors.forename: Chien-Yu
authors.initials: CY
authors.lastname: Chen
authors.forename: Hsiao-Feng
authors.initials: HF
authors.lastname: Lo
authors.forename: Shih-Tong
authors.initials: ST
authors.lastname: Jeng
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec, 2, Academia Rd, Nankang, Taipei 11529, Taiwan. ochenlf@gate.sinica.edu.tw.
authors.forename: Long-Fang O
authors.initials: LF
authors.lastname: Chen
mesh_terms: D002851:Chromatography, High Pressure Liquid; D054728:Cucurbitacins / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D004798:Enzymes / Q000235:genetics / Q000378:metabolism; D015723:Gene Library; D018745:Genome, Plant; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D021241:Spectrometry, Mass, Electrospray Ionization; D029645:Thymelaeaceae / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism
chemical_list: D004798:Enzymes; D010940:Plant Proteins; D054728:Cucurbitacins