title: The effect of red light and far-red light conditions on secondary metabolism in agarwood.
abstract: BACKGROUND
  Agarwood, a heartwood derived from Aquilaria trees, is a valuable commodity that has seen prevalent use among many cultures. In particular, it is widely used in herbal medicine and many compounds in agarwood are known to exhibit medicinal properties. Although there exists much research into medicinal herbs and extraction of high value compounds, few have focused on increasing the quantity of target compounds through stimulation of its related pathways in this species.
  
  
  RESULTS
  In this study, we observed that cucurbitacin yield can be increased through the use of different light conditions to stimulate related pathways and conducted three types of high-throughput sequencing experiments in order to study the effect of light conditions on secondary metabolism in agarwood. We constructed genome-wide profiles of RNA expression, small RNA, and DNA methylation under red light and far-red light conditions. With these profiles, we identified a set of small RNA which potentially regulates gene expression via the RNA-directed DNA methylation pathway.
  
  
  CONCLUSIONS
  We demonstrate that light conditions can be used to stimulate pathways related to secondary metabolism, increasing the yield of cucurbitacins. The genome-wide expression and methylation profiles from our study provide insight into the effect of light on gene expression for secondary metabolism in agarwood and provide compelling new candidates towards the study of functional secondary metabolic components.
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, 11529, Nankang, Taipei, Taiwan. tony.cy.kuo@gmail.com.|Department of Bio-industrial Mechatronics Engineering, National Taiwan University, Taipei, 106, Taiwan. tony.cy.kuo@gmail.com.
authors.forename: Tony Chien-Yen
authors.initials: TC
authors.lastname: Kuo
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, 11529, Nankang, Taipei, Taiwan. tim19850301@gmail.com.|Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 106, Taiwan. tim19850301@gmail.com.
authors.forename: Chuan-Hung
authors.initials: CH
authors.lastname: Chen
authors.affiliation: Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan. sophia@iis.sinica.edu.tw.
authors.forename: Shu-Hwa
authors.initials: SH
authors.lastname: Chen
authors.affiliation: Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan. lindalu@iis.sinica.edu.tw.
authors.forename: I-Hsuan
authors.initials: IH
authors.lastname: Lu
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, 11529, Nankang, Taipei, Taiwan. meiju@gate.sinica.edu.tw.
authors.forename: Mei-Ju
authors.initials: MJ
authors.lastname: Chu
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, 11529, Nankang, Taipei, Taiwan. bolch@gate.sinica.edu.tw.
authors.forename: Li-Chun
authors.initials: LC
authors.lastname: Huang
authors.affiliation: Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan. cylin@iis.sinica.edu.tw.|Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, 350, Taiwan. cylin@iis.sinica.edu.tw.|Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, 106, Taiwan. cylin@iis.sinica.edu.tw.
authors.forename: Chung-Yen
authors.initials: CY
authors.lastname: Lin
authors.affiliation: Department of Bio-industrial Mechatronics Engineering, National Taiwan University, Taipei, 106, Taiwan. cychen@mars.csie.ntu.edu.tw.|Center for Systems Biology, National Taiwan University, Taipei, 106, Taiwan. cychen@mars.csie.ntu.edu.tw.
authors.forename: Chien-Yu
authors.initials: CY
authors.lastname: Chen
authors.affiliation: Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, 106, Taiwan. hflo@ntu.edu.tw.
authors.forename: Hsiao-Feng
authors.initials: HF
authors.lastname: Lo
authors.affiliation: Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 106, Taiwan. stjeng@ntu.edu.tw.
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, 11529, Nankang, Taipei, Taiwan. ochenlf@gate.sinica.edu.tw.
authors.forename: Long-Fang O
authors.initials: LF
authors.lastname: Chen
mesh_terms: D001483:Base Sequence; D016000:Cluster Analysis; D054728:Cucurbitacins / Q000378:metabolism; D019175:DNA Methylation / Q000235:genetics / Q000528:radiation effects; D018506:Gene Expression Regulation, Plant / Q000528:radiation effects; D063990:Gene Ontology; D008027:Light; D064210:Secondary Metabolism / Q000235:genetics / Q000528:radiation effects*; D017423:Sequence Analysis, RNA; D029645:Thymelaeaceae / Q000235:genetics / Q000378:metabolism* / Q000528:radiation effects*; D014934:Wood / Q000235:genetics / Q000378:metabolism* / Q000528:radiation effects*
chemical_list: D054728:Cucurbitacins