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      The effect of red light and far-red light conditions on secondary metabolism in Agarwood

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          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.

          Electronic supplementary material

          The online version of this article (doi:10.1186/s12870-015-0537-y) contains supplementary material, which is available to authorized users.

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          Most cited references37

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          Origins and Mechanisms of miRNAs and siRNAs.

          Over the last decade, approximately 20-30 nucleotide RNA molecules have emerged as critical regulators in the expression and function of eukaryotic genomes. Two primary categories of these small RNAs--short interfering RNAs (siRNAs) and microRNAs (miRNAs)--act in both somatic and germline lineages in a broad range of eukaryotic species to regulate endogenous genes and to defend the genome from invasive nucleic acids. Recent advances have revealed unexpected diversity in their biogenesis pathways and the regulatory mechanisms that they access. Our understanding of siRNA- and miRNA-based regulation has direct implications for fundamental biology as well as disease etiology and treatment.
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            Small silencing RNAs: an expanding universe.

            Since the discovery in 1993 of the first small silencing RNA, a dizzying number of small RNA classes have been identified, including microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs). These classes differ in their biogenesis, their modes of target regulation and in the biological pathways they regulate. There is a growing realization that, despite their differences, these distinct small RNA pathways are interconnected, and that small RNA pathways compete and collaborate as they regulate genes and protect the genome from external and internal threats.
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              Streaming fragment assignment for real-time analysis of sequencing experiments

              We present eXpress, a software package for highly efficient probabilistic assignment of ambiguously mapping sequenced fragments. eXpress uses a streaming algorithm with linear run time and constant memory use. It can determine abundances of sequenced molecules in real time, and can be applied to ChIP-seq, metagenomics and other large-scale sequencing data. We demonstrate its use on RNA-seq data, showing greater efficiency than other quantification methods.
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                Author and article information

                Contributors
                +886-2-27871184 , tony.cy.kuo@gmail.com
                tim19850301@gmail.com
                sophia@iis.sinica.edu.tw
                lindalu@iis.sinica.edu.tw
                meiju@gate.sinica.edu.tw
                bolch@gate.sinica.edu.tw
                cylin@iis.sinica.edu.tw
                cychen@mars.csie.ntu.edu.tw
                hflo@ntu.edu.tw
                stjeng@ntu.edu.tw
                ochenlf@gate.sinica.edu.tw
                Journal
                BMC Plant Biol
                BMC Plant Biol
                BMC Plant Biology
                BioMed Central (London )
                1471-2229
                12 June 2015
                12 June 2015
                2015
                : 15
                : 139
                Affiliations
                [ ]Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, 11529 Nankang, Taipei Taiwan
                [ ]Department of Bio-industrial Mechatronics Engineering, National Taiwan University, Taipei, 106 Taiwan
                [ ]Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 106 Taiwan
                [ ]Institute of Information Science, Academia Sinica, Taipei, 115 Taiwan
                [ ]Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, 350 Taiwan
                [ ]Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, 106 Taiwan
                [ ]Center for Systems Biology, National Taiwan University, Taipei, 106 Taiwan
                [ ]Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, 106 Taiwan
                Article
                537
                10.1186/s12870-015-0537-y
                4464252
                26067652
                9b194176-b358-4dc7-a0a1-d29cfda1425a
                © Kou et al. 2015

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 1 February 2015
                : 12 March 2015
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2015

                Plant science & Botany
                agarwood,aquilaria agallocha,genome,secondary metabolism,red light,cucurbitacin
                Plant science & Botany
                agarwood, aquilaria agallocha, genome, secondary metabolism, red light, cucurbitacin

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