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Transcriptome and Metabolome Analysis in Shoot and Root Of Park et al. BMC Genomics (2016) 17:303 DOI 10.1186/s12864-016-2616-3 RESEARCH ARTICLE Open Access Transcriptome and metabolome analysis in shoot and root of Valeriana fauriei Yun Ji Park1, Xiaohua Li1, Seung Jae Noh2, Jae Kwang Kim3, Soon Sung Lim4, Nam Il Park5, Soonok Kim6, Yeon Bok Kim7, Young Ock Kim7, Sang Won Lee7, Mariadhas Valan Arasu8, Naif Abdullah Al-Dhabi8 and Sang Un Park1* Abstract Background: Valeriana fauriei is commonly used in the treatment of cardiovascular diseases in many countries. Several constituents with various pharmacological properties are present in the roots of Valeriana species. Although many researches on V. fauriei have been done since a long time, further studies in the discipline make a limit due to inadequate genomic information. Hence, Illumina HiSeq 2500 system was conducted to obtain the transcriptome data from shoot and root of V. fauriei. Results: A total of 97,595 unigenes were noticed from 346,771,454 raw reads after preprocessing and assembly. Of these, 47,760 unigens were annotated with Uniprot BLAST hits and mapped to COG, GO and KEGG pathway. Also, 70,013 and 88,827 transcripts were expressed in root and shoot of V. fauriei, respectively. Among the secondary metabolite biosynthesis, terpenoid backbone and phenylpropanoid biosynthesis were large groups, where transcripts was involved. To characterize the molecular basis of terpenoid, carotenoid, and phenylpropanoid biosynthesis, the levels of transcription were determined by qRT-PCR. Also, secondary metabolites content were measured using GC/MS and HPLC analysis for that gene expression correlated with its accumulation respectively between shoot and root of V. fauriei. Conclusions: We have identified the transcriptome using Illumina HiSeq system in shoot and root of V. fauriei. Also, we have demonstrated gene expressions associated with secondary metabolism such as terpenoid, carotenoid, and phenylpropanoid. Keywords: Valeriana fauriei, Illumina HiSeq system, Digital gene expression, Terpenoid, Carotenoid, Phenylpropanoid Background isolated more than 150 compounds from Valeriana The genus Valeriana, containing over 250 species grown plants, such as monoterpenes, sesquiterpenes, iridoids, in Europe, Britain, and Asia [1, 2]. The roots of Valeri- alkaloids, and so on [5]. It has been reported that flavo- ana plants are used mainly for medicinal purposes. The noids and alkaloids are primarily observed in the aerial roots have been known to contain several photochemical parts and sesquiterpenes and iridoids noticed in rhi- constituents with pharmacological properties including zomes and roots [6, 7]. Among these constituents, hypnotic, sedative, antispasmodic, mild anodyne, valerenic acid is responsible for the sedative effects and hypotensive and carminative effects [3]. Among them, its derivatives are produced in roots and rhizomes as Valeriana fauriei, which is found widely in the northeast principal compounds of Valeriana species [8, 9]. of China, South Korea, and Japan, has been used in folks Terpenes, one of the major secondary metabolites in for hundreds of years (Fig. 1) [4]. Researchers have medicinal plants, have many volatile representatives such as isoprenes (C5), monoterpenes (C10), sesquiterpenes (C15), even some diterpenes (C20), and triterepenes * Correspondence: [email protected] (C30) [10]. Members of this family serve many import- 1Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 305-764, Korea ant functions like protecting the plants from many Full list of author information is available at the end of the article © 2016 Park et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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. Park et al. BMC Genomics (2016) 17:303 Page 2 of 16 insects, pest, herbivores and microbial pathogens such produce α- and β-carotene by enzymatic catalytic activ- as bacteria and fungi [11]. All terpenes are assembled ity of two lycopene cyclases, lycopene β-cyclase (LCYB) from the basic unit of isoprenes, isopentenyl diphos- and lycopene ε-cyclase (LCYE) [18]. α-carotene is phate (IPP) and dimethylallyl diphosphate (DMAPP). hydroxylated into lutein by both β-ring hydroxylase These universal five carbon precursors are derived from (CHXB) and ε-ring hydroxylase (CHXE). In the other two alternate biosynthetic pathways: mevalonate (MVA) bransch, β-carotene is transformed into zeaxanthin; pathway from acetyl-CoA and the 2-C-methylerythritol process is catalyzed by CHXB. Next, zeaxanthin epoxi- 4-phosphate (MEP) pathway from glycerol and pyruvate dase (ZEP) allows synthesis of violaxanthin from zeaxan- (Additional file 1) [12]. Recent report claimed that even thin. At last, the enzymatic activity of nine-cis- though the operation of this pathway is independent, epoxycarotenoid dioxygenases (NCEDs) is responsible some metabolic connection were observed between the for the synthesis of abscisic acid as the final product two pathways [13]. [17]. Along the pathway, the oxidative activity of the The MVA pathway initiates with the formation of specific enzymes generate apocarotenoids which is fur- acetoacetyl-CoA by acetocetyl-CoA thiolase (AACT). ther degraded by carotenoid cleavage dioxygenases The HMG-CoA synthase (HMGS) catalyzes the synthe- (CCDs) [19]. sis of 3-hydroxy-3-methylglutaryl-CoA with one acetyl- Phenolic compounds, widely distributed in higher CoA and one acetoacetyl-CoA. Next, HMG-CoA plants, belong to one of the major classes of secondary reductase (HMGR) synthesizes the MVA. Further, metabolites including lignins, flavonols, isoflavonoids and enzymes such as mevalonate kinase (MK), phosphome- anthocyanins [20]. These compounds contribute many valonate kinase (PMK), and mevalonate diphosphate de- important functional aspects of plant life such as UV sun- carboxylase (MVD) catalyze the formation of IPP. The screens, pigments signaling. Additionally, accumulation of first step in MEP pathway, pyruvate and glyceraldehyde- phenolic compounds is stimulated by biotic and abiotic 3-phosphate combined and produce 1-deoxy-D-xylulose responses. Currently, many researchers have been focused 5-phosphate by DOXP synthase (DXS) which is mainly on the improvement of phenolic compounds in plants, be- observed in plastids. Then, the conversion of 1-deoxy-D- cause of its health promoting properties and curing xylulose-5-phosphate to 2-C-methyl-D-erythritol properties to cancers, neurodegenerative diseases, cardio- 4-phosphate is carried out by DOXP reductoisomerase vascular diseases, osteoporosis and diabetes respectively (DXR). MEP is transformed into 1-hydroxy-2-methyl-2- [21]. Phenolic compounds are synthesized through the (E)-butenyl 4-phosphate by the action of various phenylpropanoid pathway and its biosynthesis starts with catalytic enzymes. Enzyme (E)-4-hydroxy-3-methylbut the condensation of the phenylalanine which is end prod- 2-enyl diphosphate reductase (HDR) catalyzes the uct of shikimate pathway (Additional file 3). In the first synthesis of IPP and DMAPP [12]. IPP and DMAPP are step, deamination reaction involved by the action of formed by the action of enzymes geranyl diphosphate phenylalanine ammonia-lyase (PAL) for the generation of synthase (GPS) and farnesyl diphosphate synthase (FPS), trans-cinnamic acid [22]. Next, cinnamate 4-hydroxylase respectively [10]. IPP and DMAPP are the backbone for (C4H) and 4-coumaroyl CoA ligase (4CL) involved in the the synthesis of all terpenes. production of other intermediate metabolites [20]. In sev- Carotenoids, the natural C40 isoprenoid products, are eral side branches, p-coumarate acid 3-hydroxylase (C3H) essential hydrophobic plant compounds which contrib- converts p-coumaric acid to caffeic acid which is trans- ute to yellow, orange or red color [14]. Carotenoids play formed to ferulic acid, carried out by the enzyme caffeate an important role in photosynthesis, photomorphogen- O-mehtyltransferase (COMT) [22]. Also, the enzyme esis, and photoprotection. It is also mainly involved in hydroxycinnamoyl-CoA quinate hydroxyl cinnamoyl the production of abscisic acid. The main carotenoid transferase (HQT)isinvolvedinsynthesisofp-coumaroyl- biosynthetic pathway was identified in many plants and quinate from p-coumaroyl CoA which is then converted studied extensively. The pathway begins with condensa- to chlorogenic acid by C3H [21]. Finally, chalcone syn- tion of 3 molecules of geranyl-geranylpyrophosphate, a thase (CHS), catalyzes naringenin-chalcone, which is the precursors from the upstream MEP pathway for produc- derivative of the flavanoids. In downstream steps, various tion of 15-cis-phytoene catalyzed by phytoene synthase enzymes such as isomerases, reductases, and hydroxylases (PSY) (Additional file 2) [15]. Then, 15-cis-phytoene is involved in the alternation of the basic flavonoid skeleton, converted to lycopene, the first yellow carotenoid, leading to the different flavonoid subclasses [23]. through desaturation reactions which are synthesized by Recently, whole transcriptome sequencing using next- both phytoene
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