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Zhang D, Li W, Xia EH, Zhang QJ, Liu Y, Zhang Y, Tong Y, Zhao Y, Niu YC, Xu JH, Gao LZ. The Medicinal Herb Panax notoginseng Genome Provides Insights into Ginsenoside Biosynthesis and Genome Evolution. MOLECULAR PLANT 2017; 10:903-907. [PMID: 28315473 DOI: 10.1016/j.molp.2017.02.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 02/27/2017] [Accepted: 02/27/2017] [Indexed: 05/21/2023]
Affiliation(s)
- Dan Zhang
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China; Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Wei Li
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China; Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - En-Hua Xia
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China; Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Qun-Jie Zhang
- Agrobiological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yuan Liu
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China; Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Yun Zhang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Yan Tong
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Yuan Zhao
- Yunnan Agricultural University, Kunming 650201, China
| | | | - Jia-Huan Xu
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China; Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Li-Zhi Gao
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China; Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China.
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Zhang J, Li X, Lu F, Wang S, An Y, Su X, Li X, Ma L, Han G. De novo Sequencing and Transcriptome Analysis Reveal Key Genes Regulating Steroid Metabolism in Leaves, Roots, Adventitious Roots and Calli of Periploca sepium Bunge. FRONTIERS IN PLANT SCIENCE 2017; 8:594. [PMID: 28484475 PMCID: PMC5399629 DOI: 10.3389/fpls.2017.00594] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 03/31/2017] [Indexed: 06/07/2023]
Abstract
Periploca sepium Bunge is a traditional medicinal plant, whose root bark is important for Chinese herbal medicine. Its major bioactive compounds are C21 steroids and periplocin, a kind of cardiac glycoside, which are derived from the steroid synthesis pathway. However, research on P. sepium genome or transcriptomes and their related genes has been lacking for a long time. In this study we estimated this species nuclear genome size at 170 Mb (using flow cytometry). Then, RNA sequencing of four different tissue samples of P. sepium (leaves, roots, adventitious roots, and calli) was done using the sequencing platform Illumina/Solexa Hiseq 2,500. After de novo assembly and quantitative assessment, 90,375 all-transcripts and 71,629 all-unigenes were finally generated. Annotation efforts that used a number of public databases resulted in detailed annotation information for the transcripts. In addition, differentially expressed genes (DEGs) were identified by using digital gene profiling based on the reads per kilobase of transcript per million reads mapped (RPKM) values. Compared with the leaf samples (L), up-regulated genes and down-regulated genes were eventually obtained. To deepen our understanding of these DEGs, we performed two enrichment analyses: gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Here, the analysis focused upon the expression characteristics of those genes involved in the terpene metabolic pathway and the steroid biosynthesis pathway, to better elucidate the molecular mechanism of bioactive steroid synthesis in P. sepium. The bioinformatics analysis enabled us to find many genes that are involved in bioactive steroid biosynthesis. These genes encoded acetyl-CoA acetyltransferase (ACAT), HMG-CoA synthase (HMGS), HMG-CoA reductase (HMGR), mevalonate kinase (MK), phosphomevalonate kinase (PMK), mevalonate diphosphate decarboxylase (MDD), isopentenylpyrophosphate isomerase (IPPI), farnesyl pyrophosphate synthase (FPS), squalene synthase (SS), squalene epoxidase (SE), cycloartenol synthase (CAS), sterol C-24 methyltransferase (SMT1), sterol-4alpha-methyl oxidase 1 (SMO1), sterol 14alpha-demethylase (CYP51/14-SDM), delta(14)-sterol reductase (FK/14SR), C-8,7 sterol isomerase (HYD1), sterol-4alpha-methyl oxidase 2 (SMO2), delta(7)-sterol-C5(6)-desaturase (STE1/SC5DL), 7-dehydrocholesterol reductase (DWF5/DHCR7), delta (24)-sterol reductase (DWF1/DHCR24), sterol 22-desaturase (CYP710A), progesterone 5beta-reductase (5β-POR), 3-beta-hydroxysteroid dehydrogenase (3β-HSD). This research will be helpful to further understand the mechanism of bioactive steroid biosynthesis in P. sepium, namely C21 steroid and periplocin biosynthesis.
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Affiliation(s)
- Jian Zhang
- Key Lab of Industrial Fermentation Microbiology, Tianjin University of Science and Technology, Ministry of EducationTianjin, China
- School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese MedicineTianjin, China
- College of Bioengineering, Tianjin University of Science and TechnologyTianjin, China
| | - Xinglin Li
- Key Lab of Industrial Fermentation Microbiology, Tianjin University of Science and Technology, Ministry of EducationTianjin, China
- College of Bioengineering, Tianjin University of Science and TechnologyTianjin, China
| | - Fuping Lu
- Key Lab of Industrial Fermentation Microbiology, Tianjin University of Science and Technology, Ministry of EducationTianjin, China
- College of Bioengineering, Tianjin University of Science and TechnologyTianjin, China
| | - Shanying Wang
- Key Lab of Industrial Fermentation Microbiology, Tianjin University of Science and Technology, Ministry of EducationTianjin, China
- College of Bioengineering, Tianjin University of Science and TechnologyTianjin, China
| | - Yunhe An
- Beijing Center for Physical and Chemical AnalysisBeijing, China
| | - Xiaoxing Su
- Beijing Center for Physical and Chemical AnalysisBeijing, China
| | - Xiankuan Li
- School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese MedicineTianjin, China
| | - Lin Ma
- School of Traditional Chinese Materia Medica, Tianjin University of Traditional Chinese MedicineTianjin, China
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Biswas T, Mathur AK, Mathur A. A literature update elucidating production of Panax ginsenosides with a special focus on strategies enriching the anti-neoplastic minor ginsenosides in ginseng preparations. Appl Microbiol Biotechnol 2017; 101:4009-4032. [PMID: 28411325 DOI: 10.1007/s00253-017-8279-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/22/2017] [Accepted: 03/29/2017] [Indexed: 12/31/2022]
Abstract
Ginseng, an oriental gift to the world of healthcare and preventive medicine, is among the top ten medicinal herbs globally. The constitutive triterpene saponins, ginsenosides, or panaxosides are attributed to ginseng's miraculous efficacy towards anti-aging, rejuvenating, and immune-potentiating benefits. The major ginsenosides such as Rb1, Rb2, Rc, Rd., Re, and Rg1, formed after extensive glycosylations of the aglycone "dammaranediol," dominate the chemical profile of this genus in vivo and in vitro. Elicitations have successfully led to appreciable enhancements in the production of these major ginsenosides. However, current research on ginseng biotechnology has been focusing on the enrichment or production of the minor ginsenosides (the less glycosylated precursors of the major ginsenosides) in ginseng preparations, which are either absent or are produced in very low amounts in nature or via cell cultures. The minor ginsenosides under current scientific scrutiny include diol ginsenosides such as Rg3, Rh2, compound K, and triol ginsenosides Rg2 and Rh1, which are being touted as the next "anti-neoplastic pharmacophores," with better bioavailability and potency as compared to the major ginsenosides. This review aims at describing the strategies for ginsenoside production with special attention towards production of the minor ginsenosides from the major ginsenosides via microbial biotransformation, elicitations, and from heterologous expression systems.
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Affiliation(s)
- Tanya Biswas
- Plant Biotechnology Division, Central Institute of Medicinal & Aromatic Plants; Council of Scientific & Industrial Research, PO- CIMAP, Lucknow, 226015, India
| | - A K Mathur
- Plant Biotechnology Division, Central Institute of Medicinal & Aromatic Plants; Council of Scientific & Industrial Research, PO- CIMAP, Lucknow, 226015, India
| | - Archana Mathur
- Plant Biotechnology Division, Central Institute of Medicinal & Aromatic Plants; Council of Scientific & Industrial Research, PO- CIMAP, Lucknow, 226015, India.
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Nguyen NQ, Lee OR. Overexpression of ginseng UGT72AL1 causes organ fusion in the axillary leaf branch of Arabidopsis. J Ginseng Res 2017; 41:419-427. [PMID: 28701886 PMCID: PMC5489871 DOI: 10.1016/j.jgr.2017.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 03/09/2017] [Accepted: 03/14/2017] [Indexed: 11/20/2022] Open
Abstract
Background Glycosylation of natural compounds increases the diversity of secondary metabolites. Glycosylation steps are implicated not only in plant growth and development, but also in plant defense responses. Although the activities of uridine-dependent glycosyltransferases (UGTs) have long been recognized, and genes encoding them in several higher plants have been identified, the specific functions of UGTs in planta remain largely unknown. Methods Spatial and temporal patterns of gene expression were analyzed by quantitative reverse transcription (qRT)-polymerase chain reaction (PCR) and GUS histochemical assay. In planta transformation in heterologous Arabidopsis was generated by floral dipping using Agrobacterium tumefaciens (C58C1). Protein localization was analyzed by confocal microscopy via fluorescent protein tagging. Results PgUGT72AL1 was highly expressed in the rhizome, upper root, and youngest leaf compared with the other organs. GUS staining of the promoter: GUS fusion revealed high expression in different organs, including axillary leaf branch. Overexpression of PgUGT72AL1 resulted in a fused organ in the axillary leaf branch. Conclusion PgUGT72AL1, which is phylogenetically close to PgUGT71A27, is involved in the production of ginsenoside compound K. Considering that compound K is not reported in raw ginseng material, further characterization of this gene may shed light on the biological function of ginsenosides in ginseng plant growth and development. The organ fusion phenotype could be caused by the defective growth of cells in the boundary region, commonly regulated by phytohormones such as auxins or brassinosteroids, and requires further analysis.
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Affiliation(s)
| | - Ok Ran Lee
- Corresponding author. Department of Plant Biotechnology, College of Agriculture and Life Science, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea.Department of Plant BiotechnologyCollege of Agriculture and Life ScienceChonnam National University77 Yongbong-ro, Buk-guGwangju61186Republic of Korea
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Yang Y, Ge F, Sun Y, Liu D, Chen C. Strengthening Triterpene Saponins Biosynthesis by Over-Expression of Farnesyl Pyrophosphate Synthase Gene and RNA Interference of Cycloartenol Synthase Gene in Panax notoginseng Cells. Molecules 2017; 22:molecules22040581. [PMID: 28379198 PMCID: PMC6153935 DOI: 10.3390/molecules22040581] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 03/20/2017] [Accepted: 03/30/2017] [Indexed: 01/24/2023] Open
Abstract
To conform to the multiple regulations of triterpene biosynthesis, the gene encoding farnesyl pyrophosphate synthase (FPS) was transformed into Panax notoginseng (P. notoginseng) cells in which RNA interference (RNAi) of the cycloartenol synthase (CAS) gene had been accomplished. Transgenic cell lines showed both higher expression levels of FPS and lower expression levels of CAS compared to the wild-type (WT) cells. In the triterpene and phytosterol analysis, transgenic cell lines provided a higher accumulation of total triterpene saponins, and a lower amount of phytosterols in comparison with the WT cells. Compared with the cells in which RNAi of the CAS gene was achieved, the cells with simultaneously over-expressed FPS and silenced CAS showed higher triterpene contents. These results demonstrate that over-expression of FPS can break the rate-limiting reaction catalyzed by FPS in the triterpene saponins biosynthetic pathway; and inhibition of CAS expression can decrease the synthesis metabolic flux of the phytosterol branch. Thus, more precursors flow in the direction of triterpene synthesis, and ultimately promote the accumulation of P. notoginseng saponins. Meanwhile, silencing and over-expressing key enzyme genes simultaneously is more effective than just manipulating one gene in the regulation of saponin biosynthesis.
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Affiliation(s)
- Yan Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China.
- School of Biotechnology and Engineering, Dianxi Science and Technology Normal University, Lincang 677000, China.
| | - Feng Ge
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China.
| | - Ying Sun
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China.
| | - Diqiu Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China.
| | - Chaoyin Chen
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China.
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Natural products against Alzheimer's disease: Pharmaco-therapeutics and biotechnological interventions. Biotechnol Adv 2016; 35:178-216. [PMID: 28043897 DOI: 10.1016/j.biotechadv.2016.12.005] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 12/19/2016] [Accepted: 12/23/2016] [Indexed: 12/30/2022]
Abstract
Alzheimer's disease (AD) is a severe, chronic and progressive neurodegenerative disease associated with memory and cognition impairment ultimately leading to death. It is the commonest reason of dementia in elderly populations mostly affecting beyond the age of 65. The pathogenesis is indicated by accumulation of the amyloid-beta (Aβ) plaques and neurofibrillary tangles (NFT) in brain tissues and hyperphosphorylation of tau protein in neurons. The main cause is considered to be the formation of reactive oxygen species (ROS) due to oxidative stress. The current treatment provides only symptomatic relief by offering temporary palliative therapy which declines the rate of cognitive impairment associated with AD. Inhibition of the enzyme acetylcholinesterase (AChE) is considered as one of the major therapeutic strategies offering only symptomatic relief and moderate disease-modifying effect. Other non-cholinergic therapeutic approaches include antioxidant and vitamin therapy, stem cell therapy, hormonal therapy, use of antihypertensive or lipid-lowering medications and selective phosphodiesterase (PDE) inhibitors, inhibition of β-secretase and γ-secretase and Aβ aggregation, inhibition of tau hyperphosphorylation and intracellular NFT, use of nonsteroidal anti-inflammatory drugs (NSAIDs), transition metal chelators, insulin resistance drugs, etanercept, brain-derived neurotrophic factor (BDNF) etc. Medicinal plants have been reported for possible anti-AD activity in a number of preclinical and clinical trials. Ethnobotany, being popular in China and in the Far East and possibly less emphasized in Europe, plays a substantial role in the discovery of anti-AD agents from botanicals. Chinese Material Medica (CMM) involving Chinese medicinal plants has been used traditionally in China in the treatment of AD. Ayurveda has already provided numerous lead compounds in drug discovery and many of these are also undergoing clinical investigations. A number of medicinal plants either in their crude forms or as isolated compounds have exhibited to reduce the pathological features associated with AD. In this present review, an attempt has been made to elucidate the molecular mode of action of various plant extracts, phytochemicals and traditional herbal formulations investigated against AD as reported in various preclinical and clinical tests. Herbal synergism often found in polyherbal formulations were found effective to combat disease heterogeneity as found in complex pathogenesis of AD. Finally a note has been added to describe biotechnological improvement, genetic and genomic resources and mathematical and statistical techniques for empirical model building associated with anti-AD plant secondary metabolites and their source botanicals.
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Wang J, Li J, Li J, Liu S, Wu X, Li J, Gao W. Transcriptome profiling shows gene regulation patterns in ginsenoside pathway in response to methyl jasmonate in Panax Quinquefolium adventitious root. Sci Rep 2016; 6:37263. [PMID: 27876840 PMCID: PMC5120341 DOI: 10.1038/srep37263] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 10/20/2016] [Indexed: 12/15/2022] Open
Abstract
Here, we combine elicitors and transcriptomics to investigate the inducible biosynthesis of the ginsenoside from the Panax quinquefolium. Treatment of P. quinquefolium adventitious root with methyl jasmonate (MJ) results in an increase in ginsenoside content (43.66 mg/g compared to 8.32 mg/g in control group). Therefore, we sequenced the transcriptome of native and MJ treated adventitious root in order to elucidate the key differentially expressed genes (DEGs) in the ginsenoside biosynthetic pathway. Through DEG analysis, we found that 5,759 unigenes were up-regulated and 6,389 unigenes down-regulated in response to MJ treatment. Several defense-related genes (48) were identified, participating in salicylic acid (SA), jasmonic acid (JA), nitric oxide (NO) and abscisic acid (ABA) signal pathway. Additionally, we mapped 72 unigenes to the ginsenoside biosynthetic pathway. Four cytochrome P450s (CYP450) were likely to catalyze hydroxylation at C-16 (c15743_g1, c39772_g1, c55422_g1) and C-30 (c52011_g1) of the triterpene backbone. UDP-xylose synthases (c52571_g3) was selected as the candidate, which was likely to involve in ginsenoside Rb3 biosynthesis.
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Affiliation(s)
- Juan Wang
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Jinxin Li
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Jianli Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Shujie Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xiaolei Wu
- Tianjin ZhongXin Pharmaceuticals R&D Center, Tianjin 300457, China
| | - Jing Li
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Wenyuan Gao
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
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Sun HP, Li F, Ruan QM, Zhong XH. Identification and validation of reference genes for quantitative real-time PCR studies in Hedera helix L. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 108:286-294. [PMID: 27474936 DOI: 10.1016/j.plaphy.2016.07.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/21/2016] [Accepted: 07/21/2016] [Indexed: 06/06/2023]
Abstract
Reference gene evaluation and selection are necessary steps in gene expression analysis, especially in new plant varieties, through reverse transcription quantitative real-time PCR (RT-qPCR). Hedera helix L. is an important traditional medicinal plant recorded in European Pharmacopoeia. Research on gene expression in H. helix has not been widely explored, and no RT-qPCR studies have been reported. Thus, it is important and necessary to identify and validate suitable reference genes to for normalizing RT-qPCR results. In our study, 14 candidate protein-coding reference genes were selected. Their expression stability in five tissues (root, stem, leaf, petiole and shoot tip) and under seven abiotic stress conditions (cold, heat, drought, salinity, UV-C irradiation, abscisic acid and methyl jasmonate) were evaluated using geNorm and NormFinder. This study is the first to evaluate the stability of reference genes in H. helix. The results show that different reference genes should be chosen for normalization on the basis of various experimental conditions. F-box was more stable than the other selected genes under all analysis conditions except ABA treatment; 40S was the most stable reference gene under ABA treatment; in contrast, EXP and UBQ were the most unstable reference genes. The expressions of HhSE and Hhβ-AS, which are two genes related to the biosynthetic pathway of triterpenoid saponins, were also examined for reference genes in different tissues and under various cold stress conditions. The validation results confirmed the applicability and accuracy of reference genes. Additionally, this study provides a basis for the accurate and widespread use of RT-qPCR in selecting genes from the genome of H. helix.
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Affiliation(s)
- Hua-Peng Sun
- Horticulture & Landscape College, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Fang Li
- Horticulture & Landscape College, Hunan Agricultural University, Changsha, Hunan 410128, China; National Center for Citrus Improvement, Changsha, Hunan 410128, China
| | - Qin-Mei Ruan
- Horticulture & Landscape College, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Xiao-Hong Zhong
- Horticulture & Landscape College, Hunan Agricultural University, Changsha, Hunan 410128, China.
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Liu WJ, Lv HZ, He L, Song JY, Sun C, Luo HM, Chen SL. Cloning and Bioinformatic Analysis of HMGS and HMGR Genes from Panax notoginseng. CHINESE HERBAL MEDICINES 2016. [DOI: 10.1016/s1674-6384(16)60061-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Subtractive transcriptome analysis of leaf and rhizome reveals differentially expressed transcripts in Panax sokpayensis. Funct Integr Genomics 2016; 16:619-639. [PMID: 27586658 DOI: 10.1007/s10142-016-0517-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 07/16/2016] [Accepted: 07/19/2016] [Indexed: 01/01/2023]
Abstract
In the present study, suppression subtractive hybridization (SSH) strategy was used to identify rare and differentially expressed transcripts in leaf and rhizome tissues of Panax sokpayensis. Out of 1102 randomly picked clones, 513 and 374 high quality expressed sequenced tags (ESTs) were generated from leaf and rhizome subtractive libraries, respectively. Out of them, 64.92 % ESTs from leaf and 69.26 % ESTs from rhizome SSH libraries were assembled into different functional categories, while others were of unknown function. In particular, ESTs encoding galactinol synthase 2, ribosomal RNA processing Brix domain protein, and cell division cycle protein 20.1, which are involved in plant growth and development, were most abundant in the leaf SSH library. Other ESTs encoding protein KIAA0664 homologue, ubiquitin-activating enzyme e11, and major latex protein, which are involved in plant immunity and defense response, were most abundant in the rhizome SSH library. Subtractive ESTs also showed similarity with genes involved in ginsenoside biosynthetic pathway, namely farnesyl pyrophosphate synthase, squalene synthase, and dammarenediol synthase. Expression profiles of selected ESTs validated the quality of libraries and confirmed their differential expression in the leaf, stem, and rhizome tissues. In silico comparative analyses revealed that around 13.75 % of unigenes from the leaf SSH library were not represented in the available leaf transcriptome of Panax ginseng. Similarly, around 18.12, 23.75, 25, and 6.25 % of unigenes from the rhizome SSH library were not represented in available root/rhizome transcriptomes of P. ginseng, Panax notoginseng, Panax quinquefolius, and Panax vietnamensis, respectively, indicating a major fraction of novel ESTs. Therefore, these subtractive transcriptomes provide valuable resources for gene discovery in P. sokpayensis and would complement the available transcriptomes from other Panax species.
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Sharma S, Shrivastava N. Renaissance in phytomedicines: promising implications of NGS technologies. PLANTA 2016; 244:19-38. [PMID: 27002972 DOI: 10.1007/s00425-016-2492-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 02/19/2016] [Indexed: 06/05/2023]
Abstract
Medicinal plant research is growing significantly in faith to discover new and more biologically compatible phytomedicines. Deposition of huge genome/trancriptome sequence data assisted by NGS technologies has revealed the new possibilities for producing upgraded bioactive molecules in medicinal plants. Growing interest of investors and consumers in the herbal drugs raises the need for extensive research to open the facts and details of every inch of life canvas of medicinal plants to produce improved quality of phytomedicines. As in agriculture crops, knowledge emergence from medicinal plant's genome/transcriptome, can be used to assure their amended quality and these improved varieties are then transported to the fields for cultivation. Genome studies generate huge sequence data which can be exploited further for obtaining information regarding genes/gene clusters involved in biosynthesis as well as regulation. This can be achieved rapidly at a very large scale with NGS platforms. Identification of new RNA molecules has become possible, which can lead to the discovery of novel compounds. Sequence information can be combined with advanced phytochemical and bioinformatics tools to discover functional herbal drugs. Qualitative and quantitative analysis of small RNA species put a light on the regulatory aspect of biosynthetic pathways for phytomedicines. Inter or intra genomic as well as transcriptomic interactive processes for biosynthetic pathways can be elucidated in depth. Quality management of herbal material will also become rapid and high throughput. Enrichment of sequence information will be used to engineer the plants to get more efficient phytopharmaceuticals. The present review comprises of role of NGS technologies to boost genomic studies of pharmaceutically important plants and further, applications of sequence information aiming to produce enriched phytomedicines. Emerging knowledge from the medicinal plants genome/transcriptome can give birth to deep understanding of the processes responsible for biosynthesis of medicinally important compounds.
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Affiliation(s)
- Sonal Sharma
- B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Sarkhej - Gandhinagar Highway, Ahmedabad, Gujarat, India
- Nirma University, Ahmedabad, Gujarat, India
| | - Neeta Shrivastava
- B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Sarkhej - Gandhinagar Highway, Ahmedabad, Gujarat, India.
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Ma CH, Gao ZJ, Zhang JJ, Zhang W, Shao JH, Hai MR, Chen JW, Yang SC, Zhang GH. Candidate Genes Involved in the Biosynthesis of Triterpenoid Saponins in Platycodon grandiflorum Identified by Transcriptome Analysis. FRONTIERS IN PLANT SCIENCE 2016; 7:673. [PMID: 27242873 PMCID: PMC4871891 DOI: 10.3389/fpls.2016.00673] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/02/2016] [Indexed: 05/28/2023]
Abstract
BACKGROUND Platycodon grandiflorum is the only species in the genus Platycodon of the family Campanulaceae, which has been traditionally used as a medicinal plant for its lung-heat-clearing, antitussive, and expectorant properties in China, Japanese, and Korean. Oleanane-type triterpenoid saponins were the main chemical components of P. grandiflorum and platycodin D was the abundant and main bioactive component, but little is known about their biosynthesis in plants. Hence, P. grandiflorum is an ideal medicinal plant for studying the biosynthesis of Oleanane-type saponins. In addition, the genomic information of this important herbal plant is unavailable. PRINCIPAL FINDINGS A total of 58,580,566 clean reads were obtained, which were assembled into 34,053 unigenes, with an average length of 936 bp and N50 of 1,661 bp by analyzing the transcriptome data of P. grandiflorum. Among these 34,053 unigenes, 22,409 unigenes (65.80%) were annotated based on the information available from public databases, including Nr, NCBI, Swiss-Prot, KOG, and KEGG. Furthermore, 21 candidate cytochrome P450 genes and 17 candidate UDP-glycosyltransferase genes most likely involved in triterpenoid saponins biosynthesis pathway were discovered from the transcriptome sequencing of P. grandiflorum. In addition, 10,626 SSRs were identified based on the transcriptome data, which would provide abundant candidates of molecular markers for genetic diversity and genetic map for this medicinal plant. CONCLUSION The genomic data obtained from P. grandiflorum, especially the identification of putative genes involved in triterpenoid saponins biosynthesis pathway, will facilitate our understanding of the biosynthesis of triterpenoid saponins at molecular level.
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Affiliation(s)
- Chun-Hua Ma
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural UniversityKunming, China
| | - Zheng-Jie Gao
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural UniversityKunming, China
| | - Jia-Jin Zhang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural UniversityKunming, China
| | - Wei Zhang
- The Life Science and Technology College, Honghe UniversityMengzi, China
| | - Jian-Hui Shao
- National Engineering Research Center for Agricultural Biodiversity Applied Technology, Yunnan Agricultural UniversityKunming, China
| | - Mei-Rong Hai
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural UniversityKunming, China
| | - Jun-Wen Chen
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural UniversityKunming, China
| | - Sheng-Chao Yang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural UniversityKunming, China
| | - Guang-Hui Zhang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural UniversityKunming, China
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Gao Y, He X, Wu B, Long Q, Shao T, Wang Z, Wei J, Li Y, Ding W. Time-Course Transcriptome Analysis Reveals Resistance Genes of Panax ginseng Induced by Cylindrocarpon destructans Infection Using RNA-Seq. PLoS One 2016; 11:e0149408. [PMID: 26890788 PMCID: PMC4758610 DOI: 10.1371/journal.pone.0149408] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 02/01/2016] [Indexed: 11/18/2022] Open
Abstract
Panax ginseng C. A. Meyer is a highly valued medicinal plant. Cylindrocarpon destructans is a destructive pathogen that causes root rot and significantly reduces the quality and yield of P. ginseng. However, an efficient method to control root rot remains unavailable because of insufficient understanding of the molecular mechanism underlying C. destructans-P. ginseng interaction. In this study, C. destructans-induced transcriptomes at different time points were investigated using RNA sequencing (RNA-Seq). De novo assembly produced 73,335 unigenes for the P. ginseng transcriptome after C. destructans infection, in which 3,839 unigenes were up-regulated. Notably, the abundance of the up-regulated unigenes sharply increased at 0.5 d postinoculation to provide effector-triggered immunity. In total, 24 of 26 randomly selected unigenes can be validated using quantitative reverse transcription (qRT)-PCR. Gene ontology enrichment analysis of these unigenes showed that “defense response to fungus”, “defense response” and “response to stress” were enriched. In addition, differentially expressed transcription factors involved in the hormone signaling pathways after C. destructans infection were identified. Finally, differentially expressed unigenes involved in reactive oxygen species and ginsenoside biosynthetic pathway during C. destructans infection were indentified. To our knowledge, this study is the first to report on the dynamic transcriptome triggered by C. destructans. These results improve our understanding of disease resistance in P. ginseng and provide a useful resource for quick detection of induced markers in P. ginseng before the comprehensive outbreak of this disease caused by C. destructans.
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Affiliation(s)
- Yuan Gao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoli He
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bin Wu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qiliang Long
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tianwei Shao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zi Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianhe Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yong Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wanlong Ding
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Zhao YM, Zhou T, Li ZH, Zhao GF. Characterization of Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers in Two Species of Gynostemma (Cucurbitaceae). Molecules 2015; 20:21214-31. [PMID: 26633323 PMCID: PMC6332360 DOI: 10.3390/molecules201219758] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 11/05/2015] [Accepted: 11/09/2015] [Indexed: 01/16/2023] Open
Abstract
Gynostemma pentaphyllum is an important medicinal herb of the Cucurbitaceae family, but limited genomic data have hindered genetic studies. In this study, transcriptomes of two closely-related Gynostemma species, Gynostemma cardiospermum and G. pentaphyllum, were sequenced using Illumina paired-end sequencing technology. A total of 71,607 nonredundant unigenes were assembled. Of these unigenes, 60.45% (43,288) were annotated based on sequence similarity search with known proteins. A total of 11,059 unigenes were identified in the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) database. A total of 3891 simple sequence repeats (SSRs) were detected in 3526 nonredundant unigenes, 2596 primer pairs were designed and 360 of them were randomly selected for validation. Of these, 268 primer pairs yielded clear products among six G. pentaphyllum samples. Thirty polymorphic SSR markers were used to test polymorphism and transferability in Gynostemma. Finally, 15 SSR makers that amplified in all 12 Gynostemma species were used to assess genetic diversity. Our results generated a comprehensive sequence resource for Gynostemma research.
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Affiliation(s)
- Yue-Mei Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China.
- College of Biopharmaceutical and Food Engineering, Shangluo University, Beixin Street, Shangluo 726000, China.
| | - Tao Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China.
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China.
| | - Gui-Fang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China.
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Wu B, Long Q, Gao Y, Wang Z, Shao T, Liu Y, Li Y, Ding W. Comprehensive characterization of a time-course transcriptional response induced by autotoxins in Panax ginseng using RNA-Seq. BMC Genomics 2015; 16:1010. [PMID: 26608743 PMCID: PMC4659204 DOI: 10.1186/s12864-015-2151-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 10/27/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As a valuable medicinal plant, the yield of Panax ginseng is seriously affected by autotoxicity, which is a common phenomenon due to continuous cropping. However, the mechanism of autotoxicity in P. ginseng is still unknown. RESULTS In total, high throughput sequencing of 18 RNA-Seq libraries produced 996,000,000 100-nt reads that were assembled into 72,732 contigs. Compared with control, 3697 and 2828 genes were significantly up- and down-regulated across different tissues and time points, respectively. Gene Ontology enrichment analysis showed that 'enzyme inhibitor activity', 'carboxylesterase activity', 'pectinesterase activity', 'centrosome cycle and duplication' and 'mitotic spindle elongation' were enriched for the up-regulated genes. Transcription factors including AP2s/ERFs, MYBs, and WRKYs were up-regulated in roots after benzoic acid treatment. Moreover, reactive oxygen species, peroxidases and superoxide dismutase contigs were up-regulated in roots after benzoic acid treatment. Physiological and biochemical indexes showed that the proline and malondialdehyde content were restored to lower levels at a later stage after benzoic acid treatment. Benzoic acid inhibited the root hair development in a dose-dependent manner, and several differential expressed genes potentially involved in hair development were identified. Several key contigs in the flavonoid and ginsenoside biosynthesis pathways were repressed. Finally, 58,518 alternative splicing (AS) events from 12,950 genes were found after benzoic acid treatment. Interestingly, contigs in the ginsenoside biosynthetic pathway underwent AS, providing useful information about post-transcriptional regulation in P. ginseng. CONCLUSIONS This study revealed the stress-response molecular mechanisms in P. ginseng induced by benzoic acid.
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Affiliation(s)
- Bin Wu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Qiliang Long
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Yuan Gao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Zi Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Tianwei Shao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Yanan Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Yong Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Wanlong Ding
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
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Zhen G, Zhang L, Du Y, Yu R, Liu X, Cao F, Chang Q, Deng X, Xia M, He H. De novo assembly and comparative analysis of root transcriptomes from different varieties of Panax ginseng C. A. Meyer grown in different environments. SCIENCE CHINA-LIFE SCIENCES 2015; 58:1099-110. [PMID: 26563176 DOI: 10.1007/s11427-015-4961-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 06/16/2013] [Indexed: 12/22/2022]
Abstract
Panax ginseng C. A. Meyer is an important traditional herb in eastern Asia. It contains ginsenosides, which are primary bioactive compounds with medicinal properties. Although ginseng has been cultivated since at least the Ming dynasty to increase production, cultivated ginseng has lower quantities of ginsenosides and lower disease resistance than ginseng grown under natural conditions. We extracted root RNA from six varieties of fifth-year P. ginseng cultivars representing four different growth conditions, and performed Illumina paired-end sequencing. In total, 163,165,706 raw reads were obtained and used to generate a de novo transcriptome that consisted of 151,763 contigs (76,336 unigenes), of which 100,648 contigs (66.3%) were successfully annotated. Differential expression analysis revealed that most differentially expressed genes (DEGs) were upregulated (246 out of 258, 95.3%) in ginseng grown under natural conditions compared with that grown under artificial conditions. These DEGs were enriched in gene ontology (GO) terms including response to stimuli and localization. In particular, some key ginsenoside biosynthesis-related genes, including HMG-CoA synthase (HMGS), mevalonate kinase (MVK), and squalene epoxidase (SE), were upregulated in wild-grown ginseng. Moreover, a high proportion of disease resistance-related genes were upregulated in wild-grown ginseng. This study is the first transcriptome analysis to compare wild-grown and cultivated ginseng, and identifies genes that may produce higher ginsenoside content and better disease resistance in the wild; these genes may have the potential to improve cultivated ginseng grown in artificial environments.
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Affiliation(s)
- Gang Zhen
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China
- School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Lei Zhang
- Frontier Laboratories of Systems Crop Design Co., Ltd., Beijing, 100085, China
| | - YaNan Du
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China
- School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - RenBo Yu
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China
- School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - XinMin Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - FangRui Cao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Qi Chang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - XingWang Deng
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China.
- School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China.
| | - Mian Xia
- Frontier Laboratories of Systems Crop Design Co., Ltd., Beijing, 100085, China.
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China.
- School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China.
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67
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Wei R, Qiu D, Wilson IW, Zhao H, Lu S, Miao J, Feng S, Bai L, Wu Q, Tu D, Ma X, Tang Q. Identification of novel and conserved microRNAs in Panax notoginseng roots by high-throughput sequencing. BMC Genomics 2015; 16:835. [PMID: 26490136 PMCID: PMC4618736 DOI: 10.1186/s12864-015-2010-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 10/03/2015] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are small, non-coding RNAs that are important regulators of gene expression, and play major roles in plant development and their response to the environment. Root extracts from Panax notoginseng contain triterpene saponins as their principal bioactive constituent, and demonstrate medicinal properties. To investigate the novel and conserved miRNAs in P. notoginseng, three small RNA libraries constructed from 1-, 2-, and 3-year-old roots in which root saponin levels vary underwent high-throughput sequencing. METHODS P. notoginseng roots, purified from 1-, 2-, and 3-year-old roots, were extracted for RNA, respectively. Three small libraries were constructed and subjected to next generation sequencing. RESULTS Sequencing of the three libraries generated 67,217,124 clean reads from P. notoginseng roots. A total of 316 conserved miRNAs (belonging to 67 miRNA families and one unclassified family) and 52 novel miRNAs were identified. MIR156 and MIR166 were the largest miRNA families, while miR156i and miR156g showed the highest abundance of miRNA species. Potential miRNA target genes were predicted and annotated using Cluster of Orthologous Groups, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes. Comparing these miRNAs between root samples revealed 33 that were differentially expressed between 2- and 1-year-old roots (8 increased, 25 decreased), 27 differentially expressed between 3- and 1-year-old roots (7 increased, 20 decreased), and 29 differentially expressed between 3- and 2-year-old roots (8 increased, 21 decreased). Two significantly differentially expressed miRNAs and four miRNAs predicted to target genes involved in the terpenoid backbone biosynthesis pathway were selected and validated by quantitative reverse transcription PCR. Furthermore, the expression patterns of these six miRNAs were analyzed in P. notoginseng roots, stems, and leaves at different developmental stages. CONCLUSIONS This study identified a large number of P. notoginseng miRNAs and their target genes, functional annotations, and gene expression patterns. It provides the first known miRNA profiles of the P. notoginseng root development cycle.
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Affiliation(s)
- Rongchang Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China. .,Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China.
| | - Deyou Qiu
- Department of Molecular Biology, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
| | - Iain W Wilson
- CSIRO Agriculture, PO Box 1600, Canberra, ACT 2001, Australia.
| | - Huan Zhao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
| | - Jianhua Miao
- Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China.
| | - Shixin Feng
- Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China.
| | - Longhua Bai
- Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China.
| | - Qinghua Wu
- Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China.
| | - Dongping Tu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
| | - Xiaojun Ma
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
| | - Qi Tang
- Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China. .,Hunan Provincial Key Laboratory of Crop Germplasm innovation and Utilization and National Chinese Medicinal Herbs (Hunan) Technology Center, Hunan Agricultural University, Changsha, 410128, China.
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Analysis of Polygala tenuifolia Transcriptome and Description of Secondary Metabolite Biosynthetic Pathways by Illumina Sequencing. Int J Genomics 2015; 2015:782635. [PMID: 26543847 PMCID: PMC4620389 DOI: 10.1155/2015/782635] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/03/2015] [Indexed: 12/29/2022] Open
Abstract
Radix polygalae, the dried roots of Polygala tenuifolia and P. sibirica, is one of the most well-known traditional Chinese medicinal plants. Radix polygalae contains various saponins, xanthones, and oligosaccharide esters and these compounds are responsible for several pharmacological properties. To provide basic breeding information, enhance molecular biological analysis, and determine secondary metabolite biosynthetic pathways of P. tenuifolia, we applied Illumina sequencing technology and de novo assembly. We also applied this technique to gain an overview of P. tenuifolia transcriptome from samples with different years. Using Illumina sequencing, approximately 67.2% of unique sequences were annotated by basic local alignment search tool similarity searches against public sequence databases. We classified the annotated unigenes by using Nr, Nt, GO, COG, and KEGG databases compared with NCBI. We also obtained many candidates CYP450s and UGTs by the analysis of genes in the secondary metabolite biosynthetic pathways, including putative terpenoid backbone and phenylpropanoid biosynthesis pathway. With this transcriptome sequencing, future genetic and genomics studies related to the molecular mechanisms associated with the chemical composition of P. tenuifolia may be improved. Genes involved in the enrichment of secondary metabolite biosynthesis-related pathways could enhance the potential applications of P. tenuifolia in pharmaceutical industries.
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69
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Zhang S, Wu Y, Jin J, Hu B, Zeng W, Zhu W, Zheng Y, Chen P. De novo characterization of Panax japonicus C. A. Mey transcriptome and genes related to triterpenoid saponin biosynthesis. Biochem Biophys Res Commun 2015; 466:450-5. [PMID: 26365354 DOI: 10.1016/j.bbrc.2015.09.048] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 09/08/2015] [Indexed: 11/26/2022]
Abstract
Panax japonicus C.A.Mey, the traditional medicinal herb in the Araliaceae family, has been used as a tonic, anti-inflammatory and haemostatic agent in China for more than thousand years. Its clinical effects are mainly due to the presence of triterpenoid saponins. However, little is known at the genetic level about how saponins are biosynthesized in this plant. We have therefore performed the de novo transcriptome assembly and high throughput RNA-seq analysis for P. japonicus. 66,403 unigenes were assembled from 19.6 Gbp raw data, and 34,639 unigenes were annotated. After annotation, 29 unigenes involved in putative backbone biosynthesis of triterpenoid saponin were selected. Additionally, 34 Cytochrome P450 and 18 UDP-glycosyltransferase unigenes were predicted based on the annotation, which were related to the saponin backbone modification. The expression level of related key genes were further verified by qPCR analysis. The results of this study provide the most comprehensive expressed sequence resources for P. japonicus, which will enlarge the available P. japonicus gene pool and facilitate further genome-wide research and analyses in this species.
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Affiliation(s)
- Shaopeng Zhang
- School of Biology & Pharmacy Engineering, Wuhan Polytechnic University, Wuhan, 430023, PR China
| | - Yayun Wu
- School of Biology & Pharmacy Engineering, Wuhan Polytechnic University, Wuhan, 430023, PR China
| | - Jian Jin
- School of Biology & Pharmacy Engineering, Wuhan Polytechnic University, Wuhan, 430023, PR China
| | - Bingxiong Hu
- School of Biology & Pharmacy Engineering, Wuhan Polytechnic University, Wuhan, 430023, PR China
| | - Wanyong Zeng
- School of Biology & Pharmacy Engineering, Wuhan Polytechnic University, Wuhan, 430023, PR China
| | - Wenjun Zhu
- School of Biology & Pharmacy Engineering, Wuhan Polytechnic University, Wuhan, 430023, PR China
| | - Yonglian Zheng
- School of Biology & Pharmacy Engineering, Wuhan Polytechnic University, Wuhan, 430023, PR China.
| | - Ping Chen
- School of Biology & Pharmacy Engineering, Wuhan Polytechnic University, Wuhan, 430023, PR China.
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70
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De novo sequencing transcriptome of endemic Gentiana straminea (Gentianaceae) to identify genes involved in the biosynthesis of active ingredients. Gene 2015; 575:160-70. [PMID: 26358503 DOI: 10.1016/j.gene.2015.08.055] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Revised: 08/13/2015] [Accepted: 08/26/2015] [Indexed: 11/24/2022]
Abstract
Gentiana straminea is a popular Tibetan medicine that has been used for thousands of years in China to treat various diseases and conditions. Although it has multiple pharmaceutical purposes and important economic plant resource in China, transcriptome and molecular base still known limited. In flowering season, samples were collected from different tissues, using the NGS Illumina. Solexa platform, about 58.85 million sequencing reads were generated and assembled de novo, yielding 78,764 high quality unigenes with an average length of 1090bp. Gene Ontology (GO), KEGG pathway mapping showed that 49,033 of these were identified as putative homologs of annotated sequences in the protein databases. Among them, candidate genes associated with iridoid, flavonoid and anthocyanin were identified. Further the key enzymes involved to iridoid and flavonoid synthesis pathway were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR) on different tissues, the flower and root had the higher expression than leaves. In addition, 7591 SSR markers were identified from the unigenes of the G. straminea transcriptome. The foundation of G. straminea provided the important resource for facilitating to study molecular and functional genomics of it and related this species on the Qinghai-Tibet Plateau.
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71
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Wei W, Wang P, Wei Y, Liu Q, Yang C, Zhao G, Yue J, Yan X, Zhou Z. Characterization of Panax ginseng UDP-Glycosyltransferases Catalyzing Protopanaxatriol and Biosyntheses of Bioactive Ginsenosides F1 and Rh1 in Metabolically Engineered Yeasts. MOLECULAR PLANT 2015; 8:1412-24. [PMID: 26032089 DOI: 10.1016/j.molp.2015.05.010] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 05/22/2015] [Accepted: 05/24/2015] [Indexed: 05/27/2023]
Abstract
Ginsenosides, the main pharmacologically active natural compounds in ginseng (Panax ginseng), are mostly the glycosylated products of protopanaxadiol (PPD) and protopanaxatriol (PPT). No uridine diphosphate glycosyltransferase (UGT), which catalyzes PPT to produce PPT-type ginsenosides, has yet been reported. Here, we show that UGTPg1, which has been demonstrated to regio-specifically glycosylate the C20-OH of PPD, also specifically glycosylates the C20-OH of PPT to produce bioactive ginsenoside F1. We report the characterization of four novel UGT genes isolated from P. ginseng, sharing high deduced amino acid identity (>84%) with UGTPg1. We demonstrate that UGTPg100 specifically glycosylates the C6-OH of PPT to produce bioactive ginsenoside Rh1, and UGTPg101 catalyzes PPT to produce F1, followed by the generation of ginsenoside Rg1 from F1. However, UGTPg102 and UGTPg103 were found to have no detectable activity on PPT. Through structural modeling and site-directed mutagenesis, we identified several key amino acids of these UGTs that may play important roles in determining their activities and substrate regio-specificities. Moreover, we constructed yeast recombinants to biosynthesize F1 and Rh1 by introducing the genetically engineered PPT-producing pathway and UGTPg1 or UGTPg100. Our study reveals the possible biosynthetic pathways of PPT-type ginsenosides in Panax plants, and provides a sound manufacturing approach for bioactive PPT-type ginsenosides in yeast via synthetic biology strategies.
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Affiliation(s)
- Wei Wei
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Pingping Wang
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yongjun Wei
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qunfang Liu
- State Key Laboratory of Drug Research, Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, China
| | - Chengshuai Yang
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Guoping Zhao
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jianmin Yue
- State Key Laboratory of Drug Research, Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Xing Yan
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Zhihua Zhou
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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Jayakodi M, Lee SC, Lee YS, Park HS, Kim NH, Jang W, Lee HO, Joh HJ, Yang TJ. Comprehensive analysis of Panax ginseng root transcriptomes. BMC PLANT BIOLOGY 2015; 15:138. [PMID: 26063328 PMCID: PMC4464628 DOI: 10.1186/s12870-015-0527-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/20/2015] [Indexed: 05/21/2023]
Abstract
BACKGROUND Korean ginseng (Panax ginseng C.A. Meyer) is a highly effective medicinal plant containing ginsenosides with various pharmacological activities, whose roots are produced commercially for crude drugs. RESULTS Here, we used the Illumina platform to generate over 232 million RNA sequencing reads from four root samples, including whole roots from one-year-old plants and three types of root tissue from six-year-old plants (i.e., main root bodies, rhizomes, and lateral roots). Through de novo assembly and reference-assisted selection, we obtained a non-redundant unigene set consisting of 55,949 transcripts with an average length of 1,250 bp. Among transcripts in the unigene set, 94 % were functionally annotated via similarity searches against protein databases. Approximately 28.6 % of the transcripts represent novel gene sequences that have not previously been reported for P. ginseng. Digital expression profiling revealed 364 genes showing differential expression patterns among the four root samples. Additionally, 32 were uniquely expressed in one-year-old roots, while seven were uniquely expressed in six-year-old root tissues. We identified 38 transcripts encoding enzymes involved in ginsenoside biosynthesis pathways and 189 encoding UDP-glycosyltransferases. CONCLUSION Our analysis provides new insights into the role of the root transcriptome in development and secondary metabolite biosynthesis in P. ginseng.
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Affiliation(s)
- Murukarthick Jayakodi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Sang-Choon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Yun Sun Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Hyun-Seung Park
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Nam-Hoon Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Woojong Jang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Hyun Oh Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Ho Jun Joh
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, 232-916, Republic of Korea.
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Chen J, Wu XT, Xu YQ, Zhong Y, Li YX, Chen JK, Li X, Nan P. Global transcriptome analysis profiles metabolic pathways in traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao. BMC Genomics 2015; 16 Suppl 7:S15. [PMID: 26099797 PMCID: PMC4474414 DOI: 10.1186/1471-2164-16-s7-s15] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao (A. mongolicus, family Leguminosae) is one of the most important traditional Chinese herbs. Among many secondary metabolites it produces, the effective bioactive constituents include isoflavonoids and triterpene saponins. The genomic resources regarding the biosynthesis of these metabolites in A. mongolicus are limited. Although roots are the primary material harvested for medical use, the biosynthesis of the bioactive compounds and its regulation in A. mongolicus are not well understood. Therefore, a global transcriptome analysis on A. mongolicus tissues was performed to identify the genes essential for the metabolism and to profile their expression patterns in greater details. RESULTS RNA-sequencing was performed for three different A. mongolicus tissues: leaf, stem, and root, using the Illumina Hiseq2000 platform. A total of 159.5 million raw sequence reads were generated, and assembled into 186,324 unigenes with an N50 of 1,524bp. Among them, 129,966 unigenes (~69.7%) were annotated using four public databases (Swiss-Prot, TrEMBL, CDD, Pfam), and 90,202, 63,946, and 78,326 unigenes were found to express in leaves, roots, and stems, respectively. A total of 8,025 transcription factors (TFs) were identified, in which the four largest families, bHLH, MYB, C3H, and WRKY, were implicated in regulation of tissue development, metabolisms, stress response, etc. Unigenes associated with secondary metabolism, especially those with isolavonoids and triterpene saponins biosynthesis were characterized and profiled. Most genes involved in the isoflavonoids biosynthesis had the lowest expression in the leaves, and the highest in the stems. For triterpene saponin biosynthesis, we found the genes in MVA and non-MVA pathways were differentially expressed among three examined tissues, indicating the parallel but compartmentally separated biosynthesis pathways of IPP and DMAPP in A. mongolicus. The first committed enzyme in triterpene saponin biosynthesis from A. mongolicus, cycloartenol synthase (AmCAS), which belongs to the oxidosqualene cyclase family, was cloned by us to study the astragalosides biosynthesis. Further co-expression analysis indicated the candidate CYP450s and glycosyltransferases (GTs) in the cascade of triterpene saponins biosynthesis. The presence of the large CYP450 families in A. mongolicus was further compared with those from Medicago truncatula and Arabidopsis thaliana, and the diversity and phylegenetic relationships of the CYP450 families were established. CONCLUSION A transcriptome study was performed for A. mongolicus tissues to construct and profile their metabolic pathways, especially for the important bioactive molecules. The results revealed a comprehensive profile for metabolic activities among tissues, pointing to the equal importance of leaf, stem, and root in A. mongolicus for the production of bioactive compounds. This work provides valuable resources for bioengineering and in vitro synthesis of the natural compounds for medical research and for potential drug development.
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Affiliation(s)
- Jing Chen
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xue-Ting Wu
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yi-Qin Xu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yang Zhong
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
- Institute of Biodiversity Science and Geobiology, Tibet University, Lhasa 850000, China
| | - Yi-Xue Li
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai 201203, China
| | - Jia-Kuan Chen
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Peng Nan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
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Chen JJ, Wang Y. Microsatellite Development and Potential Application in Authentication, Conservation, and Genetic Improvement of Chinese Medicinal Plants. CHINESE HERBAL MEDICINES 2015. [DOI: 10.1016/s1674-6384(15)60029-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Liu MH, Yang BR, Cheung WF, Yang KY, Zhou HF, Kwok JSL, Liu GC, Li XF, Zhong S, Lee SMY, Tsui SKW. Transcriptome analysis of leaves, roots and flowers of Panax notoginseng identifies genes involved in ginsenoside and alkaloid biosynthesis. BMC Genomics 2015; 16:265. [PMID: 25886736 PMCID: PMC4399409 DOI: 10.1186/s12864-015-1477-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 03/23/2015] [Indexed: 11/10/2022] Open
Abstract
Background Panax notoginseng (Burk.) F.H. Chen is one of the most highly valued medicinal plants in the world. The major bioactive molecules are triterpene saponins, which are also known as ginsenosides. However, its large genome size has hindered the assembly of a draft genome by whole genome sequencing. Hence, genomic and transcriptomic details about P. notoginseng, especially its biosynthetic pathways and gene expression in different parts of the plant, have remained largely unknown until now. Results In this study, RNA sequencing of three different P. notoginseng tissues was performed using next generation DNA sequencing. After assembling the high quality sequencing reads into 107,340 unigenes, biochemical pathways were predicted and 9,908 unigenes were assigned to 135 KEGG pathways. Among them, 270 unigenes were identified to be involved in triterpene saponin biosynthesis. In addition, 350 and 342 unigenes were predicted to encode cytochrome P450s and glycosyltransferases, respectively, based on the annotation results, some of which encode enzymes responsible for the conversion of the triterpene saponin backbone into different ginsenosides. In particular, one unigene predominately expressed in the root was annotated as CYP716A53v2, which probably participates in the formation of protopanaxatriol from protopanaxadiol in P. notoginseng. The differential expression of this gene was further confirmed by real-time PCR. Conclusions We have established a global transcriptome dataset for P. notoginseng and provided additional genetic information for further genome-wide research and analyses. Candidate genes involved in ginsenoside biosynthesis, including putative cytochrome P450s and glycosyltransferases were obtained. The transcriptomes in different plant tissues also provide invaluable resources for future study of the differences in physiological processes and secondary metabolites in different parts of P. notoginseng. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1477-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ming-Hua Liu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Bin-Rui Yang
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China.
| | - Wai-Fung Cheung
- Beijing Genomics Institute - Shenzhen, Shenzhen, 518083, China. .,Present correspondence: Groken Bioscience, Hong Kong, China.
| | - Kevin Yi Yang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China. .,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China.
| | - He-Feng Zhou
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China.
| | - Jamie Sui-Lam Kwok
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Guo-Cheng Liu
- Beijing Genomics Institute - Shenzhen, Shenzhen, 518083, China.
| | - Xiao-Feng Li
- Beijing Genomics Institute - Shenzhen, Shenzhen, 518083, China.
| | - Silin Zhong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China.
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China. .,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China.
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Zhang GH, Ma CH, Zhang JJ, Chen JW, Tang QY, He MH, Xu XZ, Jiang NH, Yang SC. Transcriptome analysis of Panax vietnamensis var. fuscidicus discovers putative ocotillol-type ginsenosides biosynthesis genes and genetic markers. BMC Genomics 2015; 16:159. [PMID: 25765814 PMCID: PMC4355973 DOI: 10.1186/s12864-015-1332-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 02/09/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND P. vietnamensis var. fuscidiscus, called "Yesanqi" in Chinese, is a new variety of P. vietnamensis, which was first found in Jinping County, the southern part of Yunnan Province, China. Compared with other Panax plants, this species contains higher content of ocotillol-type saponin, majonoside R2. Despite the pharmacological importance of ocotillol-type saponins, little is known about their biosynthesis in plants. Hence, P. vietnamensis var. fuscidiscus is a suitable medicinal herbal plant species to study biosynthesis of ocotillol-type saponins. In addition, the available genomic information of this important herbal plant is lacking. RESULTS To investigate the P. vietnamensis var. fuscidiscus transcriptome, Illumina HiSeq™ 2000 sequencing platform was employed. We produced 114,703,210 clean reads, assembled into 126,758 unigenes, with an average length of 1,304 bp and N50 of 2,108 bp. Among these 126,758 unigenes, 85,214 unigenes (67.23%) were annotated based on the information available from the public databases. The transcripts encoding the known enzymes involved in triterpenoid saponins biosynthesis were identified in our Illumina dataset. A full-length cDNA of three Squalene epoxidase (SE) genes were obtained using reverse transcription PCR (RT-PCR) and the expression patterns of ten unigenes were analyzed by reverse transcription quantitative real-time PCR (RT-qPCR). Furthermore, 15 candidate cytochrome P450 genes and 17 candidate UDP-glycosyltransferase genes most likely to involve in triterpenoid saponins biosynthesis pathway were discovered from transcriptome sequencing of P. vietnamensis var. fuscidiscus. We further analyzed the data and found 21,320 simple sequence repeats (SSRs), 30 primer pairs for SSRs were randomly selected for validation of the amplification and polymorphism in 13 P. vietnamensis var. fuscidiscus accessions. Meanwhile, five major triterpene saponins in roots of P. vietnamensis var. fuscidicus were determined using high performance liquid chromatography (HPLC) and evaporative light scattering detector (ELSD). CONCLUSIONS The genomic resources generated from P. vietnamensis var. fuscidiscus provide new insights into the identification of putative genes involved in triterpenoid saponins biosynthesis pathway. This will facilitate our understanding of the biosynthesis of triterpenoid saponins at molecular level. The SSR markers identified and developed in this study show genetic diversity for this important crop and will contribute to marker-assisted breeding for P. vietnamensis var. fuscidiscus.
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Affiliation(s)
- Guang-Hui Zhang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China.
| | - Chun-Hua Ma
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China.
| | - Jia-Jin Zhang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China.
| | - Jun-Wen Chen
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China.
| | - Qing-Yan Tang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China.
| | - Mu-Han He
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China.
| | - Xiang-Zeng Xu
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China.
| | - Ni-Hao Jiang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China.
| | - Sheng-Chao Yang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China.
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Kim YJ, Zhang D, Yang DC. Biosynthesis and biotechnological production of ginsenosides. Biotechnol Adv 2015; 33:717-35. [PMID: 25747290 DOI: 10.1016/j.biotechadv.2015.03.001] [Citation(s) in RCA: 205] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 02/28/2015] [Accepted: 03/01/2015] [Indexed: 12/20/2022]
Abstract
Medicinal plants are essential for improving human health, and around 75% of the population in developing countries relies mainly on herb-based medicines for health care. As the king of herb plants, ginseng has been used for nearly 5,000 years in the oriental and recently in western medicines. Among the compounds studied in ginseng plants, ginsenosides have been shown to have multiple medical effects such as anti-oxidative, anti-aging, anti-cancer, adaptogenic and other health-improving activities. Ginsenosides belong to a group of triterpene saponins (also called ginseng saponins) that are found almost exclusively in Panax species and accumulated especially in the plant roots. In this review, we update the conserved and diversified pathway/enzyme biosynthesizing ginsenosides which have been presented. Particularly, we highlight recent milestone works on functional characterization of key genes dedicated to the production of ginsenosides, and their application in engineering plants and yeast cells for large-scale production of ginsenosides.
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Affiliation(s)
- Yu-Jin Kim
- Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Department of Oriental Medicinal Biotechnology and Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Youngin, 446-701, South Korea
| | - Dabing Zhang
- Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia.
| | - Deok-Chun Yang
- Department of Oriental Medicinal Biotechnology and Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Youngin, 446-701, South Korea.
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Cao H, Nuruzzaman M, Xiu H, Huang J, Wu K, Chen X, Li J, Wang L, Jeong JH, Park SJ, Yang F, Luo J, Luo Z. Transcriptome analysis of methyl jasmonate-elicited Panax ginseng adventitious roots to discover putative ginsenoside biosynthesis and transport genes. Int J Mol Sci 2015; 16:3035-57. [PMID: 25642758 PMCID: PMC4346879 DOI: 10.3390/ijms16023035] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 01/22/2015] [Indexed: 12/05/2022] Open
Abstract
The Panax ginseng C.A. Meyer belonging to the Araliaceae has long been used as an herbal medicine. Although public databases are presently available for this family, no methyl jasmonate (MeJA) elicited transcriptomic information was previously reported on this species, with the exception of a few expressed sequence tags (ESTs) using the traditional Sanger method. Here, approximately 53 million clean reads of adventitious root transcriptome were separately filtered via Illumina HiSeq™2000 from two samples treated with MeJA (Pg-MeJA) and equal volumes of solvent, ethanol (Pg-Con). Jointly, a total of 71,095 all-unigenes from both samples were assembled and annotated, and based on sequence similarity search with known proteins, a total of 56,668 unigenes was obtained. Out of these annotated unigenes, 54,920 were assigned to the NCBI non-redundant protein (Nr) database, 35,448 to the Swiss-prot database, 43,051 to gene ontology (GO), and 19,986 to clusters of orthologous groups (COG). Searching in the Kyoto encyclopedia of genes and genomes (KEGG) pathway database indicated that 32,200 unigenes were mapped to 128 KEGG pathways. Moreover, we obtained several genes showing a wide range of expression levels. We also identified a total of 749 ginsenoside biosynthetic enzyme genes and 12 promising pleiotropic drug resistance (PDR) genes related to ginsenoside transport.
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Affiliation(s)
- Hongzhe Cao
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Mohammed Nuruzzaman
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Hao Xiu
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Jingjia Huang
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Kunlu Wu
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Xianghui Chen
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Jijia Li
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Li Wang
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Ji-Hak Jeong
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Sun-Jin Park
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Fang Yang
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Junli Luo
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Zhiyong Luo
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
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Senthil K, Jayakodi M, Thirugnanasambantham P, Lee SC, Duraisamy P, Purushotham PM, Rajasekaran K, Nancy Charles S, Mariam Roy I, Nagappan AK, Kim GS, Lee YS, Natesan S, Min TS, Yang TJ. Transcriptome analysis reveals in vitro cultured Withania somnifera leaf and root tissues as a promising source for targeted withanolide biosynthesis. BMC Genomics 2015; 16:14. [PMID: 25608483 PMCID: PMC4310147 DOI: 10.1186/s12864-015-1214-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 01/02/2015] [Indexed: 12/19/2022] Open
Abstract
Background The production of metabolites via in vitro culture is promoted by the availability of fully defined metabolic pathways. Withanolides, the major bioactive phytochemicals of Withania somnifera, have been well studied for their pharmacological activities. However, only a few attempts have been made to identify key candidate genes involved in withanolide biosynthesis. Understanding the steps involved in withanolide biosynthesis is essential for metabolic engineering of this plant to increase withanolide production. Results Transcriptome sequencing was performed on in vitro adventitious root and leaf tissues using the Illumina platform. We obtained a total of 177,156 assembled transcripts with an average unigene length of 1,033 bp. About 13% of the transcripts were unique to in vitro adventitious roots but no unique transcripts were observed in in vitro-grown leaves. A putative withanolide biosynthetic pathway was deduced by mapping the assembled transcripts to the KEGG database, and the expression of candidate withanolide biosynthesis genes -were validated by qRT PCR. The accumulation pattern of withaferin A and withanolide A varied according to the type of tissue and the culture period. Further, we demonstrated that in vitro leaf extracts exhibit anticancer activity against human gastric adenocarcinoma cell lines at sub G1 phase. Conclusions We report here a validated large-scale transcriptome data set and the potential biological activity of in vitro cultures of W. somnifera. This study provides important information to enhance tissue-specific expression and accumulation of secondary metabolites, paving the way for industrialization of in vitro cultures of W. somnifera. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1214-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kalaiselvi Senthil
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, 641043, India.
| | - Murukarthick Jayakodi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Pankajavalli Thirugnanasambantham
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, 641043, India.
| | - Sang Choon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Pradeepa Duraisamy
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, 641043, India.
| | - Preethi M Purushotham
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, 641043, India.
| | - Kalaiselvi Rajasekaran
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, 641043, India.
| | - Shobana Nancy Charles
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, 641043, India.
| | - Irene Mariam Roy
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, 641043, India.
| | - Arul Kumar Nagappan
- Lab of Biochemistry, School of Veterinary Medicine, Gyeongsang National University, Gyeongsangnam-do, Republic of Korea.
| | - Gon Sup Kim
- Lab of Biochemistry, School of Veterinary Medicine, Gyeongsang National University, Gyeongsangnam-do, Republic of Korea.
| | - Yun Sun Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Senthil Natesan
- Genomics and Proteomics Laboratory, Centre for Plant Molecular Biology & Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, Tamil Nadu, India.
| | - Tae-Sun Min
- National Research Foundation, Seoul, Republic of Korea.
| | - Tae Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
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Unamba CIN, Nag A, Sharma RK. Next Generation Sequencing Technologies: The Doorway to the Unexplored Genomics of Non-Model Plants. FRONTIERS IN PLANT SCIENCE 2015; 6:1074. [PMID: 26734016 PMCID: PMC4679907 DOI: 10.3389/fpls.2015.01074] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/16/2015] [Indexed: 05/04/2023]
Abstract
Non-model plants i.e., the species which have one or all of the characters such as long life cycle, difficulty to grow in the laboratory or poor fecundity, have been schemed out of sequencing projects earlier, due to high running cost of Sanger sequencing. Consequently, the information about their genomics and key biological processes are inadequate. However, the advent of fast and cost effective next generation sequencing (NGS) platforms in the recent past has enabled the unearthing of certain characteristic gene structures unique to these species. It has also aided in gaining insight about mechanisms underlying processes of gene expression and secondary metabolism as well as facilitated development of genomic resources for diversity characterization, evolutionary analysis and marker assisted breeding even without prior availability of genomic sequence information. In this review we explore how different Next Gen Sequencing platforms, as well as recent advances in NGS based high throughput genotyping technologies are rewarding efforts on de-novo whole genome/transcriptome sequencing, development of genome wide sequence based markers resources for improvement of non-model crops that are less costly than phenotyping.
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Affiliation(s)
- Chibuikem I. N. Unamba
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource TechnologyPalampur, India
- Department of Plant Science and Biotechnology, Imo State UniversityOwerri, Nigeria
| | - Akshay Nag
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource TechnologyPalampur, India
| | - Ram K. Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource TechnologyPalampur, India
- *Correspondence: Ram K. Sharma ;
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81
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Md-Mustafa ND, Khalid N, Gao H, Peng Z, Alimin MF, Bujang N, Ming WS, Mohd-Yusuf Y, Harikrishna JA, Othman RY. Transcriptome profiling shows gene regulation patterns in a flavonoid pathway in response to exogenous phenylalanine in Boesenbergia rotunda cell culture. BMC Genomics 2014; 15:984. [PMID: 25407215 PMCID: PMC4289260 DOI: 10.1186/1471-2164-15-984] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 09/26/2014] [Indexed: 11/19/2022] Open
Abstract
Background Panduratin A extracted from Boesenbergia rotunda is a flavonoid reported to possess a range of medicinal indications which include anti-dengue, anti-HIV, anti-cancer, antioxidant and anti-inflammatory properties. Boesenbergia rotunda is a plant from the Zingiberaceae family commonly used as a food ingredient and traditional medicine in Southeast Asia and China. Reports on the health benefits of secondary metabolites extracted from Boesenbergia rotunda over the last few years has resulted in rising demands for panduratin A. However large scale extraction has been hindered by the naturally low abundance of the compound and limited knowledge of its biosynthetic pathway. Results Transcriptome sequencing and digital gene expression (DGE) analysis of native and phenylalanine treated Boesenbergia rotunda cell suspension cultures were carried out to elucidate the key genes differentially expressed in the panduratin A biosynthetic pathway. Based on experiments that show increase in panduratin A production after 14 days post treatment with exogenous phenylalanine, an aromatic amino acid derived from the shikimic acid pathway, total RNA of untreated and 14 days post-phenylalanine treated cell suspension cultures were extracted and sequenced using next generation sequencing technology employing an Illumina-Solexa platform. The transcriptome data generated 101, 043 unigenes with 50, 932 (50.41%) successfully annotated in the public protein databases; including 49.93% (50, 447) in the non-redundant (NR) database, 34.63% (34, 989) in Swiss-Prot, 24,07% (24, 316) in Kyoto Encyclopedia of Genes and Genomes (KEGG) and 16.26% (16, 426) in Clusters of Orthologous Groups (COG). Through DGE analysis, we found that 14, 644 unigenes were up-regulated and 14, 379 unigenes down-regulated in response to exogenous phenylalanine treatment. In the phenylpropanoid pathway leading to the proposed panduratin A production, 2 up-regulated phenylalanine ammonia-lyase (PAL), 3 up-regulated 4-coumaroyl:coenzyme A ligase (4CL) and 1 up-regulated chalcone synthase (CHS) were found. Conclusions This is the first report of Boesenbergia rotunda de novo transcriptome data that could serve as a reference for gene or enzyme functional studies in the Zingiberaceae family. Although enzymes that are directly involved in the panduratin A biosynthetic pathway were not completely elucidated, the data provides an overall picture of gene regulation patterns leading to panduratin A production. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-984) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Rofina Yasmin Othman
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia.
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82
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Identification of the protopanaxatriol synthase gene CYP6H for ginsenoside biosynthesis in Panax quinquefolius. Funct Integr Genomics 2014; 14:559-70. [DOI: 10.1007/s10142-014-0386-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 06/23/2014] [Accepted: 07/14/2014] [Indexed: 10/25/2022]
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83
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Transcriptome profiling and comparative analysis of Panax ginseng adventitious roots. J Ginseng Res 2014; 38:278-88. [PMID: 25379008 PMCID: PMC4213845 DOI: 10.1016/j.jgr.2014.05.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 11/24/2022] Open
Abstract
Background Panax ginseng Meyer is a traditional medicinal plant famous for its strong therapeutic effects and serves as an important herbal medicine. To understand and manipulate genes involved in secondary metabolic pathways including ginsenosides, transcriptome profiling of P. ginseng is essential. Methods RNA-seq analysis of adventitious roots of two P. ginseng cultivars, Chunpoong (CP) and Cheongsun (CS), was performed using the Illumina HiSeq platform. After transcripts were assembled, expression profiling was performed. Results Assemblies were generated from ∼85 million and ∼77 million high-quality reads from CP and CS cultivars, respectively. A total of 35,527 and 27,716 transcripts were obtained from the CP and CS assemblies, respectively. Annotation of the transcriptomes showed that approximately 90% of the transcripts had significant matches in public databases. We identified several candidate genes involved in ginsenoside biosynthesis. In addition, a large number of transcripts (17%) with different gene ontology designations were uniquely detected in adventitious roots compared to normal ginseng roots. Conclusion This study will provide a comprehensive insight into the transcriptome of ginseng adventitious roots, and a way for successful transcriptome analysis and profiling of resource plants with less genomic information. The transcriptome profiling data generated in this study are available in our newly created adventitious root transcriptome database (http://im-crop.snu.ac.kr/transdb/index.php) for public use.
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84
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Subramaniyam S, Mathiyalagan R, Natarajan S, Kim YJ, Jang MG, Park JH, Yang DC. Transcript expression profiling for adventitious roots of Panax ginseng Meyer. Gene 2014; 546:89-96. [PMID: 24831831 DOI: 10.1016/j.gene.2014.05.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 04/26/2014] [Accepted: 05/07/2014] [Indexed: 02/06/2023]
Abstract
Panax ginseng Meyer is one of the major medicinal plants in oriental countries belonging to the Araliaceae family which are the primary source for ginsenosides. However, very few genes were characterized for ginsenoside pathway, due to the limited genome information. Through this study, we obtained a comprehensive transcriptome from adventitious roots, which were treated with methyl jasmonic acids for different time points (control, 2h, 6h, 12h, and 24h) and sequenced by RNA 454 pyrosequencing technology. Reference transcriptome 39,304,529 (0.04GB) was obtained from 5,724,987,880 bases (5.7GB) of 22 libraries by de novo assembly and 35,266 (58.5%) transcripts were annotated with biological schemas (GO and KEGG). The digital gene expression patterns were obtained from in vitro grown adventitious root sequences which mapped to reference, from that, 3813 (6.3%) unique transcripts were involved in ≥2 fold up and downregulations. Finally, candidates for ginsenoside pathway genes were predicted from observed expression patterns. Among them, 30 transcription factors, 20 cytochromes, and 11 glycosyl transferases were predicted as ginsenoside candidates. These data can remarkably expand the existing transcriptome resources of Panax, especially to predict existence of gene networks in P. ginseng. The entity of the data provides a valuable platform to reveal more on secondary metabolism and abiotic stresses from P. ginseng in vitro grown adventitious roots.
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Affiliation(s)
- Sathiyamoorthy Subramaniyam
- Graduate School of Biotechnology & Ginseng Bank, College of Life Science, Kyung Hee University, Yongin 449-701, South Korea; Insilicogen Inc., #909, Venture Valley, 958, Gosaek-dong, Gwonseon-gu, Suwon, Gyeonggi-do 441-813, South Korea
| | - Ramya Mathiyalagan
- Graduate School of Biotechnology & Ginseng Bank, College of Life Science, Kyung Hee University, Yongin 449-701, South Korea
| | - Sathishkumar Natarajan
- Graduate School of Biotechnology & Ginseng Bank, College of Life Science, Kyung Hee University, Yongin 449-701, South Korea
| | - Yu-Jin Kim
- Graduate School of Biotechnology & Ginseng Bank, College of Life Science, Kyung Hee University, Yongin 449-701, South Korea
| | - Moon-Gi Jang
- Graduate School of Biotechnology & Ginseng Bank, College of Life Science, Kyung Hee University, Yongin 449-701, South Korea
| | - Jun-Hyung Park
- Insilicogen Inc., #909, Venture Valley, 958, Gosaek-dong, Gwonseon-gu, Suwon, Gyeonggi-do 441-813, South Korea
| | - Deok Chun Yang
- Graduate School of Biotechnology & Ginseng Bank, College of Life Science, Kyung Hee University, Yongin 449-701, South Korea.
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85
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Dong S, Liu Y, Niu J, Ning Y, Lin S, Zhang Z. De novo transcriptome analysis of the Siberian apricot (Prunus sibirica L.) and search for potential SSR markers by 454 pyrosequencing. Gene 2014; 544:220-7. [PMID: 24746601 DOI: 10.1016/j.gene.2014.04.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 04/10/2014] [Accepted: 04/17/2014] [Indexed: 11/29/2022]
Abstract
The Siberian apricot, an economically and ecologically important plant in China, contains seeds high in oil and can grow on marginal land. Although this species has multiple purposes and may be a feedstock of biofuel in China, transcriptome information and molecular research on this species remain limited. RNA-Seq technology has been widely applied to transcriptomics, genomics and the development of molecular markers, and functional gene studies. In this study, we obtained 1,243,067 high-quality reads with a mean size of 425 bp in a single run, totaling 528.4 Mb of sequence data using 454 GS FLX Titanium sequencing. All reads were assembled de novo into 46,940 unigenes with a mean size of 651 bp (range: 45-5566 bp). Assembled unigenes were annotated in multiple public databases based on similarity alignments to genes and proteins. 191 unigenes involving in lipid biosynthesis and metabolism were found, among them, expression patterns of two desaturase enzymes were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR), based on six tissues from Siberian apricot, the seeds had the highest expression. 7304 simple sequence repeats (SSR) were identified from 6509 unigenes, a total of 9930 primer pairs were designed, 50 primer pairs were randomly selected to validate of the usefulness, and 24 (48%) primer pairs produced bands of the expected size. These data provide a base of sequence information to improve agronomic characters and molecular marker-assisted breeding to alter the composition of fatty acids in seeds from this plant, and hence, facilitate its utilization as a future biodiesel feedstock.
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Affiliation(s)
- Shubin Dong
- Lab of Systematic Evolution and Biogeography of Woody Plants, College of Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Yulin Liu
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Jun Niu
- Lab of Systematic Evolution and Biogeography of Woody Plants, College of Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Yu Ning
- Lab of Systematic Evolution and Biogeography of Woody Plants, College of Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Shanzhi Lin
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Zhixiang Zhang
- Lab of Systematic Evolution and Biogeography of Woody Plants, College of Nature Conservation, Beijing Forestry University, Beijing 100083, China.
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86
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Xiang L, Li Y, Zhu Y, Luo H, Li C, Xu X, Sun C, Song J, Shi L, He L, Sun W, Chen S. Transcriptome analysis of the Ophiocordyceps sinensis fruiting body reveals putative genes involved in fruiting body development and cordycepin biosynthesis. Genomics 2014; 103:154-9. [PMID: 24440419 DOI: 10.1016/j.ygeno.2014.01.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 11/09/2013] [Accepted: 01/07/2014] [Indexed: 12/20/2022]
Abstract
Ophiocordyceps sinensis is a highly valuable and popular medicinal fungus used as a tonic and roborant for thousands of years in traditional Asian medicine. However, unsustainable harvesting practices have endangered this species and very little is known about its developmental programming, its biochemistry and genetics. To begin to address this, the transcriptome of the medicinal O. sinensis fruiting body was analyzed by high-throughput. In this O. sinensis 454-EST dataset, four mating type genes and 121 genes that may be involved in fruiting body development, especially in signal transduction and transcription regulation, were discovered. Moreover, a model was developed for the synthesis of the primary medicinal compound, cordycepin, and the putative biosynthetic enzymes identified. This transcriptome dataset provides a significant new resource for gene discovery in O. sinensis and dissection of its valuable biosynthetic and developmental pathways.
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Affiliation(s)
- Li Xiang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Ying Li
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100094, China
| | - Yingjie Zhu
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100094, China
| | - Hongmei Luo
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100094, China
| | - Chunfang Li
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100094, China
| | - Xiaolan Xu
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100094, China
| | - Chao Sun
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100094, China
| | - Jingyuan Song
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100094, China
| | - Linchun Shi
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100094, China
| | - Liu He
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100094, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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87
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Niu Y, Luo H, Sun C, Yang TJ, Dong L, Huang L, Chen S. Expression profiling of the triterpene saponin biosynthesis genes FPS, SS, SE, and DS in the medicinal plant Panax notoginseng. Gene 2014; 533:295-303. [DOI: 10.1016/j.gene.2013.09.045] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 09/10/2013] [Accepted: 09/12/2013] [Indexed: 12/22/2022]
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Putative genes involved in saikosaponin biosynthesis in Bupleurum species. Int J Mol Sci 2013; 14:12806-26. [PMID: 23783277 PMCID: PMC3709813 DOI: 10.3390/ijms140612806] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 06/13/2013] [Accepted: 06/14/2013] [Indexed: 11/26/2022] Open
Abstract
Alternative medicinal agents, such as the herb Bupleurum, are increasingly used in modern medicine to supplement synthetic drugs. First, we present a review of the currently known effects of triterpene saponins-saikosaponins of Bupleurum species. The putative biosynthetic pathway of saikosaponins in Bupleurum species is summarized, followed by discussions on identification and characterization of genes involved in the biosynthesis of saikosaponins. The purpose is to provide a brief review of gene extraction, functional characterization of isolated genes and assessment of expression patterns of genes encoding enzymes in the process of saikosaponin production in Bupleurum species, mainly B. kaoi. We focus on the effects of MeJA on saikosaponin production, transcription patterns of genes involved in biosynthesis and on functional depiction.
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Abstract
INTRODUCTION The apparent productivity crisis in the pharmaceutical industry and the economic and political rise of China have contributed to renewed interest in the application of Chinese medicine for drug discovery. AREAS COVERED The author presents an overview of the historical development and basic principles of theory and practice of Chinese herbal medicine, its materia medica and prescription formulas, and discusses the motivation for and rationale of its application to drug discovery. Furthermore, the author distinguishes the five main approaches to drug discovery from Chinese herbal medicine, based on the decreasing amount and detail of historical and clinical Chinese medicine knowledge that informed the research effort. EXPERT OPINION Many compounds that have been isolated from the Chinese materia medica exhibit pharmacological activities comparable to pharmaceutical drugs. With the exception of the antimalarial drug artemisinin, however, this knowledge has not led to the successful development of new drugs outside of China. The chance of success in a Chinese medicine-based drug discovery effort will be increased by consideration of the empirical knowledge that has been documented over many centuries in the historical materia medica and prescription literature. Most Chinese medicine-derived compounds affect more than one target and do not correspond to the one compound/one-target drug discovery paradigm. A new frontier is opening up with the development of drugs consisting of combinations of multiple compounds acting on multiple targets under the paradigm of network pharmacology. The ancient practice of combining multiple drugs in prescription formulas can serve as inspirational analogy and a practical guide.
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Affiliation(s)
- Nikolaus J Sucher
- Science, Technology, Engineering & Math (S.T.E.M), Roxbury Community College, Roxbury Crossing, MA 02120, USA.
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90
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Hao DC, Chen SL, Xiao PG, Liu M. Application of High-Throughput Sequencing in Medicinal Plant Transcriptome Studies. Drug Dev Res 2012. [DOI: 10.1002/ddr.21041] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Da-Cheng Hao
- Biotechnology Institute/School of Environment; Dalian Jiaotong University; Dalian; 116028; China
| | - Shi-Lin Chen
- Institute of Medicinal Plant Development; Chinese Academy of Medical sciences/Peking Union Medical College; Beijing; 100193; China
| | - Pei-Gen Xiao
- Institute of Medicinal Plant Development; Chinese Academy of Medical sciences/Peking Union Medical College; Beijing; 100193; China
| | - Ming Liu
- Biotechnology Institute/School of Environment; Dalian Jiaotong University; Dalian; 116028; China
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91
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Guan YF, Li GR, Wang RJ, Yi YT, Yang L, Jiang D, Zhang XP, Peng Y. Application of next-generation sequencing in clinical oncology to advance personalized treatment of cancer. CHINESE JOURNAL OF CANCER 2012; 31:463-70. [PMID: 22980418 PMCID: PMC3777453 DOI: 10.5732/cjc.012.10216] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
With the development and improvement of new sequencing technology, next-generation sequencing (NGS) has been applied increasingly in cancer genomics research over the past decade. More recently, NGS has been adopted in clinical oncology to advance personalized treatment of cancer. NGS is used to identify novel and rare cancer mutations, detect familial cancer mutation carriers, and provide molecular rationale for appropriate targeted therapy. Compared to traditional sequencing, NGS holds many advantages, such as the ability to fully sequence all types of mutations for a large number of genes (hundreds to thousands) in a single test at a relatively low cost. However, significant challenges, particularly with respect to the requirement for simpler assays, more flexible throughput, shorter turnaround time, and most importantly, easier data analysis and interpretation, will have to be overcome to translate NGS to the bedside of cancer patients. Overall, continuous dedication to apply NGS in clinical oncology practice will enable us to be one step closer to personalized medicine.
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Affiliation(s)
- Yan-Fang Guan
- Shenzhen Clinical Molecular Diagnostic Engineering Laboratory, BGI-Shenzhen, Shenzhen, Guangdong, People's Republic of China
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92
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Zhang Y, Zhang S, Han S, Li X, Qi L. Transcriptome profiling and in silico analysis of somatic embryos in Japanese larch (Larix leptolepis). PLANT CELL REPORTS 2012; 31:1637-57. [PMID: 22622308 DOI: 10.1007/s00299-012-1277-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 04/19/2012] [Accepted: 04/20/2012] [Indexed: 05/13/2023]
Abstract
UNLABELLED Japanese larch (Larix leptolepis) is an ecologically and economically important species mainly grown in northeastern China, Japan and Europe. However, erratic flowering and poor germplasm resources caused by high embryo abortion rates have hampered breeding of Larix species. Somatic embryogenesis (SE) is an effective tool for the production of L. leptolepis with desirable characteristics, such as expression of totipotency, preparation of synthetic seeds, and genetic transformation. However, public genomic resources for this species are limited. We sequenced 591,759 raw expressed sequence tags (ESTs) from a 454 sequencing cDNA library of L. leptolepis somatic embryos, resulting in 572,403 high-quality reads. These reads were assembled into 70,927 unique sequences (UniGenes), including 32,321 contigs and 38,606 singletons. After removal of low-quality sequences, 65,115 UniGenes were annotated using the UniProtKB program. Based on their sequence similarity with known proteins, the matched 30,372 sequences from 664 species were estimated to represent approximately 19,000 unique genes. Gene ontology analysis revealed 21,324 UniGenes assigned to 51 categories. By Kyoto Encyclopedia of Genes and Genomes mapping, 25,773 transcripts were associated with 160 biochemical pathways. Further analysis screened four signal transduction pathways represented by 337 enzymes and 17 secondary metabolites. In silico analysis reveals that 207 UniESTs in Larix are homologous to MAPKs genes identified from other model plants, which may be involved in regulating SE development. This study provides an initial insight into the Larix transcriptomes of the pro-embryogenic mass and is a sound basis for future studies. KEY MESSAGE We constructed a large, full-length 454 sequencing cDNA library of Larix leptolepis during somatic embryogenesis. More than 590,000 sequences were obtained and a deep-coverage EST database was constructed.
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Affiliation(s)
- Yuan Zhang
- Laboratory of Cell Biology, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
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93
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Zhang K, Pirooznia M, Arabnia HR, Yang JY, Wang L, Luo Z, Deng Y. Genomic signatures and gene networking: challenges and promises. BMC Genomics 2011; 12 Suppl 5:I1. [PMID: 22369358 PMCID: PMC3287490 DOI: 10.1186/1471-2164-12-s5-i1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
This is an editorial report of the supplement to BMC Genomics that includes 15 papers selected from the BIOCOMP'10 - The 2010 International Conference on Bioinformatics & Computational Biology as well as other sources with a focus on genomics studies. BIOCOMP'10 was held on July 12-15 in Las Vegas, Nevada. The congress covered a large variety of research areas, and genomics was one of the major focuses because of the fast development in this field. We set out to launch a supplement to BMC Genomics with manuscripts selected from this congress and invited submissions. With a rigorous peer review process, we selected 15 manuscripts that showed work in cutting-edge genomics fields and proposed innovative methodology. We hope this supplement presents the current computational and statistical challenges faced in genomics studies, and shows the enormous promises and opportunities in the genomic future.
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