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http://dx.doi.org/10.1016/j.jgr.2014.05.008

Transcriptome profiling and comparative analysis of Panax ginseng adventitious roots  

Jayakodi, Murukarthick (Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University)
Lee, Sang-Choon (Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University)
Park, Hyun-Seung (Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University)
Jang, Woojong (Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University)
Lee, Yun Sun (Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University)
Choi, Beom-Soon (Phyzen Genomics Institute)
Nah, Gyoung Ju (Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University)
Kim, Do-Soon (Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University)
Natesan, Senthil (Genomics and Proteomics Laboratory, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University)
Sun, Chao (Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College)
Yang, Tae-Jin (Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University)
Publication Information
Journal of Ginseng Research / v.38, no.4, 2014 , pp. 278-288 More about this Journal
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.
Keywords
adventitious root; de novo assembly; next-generation sequencing; Panax ginseng; transcriptome;
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1 Wen J, Zimmer EA. Phylogeny and biogeography of Panax L. (the ginseng genus, Araliaceae): inferences from ITS sequences of nuclear ribosomal DNA. Mol Phylogenet Evol 1996;6:167-77.   DOI   ScienceOn
2 Hu SY. The genus Panax (ginseng) in Chinese medicine. Econ Bot 1976;30:11-28.   DOI   ScienceOn
3 Lee FC. Facts about ginseng: the elixir of life. New Jersey: Hollym International Corporation Press; 1992.
4 Liu J, Wang S, Liu H, Yang L, Nan G. Stimulatory effect of saponin from Panax ginseng on immune function of lymphocytes in the elderly. Mech Ageing Dev 1995;83:43-53.   DOI   ScienceOn
5 Shin HR, Kim JY, Yun TK, Morgan G, Vainio H. The cancer preventive potential of Panax ginseng: a review of human and experimental evidence. Cancer Causes Control 2000;11:565-76.   DOI   ScienceOn
6 Kim SH, Park KS. Effects of Panax ginseng extract on lipid metabolism in humans. Pharmacol Res 2003;48:511-3.   DOI   ScienceOn
7 Kwon WS, Chung CM, Kim YT, Lee MG, Choi KT. Breeding process and characteristics of KG101, a superior line of Panax ginseng C.A. Meyer. Korean J Ginseng Sci 1998;22:11-7.
8 Jung JD, Park HW, Hahn Y, Hur CG, In DS, Chung HJ, Liu JR, Choi DW. Discovery of genes for ginsenoside biosynthesis by analysis of ginseng expressed sequence tags. Plant Cell Rep 2003;22:224-30.   DOI   ScienceOn
9 Sathiyamoorthy S, In JG, Gayathri S, Kim YJ, Yang DC. Generation and gene ontology based analysis of expressed sequence tags (EST) from a Panax ginseng C. A. Meyer roots. Mol Biol Rep 2010;37:3465-72.   DOI   ScienceOn
10 Choi HI, Kim NH, Kim JH, Choi BS, Ahn IO, Lee JS, Yang TJ. Development of reproducible EST-derived SSR markers and assessment of genetic diversity in Panax ginseng cultivars and related species. J Ginseng Res 2011;35:399-412.   DOI   ScienceOn
11 Luo H, Sun C, Sun Y, Wu Q, Li Y, Song J, Niu Y, Cheng X, Xu H, Li C, et al. Analysis of the transcriptome of Panax notoginseng root uncovers putative triterpene saponin-biosynthetic genes and genetic markers. BMC Genomics 2011;12(Suppl. 5):S5.
12 Sun C, Li Y, Wu Q, Luo H, Sun Y, Song J, Lui EM, Chen S. De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX titanium platform to discover putative genes involved in ginsenoside biosynthesis. BMC Genomics 2010;11:262.   DOI
13 Li C, Zhu Y, Guo X, Sun C, Luo H, Song J, Li Y, Wang L, Qian J, Chen S. Transcriptome analysis reveals ginsenosides biosynthetic genes, microRNAs and simple sequence repeats in Panax ginseng C. A. Meyer. BMC Genomics 2013;14:245.   DOI
14 Patel RK, Jain M. NGS QC toolkit: a toolkit for quality control of next generation sequencing data. PLoS One 2012;7:e30619.   DOI
15 Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005;21:3674-6.   DOI   ScienceOn
16 Schulz MH, Zerbino DR, Vingron M, Birney E. Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 2012;28:1086-92.   DOI
17 Xie Y, Wu G, Tang J, Luo R, Patterson J, Liu S, Huang W, He G, Gu S, Li S, et al. SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics 2014;30:1660-6.   DOI
18 Birol I, Jackman SD, Nielsen CB, Qian JQ, Varhol R, Stazyk G, Morin RD, Zhao Y, Hirst M, Schein JE, et al. De novo transcriptome assembly with ABySS. Bioinformatics 2009;25:2872-7.   DOI   ScienceOn
19 Velculescu VE, Kinzler KW. Gene expression analysis goes digital. Nat Biotechnol 2007;25:878-80.   DOI
20 Haralampidis K, Trojanowska M, Osbourn AE. Biosynthesis of triterpenoid saponins in plants. Adv Biochem Eng Biotechnol 2002;75:31-49.
21 Kushiro T, Shibuya M, Ebizuka Y. Beta-amyrin synthase-cloning of oxidosqualene cyclase that catalyzes the formation of the most popular triterpene among higher plants. Eur J Biochem 1998;256:238-44.   DOI   ScienceOn
22 Lee MH, Jeong JH, Seo JW, Shin CG, Kim YS, In JG, Yang DC, Yi JS, Choi YE. Enhanced triterpene and phytosterol biosynthesis in Panax ginseng overexpressing squalene synthase gene. Plant Cell Physiol 2004;8:976-84.
23 Han JY, Kwon YS, Yang DC, Jung YR, Choi YE. Expression and RNA interference-induced silencing of the dammarenediol synthase gene in Panax ginseng. Plant Cell Physiol 2006;47:1653-62.   DOI   ScienceOn
24 Achnine L, Huhman DV, Farag MA, Sumner LW, Blount JW, Dixon RA. Genomics-based selection and functional characterization of triterpene glycosyl-transferases from the model legume Medicago truncatula. Plant J 2005;41:875-87.   DOI   ScienceOn
25 Han JY, In JG, Kwon YS, Choi YE. Regulation of ginsenoside and phytosterol biosynthesis by RNA interferences of squalene epoxidase gene in Panax ginseng. Phytochemistry 2010;71:36-46.   DOI   ScienceOn
26 Han JY, Kim HJ, Kwon YS, Choi YE. The Cyt P450 enzyme CYP716A47 catalyzes the formation of protopanaxadiol from dammarenediol-II during ginsenoside biosynthesis in Panax ginseng. Plant Cell Physiol 2011;52:2062-73.   DOI
27 Han JY, Hwang HS, Choi SW, Kim HJ, Choi YE. Cytochrome P450 CYP716A53v2 catalyzes the formation of protopanaxatriol from protopanaxadiol during ginsenoside biosynthesis in Panax ginseng. Plant Cell Physiol 2012;53:1535-45.   DOI
28 Meesapyodsuk D, Balsevich J, Reed DW, Covello PS. Saponin biosynthesis in Saponaria vaccaria. cDNAs encoding beta-amyrin synthase and a triterpene carboxylic acid glucosyltransferase. Plant Physiol 2007;143:959-69.
29 Chen S, Luo H, Li Y, Sun Y, Wu Q, Niu Y, Song J, Lv A, Zhu Y, Sun C, et al. 454 EST analysis detects genes putatively involved in ginsenoside biosynthesis in Panax ginseng. Plant Cell Rep 2011;30:1593-601.   DOI
30 Xu DL, Long H, Liang JJ, Zhang J, Chen X, Li JL, Pan ZF, Deng GB, Yu MQ. De novo assembly and characterization of the root transcriptome of Aegilops variabilis during an interaction with the cereal cyst nematode. BMC Genomics 2012;13:133.   DOI
31 Zhang J, Liang S, Duan J, Wang J, Chen S, Cheng Z, Zhang Q, Liang X, Li Y. De novo assembly and characterisation of the transcriptome during seed development, and generation of genic-SSR markers in peanut (Arachis hypogaea L. BMC Genomics 2012;13:90.   DOI
32 Arican E, Albayrak G, Gozukirmizi N. Calli cultures from Abies equi-trojani (Aschers et Sinten) and changes in antioxidant defense system enzymes. J Environ Biol 2008;29:841-4.
33 Vijay N, Poelstra JW, Künstner A, Wolf JBW. Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments. Mol Ecol 2013;22:620-34.   DOI
34 Choi HI, Kim NH, Lee J, Choi BS, Kim KD, Park JY, Lee SC, Yang TJ. Evolutionary relationship of Panax ginseng and P. quinquefolius inferred from sequencing and comparative analysis of expressed sequence tags. Genet Resour Crop Evol 2013;60:1377-87.   DOI
35 Wang Z, Fang B, Chen J, Zhang X, Luo Z, Huang L, Chen X, Li Y. De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas). BMC Genomics 2010;11:726.   DOI   ScienceOn
36 Kim SI, Kim JY, Kim EA, Kwon KH, Kim KW, Cho K, Lee JH, Nam MH, Yang DC, Yoo JS, et al. Proteome analysis of hairy root from Panax ginseng C. A. Meyer using peptide fingerprinting, internal sequencing and expressed sequence tag data. Proteomics 2003;3:2379-92.   DOI   ScienceOn
37 Lee OR, Sathiyaraj G, Kim YJ, In JG, Kwon WS, Kim JH, Yang DC. Defense genes induced by pathogens and abiotic stresses in Panax ginseng C. A. Meyer. J Ginseng Res 2011;1:1-11.
38 Sathiyaraj G, Lee OR, Parvin S, Khorolragchaa A, Kim YJ, Yang DC. Transcript profiling of antioxidant genes during biotic and abiotic stresses in Panax ginseng C. A. Meyer. Mol Biol Rep 2011;38:2761-9.   DOI
39 Kushiro T, Ohno Y, Shibuya M, Ebizuka Y. In vitro conversion of 2,3-oxidosqualene into dammarenediol by Panax ginseng microsomes. Biol Pharm Bull 1997;20:292-4.   DOI   ScienceOn
40 Hu W, Liu N, Tian Y, Zhang L. Molecular cloning, expression, purification, and functional characterization of dammarenediol synthase from Panax ginseng. Biomed Res Int 2013;2013:1-7. Article ID 285740.
41 Daniel RR, Felipe HB, Natasha TH, Louise EJ, Daniel PS. Tomato root transcriptome response to a nitrogen-enriched soil patch. BMC Plant Biol 2010;10:75.   DOI
42 Wang J, Man S, Gao W, Zhang L, Huang L. Cluster analysis of ginseng tissue cultures, dynamic change of growth, total saponins, specific oxygen uptake rate in bioreactor and immuno-regulative effect of ginseng adventitious root. Ind Crops Prod 2013;41:57-63.   DOI
43 Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009;10:57-63.   DOI   ScienceOn
44 Grabherr MG, Haas BJ, Yassour M. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 2011;15:644-52.
45 Tansakul P, Shibuya M, Kushiro T, Ebizuka Y. Dammarenediol-II synthase, the first dedicated enzyme for ginsenoside biosynthesis in Panax ginseng. FEBS Lett 2006;580:5143-9.   DOI   ScienceOn
46 Garg R, Patel RK, Tyagi AK, Jain M. De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res 2011;18:53-63.   DOI
47 Ge XX, Chai LJ, Liu Z, Wu XM, Deng XX, Guo WW. Transcriptional profiling of genes involved in embryogenic, non-embryogenic calluses and somatic embryogenesis of Valencia sweet orange by SSH-based microarray. Planta 2012;236:1107-24.   DOI
48 Li D, Deng Z, Qin B, Liu X, Men Z. De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg. BMC Genomics 2012;13:192.   DOI
49 Lee JW, Kim YC, Jo IH, Seo AY, Lee JH, Kim OT, Hyun DY, Cha SW, Bang KH, Cho JH. Development of an ISSR-derived SCAR marker in Korean ginseng cultivars (Panax ginseng C. A. Meyer). J Ginseng Res 2011;35:52-9.   DOI
50 Kim TD, Han JY, Huh GH, Choi YE. Expression and functional characterization of three squalene synthase genes associated with saponin biosynthesis in Panax ginseng. Plant Cell Physiol 2011;1:125-37.