Transcriptome profiling and comparative analysis of panax ginseng adventitious roots

Journal of Ginseng Research

Volumn 38, Issue 4, 2014, Pages 278-288

  Jayakodi, Murukarthick ^a   Lee, Sang Choon ^a   Park, Hyun Seung ^a   Jang, Woojong ^a   Lee, Yun Sun ^a   Choi, Beom Soon ^b   Nah, Gyoung Ju ^a   Kim, Do Soon ^a   Natesan, Senthil ^c   Sun, Chao ^d   Yang, Tae Jin ^a  

^a Seoul National University   (South Korea)

^b Phyzen Inc   (South Korea)

^c TAMIL NADU AGRICULTURAL UNIVERSITY   (India)

^d INSTITUTE OF MEDICINAL PLANT DEVELOPMENT   (China)

Author keywords

Adventitious root; De novo assembly; Next generation sequencing; Panax ginseng; Transcriptome

Indexed keywords

GINSENG EXTRACT; GINSENOSIDE; TRANSCRIPTOME;

ADVENTITIOUS ROOT; ARTICLE; BIOSYNTHESIS; CHEONGSUN; CHUNPOONG; CULTIVAR; DATA BASE; GENE; GENE EXPRESSION PROFILING; GENE ONTOLOGY; GINSENG; METABOLISM; NONHUMAN; PRIORITY JOURNAL; RNA SEQUENCE;

EID: 84924283283     PISSN: 12268453     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jgr.2014.05.008     Document Type: Article

References (50)

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
2. Hu SY. The genus Panax (ginseng) in Chinese medicine. Econ Bot 1976;30:11-28
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
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
6. Kim SH, Park KS. Effects of Panax ginseng extract on lipid metabolism in humans. Pharmacol Res 2003;48:511-3
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. 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
9. 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
10. 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
11. 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
12. 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
13. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009;10:57-63
14. 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
15. 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
16. 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
17. Patel RK, Jain M. NGS QC toolkit: a toolkit for quality control of next generation sequencing data. PLoS One 2012;7:e30619
18. 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
19. Grabherr MG, Haas BJ, Yassour M. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 2011;15:644-52
20. 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
21. 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
22. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005;21:3674-6
23. Velculescu VE, Kinzler KW. Gene expression analysis goes digital. Nat Biotechnol 2007;25:878-80
24. Haralampidis K, Trojanowska M, Osbourn AE. Biosynthesis of triterpenoid saponins in plants. Adv Biochem Eng Biotechnol 2002;75:31-49
25. Kushiro T, Shibuya M, Ebizuka Y. Beta-amyrin synthasedcloning of oxidosqualene cyclase that catalyzes the formation of the most popular triterpene among higher plants. Eur J Biochem 1998;256:238-44
26. 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
27. 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
28. 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
29. 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
30. 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
31. 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
32. 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
33. Achnine L, Huhman DV, Farag MA, Sumner LW, Blount JW, Dixon RA. Genomics- based selection and functional characterization of triterpene glycosyltransferases from the model legume Medicago truncatula. Plant J 2005;41: 875-87
34. 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
35. 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
36. 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
37. 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
38. 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
39. 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
40. 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
41. 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
42. 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
43. 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
44. 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
45. 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
46. 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
47. 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
48. 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
49. 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
50. 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. 285740.