The spatial and temporal transcriptomic landscapes of ginseng, Panax ginseng C. A. Meyer

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Wang, Kangyu ^a   Jiang, Shicui ^a   Sun, Chunyu ^a   Lin, Yanping ^a   Yin, Rui ^a   Wang, Yi ^a   Zhang, Meiping ^a  

^a JILIN AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

GINSENOSIDE; TRANSCRIPTOME;

ANTIBODY SPECIFICITY; BIOLOGY; BIOSYNTHESIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE ONTOLOGY; GENE REGULATORY NETWORK; GENETICS; METABOLISM; MOLECULAR GENETICS; PANAX; PLANT ROOT; PROCEDURES; TIME FACTOR;

BIOSYNTHETIC PATHWAYS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE ONTOLOGY; GENE REGULATORY NETWORKS; GINSENOSIDES; MOLECULAR SEQUENCE ANNOTATION; ORGAN SPECIFICITY; PANAX; PLANT ROOTS; TIME FACTORS; TRANSCRIPTOME;

EID: 84949844013     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep18283     Document Type: Article

References (40)

1. Briskin, D. P. Medicinal plants and phytomedicines. Linking plant biochemistry and physiology to human health. Plant Physiol. 124, 507-514 (2000).
2. Popovich, D. G., Yeo, C-R. & Zhang, W. Ginsenosides derived from Asian (Panax ginseng), American ginseng (Panax quinquefolius) and potential cytoactivity. Int. J. Biomed Pharm. Sci. 6, 56-62 (2012).
3. OHara, M., Kiefer, D., Farrell, K. & Kemper, K. A review of 12 commonly used medicinal herbs. Arch. Fam. Med. 7, 523-536 (1998).
4. Chen, C. F., Chiou, W. F. & Zhang, J. T. Comparison of the pharmacological effects of Panax ginseng and Panax quinquefolium. Acta. Pharmacol. Sin. 29, 1103-1108 (2008).
5. Kim, S. K. & Park, J. H. Trends in ginseng research in 2010. J. Ginseng Res. 35, 389-398 (2011).
6. Tran, T. L., Kim, Y. R., Yang, J. L., Oh, D. R., Dao, T. T. & Oh, W. K. Dammarane triterpenes from the leaves of Panax ginseng enhance cellular immunity. Bioorg. Med. Chem. 22, 499-504 (2014).
7. Haralampidis, K., Trojanowska, M. & Osbourn, A. E. Biosynthesis of triterpenoid saponins in plants. Advances in Biochemical Engineering/Biotechnology 75, 31-49 (2002).
8. Abe, I., Rohmer, M. & Prestwich, G. D. Enzymatic cyclization of squalene and oxidosqualene to sterols and triterpenes. Chem. Rev. 93, 2189-2206 (1993).
9. Hostettmann, K. & Marston, A. Saponins. Cambridge, Cambridge University Press (1995).
10. Han, J. Y., Kwon, Y. S., Yang, D. C., Jung, Y. R. & Choi, Y. E. Expression and RNA interference-induced silencing of the dammarenediol synthase gene in Panax ginseng. Plant Cell Physiol. 47, 1653-1662 (2006).
11. Liang, Y. & Zhao, S. Progress in understanding of ginsenoside biosynthesis. Plant Biology 10, 415-421 (2008).
12. Tansakul, P., Shibuya, M., Kushiro, T. & Ebizuka, Y. Dammarenediol-II synthase, the first dedicated enzyme for ginsenoside biosynthesis, in Panax ginseng. FEBS Lett. 580, 5143-5149 (2006).
13. Kim, D. S., Chang, Y. J., Zedk, U., Zhao, P., Liu, Y. Q. & Yang, C. R. Dammarane saponins from Panax ginseng. Phytochemistry 40, 1493-1497 (1995).
14. Christensen, L. P. Ginsenosides, Chemistry, Biosynthesis, Analysis and Potential Health Effects. Adv. Food Nutr. Res. 55, 1-99 (2008).
15. Tung, N. H., Song, G. Y., Park, Y. J. & Kim, Y. H. Two new dammaranetype saponins from the leaves of Panax ginseng. Chem. Pharm. Bull. 57, 1412-1414 (2009).
16. Hong, C. P., et al. Construction of a BAC library of Korean ginseng and initial analysis of BAC-end sequences. Molecular Genetics and Genomics 271, 709-716 (2004).
17. Bang, K. H., et al. Molecular authentication and genetic polymorphism of Korean ginseng (Panax ginseng C. A. Meyer) by inter-simple sequence repeats (ISSRs) markers. J. Life Sci. 14, 425-428 (2004).
18. In, D. S., et al. Genetic relationships of Panax species by RAPD and ISSR analyses. Korean J. Med. Crop. Sci. 13, 249-253 (2005).
19. Ma, K. H., et al. Development and characterization of new microsatellite markers for ginseng (Panax ginseng C.A.Meyer). Conserv. Genet. 8, 1507-1509 (2007).
20. Van, Dan. N., et al. Development and characterization of new microsatellite markers in Panax ginseng (C.A.Meyer) from BAC end sequences. Conserv. Genet. 11, 1223-1225 (2010).
21. Jung, J. D., et al. Discovery of genes for ginsenoside biosynthesis by analysis of ginseng expressed sequence tags. Plant Cell Rep. 22, 224-230 (2003).
22. Sathiyamoorthy, S., In, J. G., Gayathri, S., Kim, Y. J. & Yang, D. C. Generation and gene ontology based analysis of expressed sequence tags (EST) from a Panax ginseng C. A. Meyer roots. Mol. Biol. Rep. 37, 3465-3472 (2010).
23. Zhai, J., et al. A plant-transformation-competent BIBAC library of ginseng (Panax ginseng C.A.Meyer) for functional genomics research and characterization of genes involved in ginsenoside biosynthesis. Mol. Breeding 31, 685-692 (2013).
24. Chen, S., et al. 454 EST analysis detects genes putatively involved in ginsenoside biosynthesis in Panax ginseng. Plant Cell Rep. 30, 1593-1601 (2011).
25. Li, C., et al. Transcriptome analysis reveals ginsenosides biosynthetic genes, microRNAs and simple sequence repeats in Panax ginseng C.A. Meyer. BMC Genomics 14, 245 (2013).
26. Jayakodi, M., et al. Transcriptome profiling and comparative analysis of Panax ginseng adventitious roots. J. Ginseng Res. 38, 278-288 (2014).
27. Jayakodi, M., et al. Comprehensive analysis of Panax ginseng root transcriptomes. BMC Plant Biol. 15, 138 (2015).
28. Nagalakshmi, U., Waern, K. & Snyder, M. RNA-seq: a method for comprehensive transcriptome analysis. Curr. Protoc. Mol. Biol. 89, 1-4 (2010).
29. Bao, J., et al. Serial Analysis of Gene Expression Study of a Hybrid Rice Strain (LYP9) and Its Parental Cultivars. Plant Physiol. 138, 1216-1231 (2005).
30. Matsumura, H., et al. Gene expression analysis of plant host-pathogen interactions by SuperSAGE. PNAS. 100, 15718-15723 (2003).
31. Poroyko, V., et al. The Maize Root Transcriptome by Serial Analysis of Gene Expression. Plant Physiol. 138, 1700-1710 (2005).
32. Soderlund, C., et al. Sequencing, Mapping, and Analysis of 27,455 Maize Full-Length cDNAs. PLoS Genet. 5, e1000740 (2009).
33. Wang, K., et al. The draft genome of a diploid cotton Gossypium raimondii. Nat. Genet. 44, 1098-103 (2012).
34. Schnable, P. S., et al. The B73 maize genome: complexity, diversity, and dynamics. Science 326, 1112-1115 (2009).
35. t Hoen, P. A. C., et al. Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nat. Biotechnol. 31, 1015-1022.
36. Pan, Q., Shai, O., Lee, L. J., Frey, B. J. & Blencowe, B. J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 40, 1413-1415 (2008).
37. Grabherr, M. G., et al. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat. Biotechnol. 29, 644-52 (2011).
38. Haas, B. J., et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat. Protoc. 8, 1494-512 (2013).
39. Conesa, A., Gotz, S., Garcia-Gomez, J. M., Terol, J., Talon, M. & Robles, M. Blast2GO: a universal tool for annotate on, visualization and analysis in functional genomics research. Bioinformatics 21, 3674-3676 (2005).
40. Theocharidis, A., Van, Dongen. S., Enright, A. J. & Freeman, T. C. Network visualization and analysis of gene expression data using BioLayout Express (3D). Nat. Protoc. 4, 1535-1550 (2009).