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International Journal of Genomics
Volume 2015, Article ID 782635, 11 pages
http://dx.doi.org/10.1155/2015/782635
Research Article

Analysis of Polygala tenuifolia Transcriptome and Description of Secondary Metabolite Biosynthetic Pathways by Illumina Sequencing

1Research Institute of Economics Crop, Shanxi Academy of Agriculture Science, Fenyang, Shanxi 032200, China
2Modern Research Center for Traditional Chinese Medicine, Shanxi University, No. 92 Wucheng Road, Taiyuan, Shanxi 030006, China
3College of Chemistry and Chemical Engineering, Shanxi University, No. 92 Wucheng Road, Taiyuan, Shanxi 030006, China
4Institute of Materia Medica, Chinese Academy of Medical Sciences, Beijing 100050, China

Received 22 June 2015; Accepted 3 August 2015

Academic Editor: Xiaohan Yang

Copyright © 2015 Hongling Tian et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. Y. Yao, M. Jia, J.-G. Wu et al., “Anxiolytic and sedative-hypnotic activities of polygalasaponins from Polygala tenuifolia in mice,” Pharmaceutical Biology, vol. 48, no. 7, pp. 801–807, 2010. View at Publisher · View at Google Scholar · View at Scopus
  2. F. S. Zhang, X. W. Li, Z. Y. Li et al., “UPLC/Q-TOF MS-based metabolomics and qRT-PCR in enzyme gene screening with key role in triterpenoid saponin biosynthesis of Polygala tenuifolia,” PLoS ONE, vol. 9, no. 8, Article ID e105765, 2014. View at Publisher · View at Google Scholar
  3. H. Seki, S. Sawai, K. Ohyama et al., “Triterpene functional genomics in licorice for identification of CYP72A154 involved in the biosynthesis of glycyrrhizin,” The Plant Cell, vol. 23, no. 11, pp. 4112–4123, 2011. View at Publisher · View at Google Scholar · View at Scopus
  4. S. Chen, H. Luo, Y. Li et al., “454 EST analysis detects genes putatively involved in ginsenoside biosynthesis in Panax ginseng,” Plant Cell Reports, vol. 30, no. 9, pp. 1593–1601, 2011. View at Publisher · View at Google Scholar · View at Scopus
  5. H. Luo, C. Sun, Y. Sun et al., “Analysis of the transcriptome of Panax notoginseng root uncovers putative triterpene saponin-biosynthetic genes and genetic markers,” BMC Genomics, vol. 12, no. 5, article S5, 2011. View at Publisher · View at Google Scholar · View at Scopus
  6. C. Sun, Y. Li, Q. Wu et al., “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, vol. 11, article 262, 2010. View at Publisher · View at Google Scholar · View at Scopus
  7. W. Gao, H.-X. Sun, H. Xiao et al., “Combining metabolomics and transcriptomics to characterize tanshinone biosynthesis in Salvia miltiorrhiza,” BMC Genomics, vol. 15, article 73, 2014. View at Publisher · View at Google Scholar · View at Scopus
  8. L. Liu, Y. Li, S. Li et al., “Comparison of next-generation sequencing systems,” Journal of Biomedicine and Biotechnology, vol. 2012, Article ID 251364, 11 pages, 2012. View at Publisher · View at Google Scholar
  9. Y. Yang, M. Xu, Q. Luo, J. Wang, and H. Li, “De novo transcriptome analysis of Liriodendron chinense petals and leaves by Illumina sequencing,” Gene, vol. 534, no. 2, pp. 155–162, 2014. View at Publisher · View at Google Scholar · View at Scopus
  10. S. Fowler and M. F. Thomashow, “Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway,” Plant Cell, vol. 14, no. 8, pp. 1675–1690, 2002. View at Publisher · View at Google Scholar · View at Scopus
  11. R. Zhai, Y. Feng, H. Wang et al., “Transcriptome analysis of rice root heterosis by RNA-Seq,” BMC Genomics, vol. 14, no. 1, article 19, 2013. View at Publisher · View at Google Scholar · View at Scopus
  12. I. Zouari, A. Salvioli, M. Chialva et al., “From root to fruit: RNA-Seq analysis shows that arbuscular mycorrhizal symbiosis may affect tomato fruit metabolism,” BMC Genomics, vol. 15, article 221, 2014. View at Publisher · View at Google Scholar · View at Scopus
  13. S. Kaur, L. W. Pembleton, N. O. I. Cogan et al., “Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers,” BMC Genomics, vol. 13, no. 1, article 104, 2012. View at Publisher · View at Google Scholar · View at Scopus
  14. U. Chandrasekaran, W. Xu, and A. Liu, “Transcriptome profiling identifies ABA mediated regulatory changes towards storage filling in developing seeds of castor bean (Ricinus communis L.),” Cell & Bioscience, vol. 4, no. 1, article 33, 2014. View at Publisher · View at Google Scholar · View at Scopus
  15. T. Zhang, X. Zhao, W. Wang et al., “Deep transcriptome sequencing of rhizome and aerial-shoot in Sorghum propinquum,” Plant Molecular Biology, vol. 84, no. 3, pp. 315–327, 2014. View at Publisher · View at Google Scholar · View at Scopus
  16. Y. Ikeya, S. Takeda, M. Tunakawa et al., “Cognitive improving and cerebral protective effects of acylated oligosaccharides in Polygala tenuifolia,” Biological and Pharmaceutical Bulletin, vol. 27, no. 7, pp. 1081–1085, 2004. View at Publisher · View at Google Scholar · View at Scopus
  17. J. M. Augustin, V. Kuzina, S. B. Andersen, and S. Bak, “Molecular activities, biosynthesis and evolution of triterpenoid saponins,” Phytochemistry, vol. 72, no. 6, pp. 435–457, 2011. View at Publisher · View at Google Scholar · View at Scopus
  18. Y. Wang, X. Wang, T.-H. Lee, S. Mansoor, and A. H. Paterson, “Gene body methylation shows distinct patterns associated with different gene origins and duplication modes and has a heterogeneous relationship with gene expression in Oryza sativa (rice),” New Phytologist, vol. 198, no. 1, pp. 274–283, 2013. View at Publisher · View at Google Scholar · View at Scopus
  19. V. Tzin and G. Galili, “The biosynthetic pathways for shikimate and aromatic amino acids in Arabidopsis thaliana,” The Arabidopsis Book, vol. 8, Article ID e0132, 2010. View at Publisher · View at Google Scholar
  20. W. Boerjan, J. Ralph, and M. Baucher, “Lignin biosynthesis,” Annual Review of Plant Biology, vol. 54, pp. 519–546, 2003. View at Publisher · View at Google Scholar · View at Scopus
  21. J. C. D'Auria and J. Gershenzon, “The secondary metabolism of Arabidopsis thaliana: growing like a weed,” Current Opinion in Plant Biology, vol. 8, no. 3, pp. 308–316, 2005. View at Publisher · View at Google Scholar · View at Scopus
  22. B. Langmead, C. Trapnell, M. Pop, and S. L. Salzberg, “Ultrafast and memory-efficient alignment of short DNA sequences to the human genome,” Genome Biology, vol. 10, no. 3, article R25, 2009. View at Publisher · View at Google Scholar · View at Scopus
  23. R. L. Tatusov, E. V. Koonin, and D. J. Lipman, “A genomic perspective on protein families,” Science, vol. 278, no. 5338, pp. 631–637, 1997. View at Publisher · View at Google Scholar · View at Scopus
  24. R. L. Tatusov, N. D. Fedorova, J. D. Jackson et al., “The COG database: an updated vesion includes eukaryotes,” BMC Bioinformatics, vol. 4, article 41, 2003. View at Publisher · View at Google Scholar · View at Scopus
  25. M. Kanehisa, S. Goto, M. Hattori et al., “From genomics to chemical genomics: new developments in KEGG,” Nucleic Acids Research, vol. 34, pp. D354–D357, 2006. View at Publisher · View at Google Scholar · View at Scopus
  26. E. M. Zdobnov and R. Apweiler, “InterProScan—an integration platform for the signature-recognition methods in InterPro,” Bioinformatics, vol. 17, no. 9, pp. 847–848, 2001. View at Publisher · View at Google Scholar · View at Scopus
  27. M. L. Wise and R. Croteau, “Monoterpene biosynthesis,” in Comprehensive Natural Products Chemistry, p. 2, Elsevier, 1998. View at Google Scholar
  28. C. A. Schuhr, T. Radykewicz, S. Sagner et al., “Quantitative assessment of crosstalk between the two isoprenoid biosynthesis pathways in plants by NMR spectroscopy,” Phytochemistry Reviews, vol. 2, no. 1-2, pp. 3–16, 2003. View at Publisher · View at Google Scholar · View at Scopus
  29. W. Eisenreich, M. Schwarz, A. Cartayrade, D. Arigoni, M. H. Zenk, and A. Bacher, “The deoxyxylulose phosphate pathway of terpenoid biosynthesis in plants and microorganisms,” Chemistry and Biology, vol. 5, no. 9, pp. R221–R233, 1998. View at Publisher · View at Google Scholar · View at Scopus
  30. J. D. Park, D. K. Rhee, and Y. H. Lee, “Biological activities and chemistry of saponins from Panax ginseng C. A. Meyer,” Phytochemistry Reviews, vol. 4, no. 2-3, pp. 159–175, 2005. View at Publisher · View at Google Scholar · View at Scopus
  31. M. Rohmer, “Mevalonate-independent methylerythritol phosphate pathway for isoprenoid biosynthesis, elucidation and distribution,” Pure and Applied Chemistry, vol. 75, no. 2-3, pp. 375–387, 2003. View at Google Scholar · View at Scopus
  32. S. Kalra, B. L. Puniya, D. Kulshreshtha et al., “De novo transcriptome sequencing reveals important molecular networks and metabolic pathways of the plant, chlorophytum borivilianum,” PLoS ONE, vol. 8, no. 12, Article ID e83336, 2013. View at Publisher · View at Google Scholar · View at Scopus
  33. A. H. Meijer, E. Souer, R. Verpoorte, and J. H. C. Hoge, “Isolation of cytochrome P450 cDNA clones from the higher plant Catharanthus roseus by a PCR strategy,” Plant Molecular Biology, vol. 22, no. 2, pp. 379–383, 1993. View at Publisher · View at Google Scholar · View at Scopus
  34. H. Seki, K. Ohyama, S. Sawai et al., “Licorice beta-amyrin 11-oxidase, a cytochrome P450 with a key role in the biosynthesis of the triterpene sweetener glycyrrhizin,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 37, pp. 14204–14209, 2008. View at Publisher · View at Google Scholar · View at Scopus
  35. M. Shibuya, M. Hoshino, Y. Katsube, H. Hayashi, T. Kushiro, and Y. Ebizuka, “Identification of β-amyrin and sophoradiol 24-hydroxylase by expressed sequence tag mining and functional expression assay,” FEBS Journal, vol. 273, no. 5, pp. 948–959, 2006. View at Publisher · View at Google Scholar · View at Scopus
  36. Y. Wang, Y. Pan, Z. Liu et al., “De novo transcriptome sequencing of radish (Raphanus sativus L.) and analysis of major genes involved in glucosinolate metabolism,” BMC Genomics, vol. 14, article 836, 2013. View at Publisher · View at Google Scholar · View at Scopus
  37. D. Meesapyodsuk, J. Balsevich, D. W. Reed, and P. S. Covello, “Saponin biosynthesis in Saponaria vaccaria. cDNAs encoding β-amyrin synthase and a triterpene carboxylic acid glucosyltransferase,” Plant Physiology, vol. 143, no. 2, pp. 959–969, 2007. View at Publisher · View at Google Scholar · View at Scopus
  38. L. Achnine, D. V. Huhman, M. A. Farag, L. W. Sumner, J. W. Blount, and R. A. Dixon, “Genomics-based selection and functional characterization of triterpene glycosyltransferases from the model legume Medicago truncatula,” Plant Journal, vol. 41, no. 6, pp. 875–887, 2005. View at Publisher · View at Google Scholar · View at Scopus
  39. K. Yonekura-Sakakibara, T. Tohge, F. Matsuda et al., “Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis,” Plant Cell, vol. 20, no. 8, pp. 2160–2176, 2008. View at Publisher · View at Google Scholar · View at Scopus
  40. R. Yin, B. Messner, T. Faus-Kessler et al., “Feedback inhibition of the general phenylpropanoid and flavonol biosynthetic pathways upon a compromised flavonol-3-O-glycosylation,” Journal of Experimental Botany, vol. 63, no. 7, pp. 2465–2478, 2012. View at Publisher · View at Google Scholar · View at Scopus
  41. J. Chen, X. Dong, Q. Li et al., “Biosynthesis of the active compounds of Isatis indigotica based on transcriptome sequencing and metabolites profiling,” BMC Genomics, vol. 14, article 857, 2013. View at Publisher · View at Google Scholar · View at Scopus