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Isolation of Gene according to the Physiological Changes of Lespedeza cuneata. G don by the Convergence Study using a Computer Program and NGS (Next Generation Sequencing)

NGS (Next Generation Sequencing)와 컴퓨터 프로그램의 융합적 연구를 통한 비수리(Lespedeza cuneata. G. don)의 생리적 변화에 따른 유용 유전자 분리

  • Ahn, Chul-Hyun (Korea National College of Agriculture and Fisheries)
  • Received : 2017.10.23
  • Accepted : 2017.12.20
  • Published : 2017.12.28

Abstract

This study was carried out to investigate the possibility of isolating the useful gene of soybean plant, anthocyanin, through NGS (Next Generation Sequencing) and molecular biology experiments. Lespedeza cuneata. G. don is a resource plant but has many useful materials. Especially, D-pinitol, which has anti-diabetic function, is contained in a large amount. However, the gene related to the biosynthesis of D-piniol has not been isolated in the non-spermatid. Lespedeza cuneata. G. don was treated with abiotic stress (drought), total RNA was extracted, and a library was constructed to perform NGS. In this way, the genes involved in D-pinitol biosynthesis were isolated and sequenced in silico. In order to support this, ononitol epimerase involved in D-pinitol amplification was identified using the Blast program and RT-PCR confirmed the increased gene expression in vitro, and the gene was isolated and identified by convergence study.

Keywords

Next Generation Sequencing;D-pinitol;Epimerase;Abiotic stress;Anti-diabetic;Functional material

References

  1. I. B. Park, J. Kim, D. J. Kim, C. H. Chung, J. Y. Oh, S. W. Park, J. Lee, K. M. Choi, K. W. Min, J. H. Park, H. S. Son, C. W. Ahn, H. Kim, S. Lee, I. B. Lee, I. Choi, S. H. Baik, "Diabetes epidemics inKorea: Reappraise nationwide survey of diabetes "Diabetesin Korea 2007"", Diabetes Metab J Vol. 37, pp. 233-239, 2013. https://doi.org/10.4093/dmj.2013.37.4.233
  2. Y. R. Lee, N. Yoon, "Anti-oxidative and anti-Diabetic effects of methanol extracts from medicinal plants", J Korean Soc Food Sci Nutr Vol. 44, pp. 681-686, 2015 https://doi.org/10.3746/jkfn.2015.44.5.681
  3. H. Hikino, M. Takahashi, K. Otake, C. Konno, "Isolation and hypoglycemic activity of eleutherans A, B, C, D, E, F, and G : Glycans of Eleutherococcus senticoccus root", J. Nat. Prod. Vol. 49, pp. 293-297, 1986. https://doi.org/10.1021/np50044a015
  4. A. Kato, T. Miura, "Hpogly-cemic action of the rhizomesof polygo-natum officinale in normal and diabetic mice", Planta. Med. Vol. 60, pp. 201-206, 1994. https://doi.org/10.1055/s-2006-959458
  5. F. S. Medina, M. J. Gamez, J. Jimenez, I. Osuna, A. Zarzuelo, "Hypoglycemic activity of Juniper Berries", PlantaMed. Vol. 60, pp. 197-203, 1994.
  6. N. Ohno, I. Suzuki, K. Sato, S. Oikawa, T. Miyazaki, T. Yadomae, 'Purification and structural characterization of anantitumor ${\beta}$-1,3-glucan isolated from hot water extract of the fruitbody of cultured Grifola frondosa", Chem. Pharm. Bull. Vol. 33, pp. 4522- 4527, 1985. https://doi.org/10.1248/cpb.33.4522
  7. G. Zhao, J. Kan, Z. Li, Z. Chen, "Structural features andimmu- nological activity of a polysaccharide from Dios-coreaopposita Thumb roots", Carbohydr Polym Vol. 61, pp. 125-131, 2005. https://doi.org/10.1016/j.carbpol.2005.04.020
  8. H. R. Park, J. S. Cho, "Effects of natural medicinal multiplantextract on blood glucose, insulin levels, and serum- malondialdehyde concentrations in strep- tozotocin-induceddiabetic rats", J East Asian Soc Dietary Life. Vol. 17, pp. 205-212, 2007.
  9. V. A. Koivisto, "Insulin therapy on type II diabetes", Diabetes Care Vol. 16, pp. 29-39, 1993. https://doi.org/10.2337/diacare.16.3.29
  10. H. A, Lee, H. S. Sim, K. J. Choi, H. B. Lee, "Hypoglycemicaction of red ginseng components (II): Investigation of effectof fat soluble fraction from red ginseng on enzymesrelated to glucose metabolism in cultured rat hapato-cytes", Korean J Ginseng Sci Vol. 22, pp. 51-59, 1998.
  11. W. H. Dillmann, "Diabetes mellitus induced changes incardiac myosin of the rat", Diabetes Vol. 29, pp. 579-582, 1980. https://doi.org/10.2337/diab.29.7.579
  12. T. Katsube, H. Tabata, Y. Ohta, Y. Yamasaki, E. Anuurad, K. Shiwaku, Y. Yamane, "Screening for antioxidant activityin edible plant products: Comparison of low-densitylipo- protein oxidation assay, DPPH radical scavenging assay, and Folin-Ciocalteu assay', J Agric Food Chem Vol. 52, pp. 2391-2396, 2004. https://doi.org/10.1021/jf035372g
  13. C. H. Kee, "The pharmacology of Chinese herbs", CRCPress. pp. 222, 1993
  14. Q. Wang, H. Kuang, Y. Su, Y. Sun, J. Feng, R. Guo, K. Chan, "Naturally derived anti-inflammatory compounds from Chinese medicinal plants", J Ethnopharmacol Vol. 146, pp. 9-39, 2013. https://doi.org/10.1016/j.jep.2012.12.013
  15. S. J. Choi, Y. S. Kim, J. H. Kim, J. S. Kim, "Screening of herbal medicines from korea with inhibitory activity on Advanced glycation end products formation (XII)", Kor. J. Pharmacogn Vol. 46, No. 3, pp. 250-259, 2015
  16. H. Y. Kim, J. Y. Ko, S. B. Song, J. I. Kim, H. I. Seo1, J. S. Lee, D. Y. Kwak, T. W. Jung, K. Y. Kim, I. S. Oh, H. S. Jeong, K. S. Woo, "Antioxidant and ${\alpha}$-Glucosidase inhibition activities of solvent fractions from methanolic extract of sericea Lespedeza (Lespedeza cuneata G. Don)", J Korean Soc Food Sci Nutr Vol. 41, No. 11, pp. 1508-1514, 2012 https://doi.org/10.3746/jkfn.2012.41.11.1508
  17. K. A. Chung, M. J. Cheong, "Effect of Lespedeza Caneata (LC) extracts on atopic dermatitis in DNCB-induced Mice" Journal of the Korea Convergence Society, Vol. 7, No. 4, pp. 67-73, 2016.
  18. E. J. Kim, J. Y. Choi, M. Yu, M. Y. K, S. H. Lee, B. H. Lee, "Total polyphenols, total flavonoid contents, and antioxidant activity of korean natural and medicinal plants", Korea J. Food Sci. Technol. Vol. 44, No. 3, pp. 337-342, 2012 https://doi.org/10.9721/KJFST.2012.44.3.337
  19. J. H. Lee, J. W. Jhoo, "Antioxidant activity of different parts of Lespedeza bicolor and isolation of antioxidant compound", Korea J. Food Sci. Technol. Vol. 44, No. 6, pp. 763-771, 2012 https://doi.org/10.9721/KJFST.2012.44.6.763
  20. H. K. Jung, K. S. Kim, Y. S. Jeong, "Wound Healing Effects of Lespedeza cuneata Extract", J Korean Soc Food Sci Nutr Vol. 43, No. 3, pp. 374-380, 2014 https://doi.org/10.3746/jkfn.2014.43.3.374
  21. J. A. Martin, Z. Wang, "Next-generation transcriptome assembly", Nat Rev Genet Vol. 12, No. 10, pp. 671-82, 2011. https://doi.org/10.1038/nrg3068
  22. B. J. Haas, A. Papanicolaou, M. Yassour, M. Grabherr, P. D. Blood, J. Bowden, M. B. Couger, D. Eccles, B. Li, M. Lieber, M. D. MacManes, M. Ott, J. Orvis, N. Pochet, F. Strozzi, N. Weeks, R Westerman, T. William, C. N. Dewey, R. Henschel, R. D. LeDuc, N. Friedman, A. Regev, "De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis", Nature Protocols Vol. 8, pp. 1494-1512, 2013 https://doi.org/10.1038/nprot.2013.084
  23. Y. Yang, S.A. Smith, "Optimizing de novo assembly of short-read RNA-seq data for phylogenomics", BMC Genomics. Vol. 14, pp. 328, 2013 https://doi.org/10.1186/1471-2164-14-328
  24. G. Pertea, X. Huang, F. Liang, V. Antonescu, R. Sultana, S. Karamycheva, Y. Lee, J. White, F. Cheung, B. Parvizi, J. Tsai, J. Quackenbush, "TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets", Bioinformatics, Vol. 19, pp. 651-652, 2003 https://doi.org/10.1093/bioinformatics/btg034
  25. X. Huang, A. Madan, "CAP3: A DNA sequence assembly program", Genome Res. Vol. 9, pp. 868-877, 1999. https://doi.org/10.1101/gr.9.9.868
  26. E. Blanco, G. Parra, R. Guigo, "Using geneid to Identify Genes", Curr Protoc Bioinformatics. Chapter 4:Unit 4.3, 2007
  27. S. M. Seo, Y. S. Jeong, Hari, D. Krisna, D. H. Shin, I. J. Lee, E. S. Park, J. D. Lee, Y. H. Hwang, "Variation of Pinitol Content for Domestic Legume Species in Korea" Korea Journal Of Crop Science Vol. 56, No. 1, pp. 50-56, 2011 https://doi.org/10.7740/kjcs.2011.56.1.050