Korean Journal of Agricultural Science (농업과학연구)

Institute of Agricultural Science, CNU (충남대학교 농업과학연구소)
권호 표지
DOI QR코드

DOI QR Code

Construction of a full-length cDNA library from Pinus koraiensis and analysis of EST dataset

잣나무(Pinus koraiensis)의 cDNA library 제작 및 EST 분석

  • Kim, Joon-Ki (Department of Horticulture, Chungnam National University) ;
  • Im, Su-Bin (Department of Horticulture, Chungnam National University) ;
  • Choi, Sun-Hee (Department of Horticulture, Chungnam National University) ;
  • Lee, Jong-Suk (Department of Horticulture, Chungnam National University) ;
  • Roh, Mark S. (USDA, Agricultural Research Service, National Arboretum, Floral and Nursery Plants Research Unit) ;
  • Lim, Yong-Pyo (Department of Horticulture, Chungnam National University)
  • Received : 2011.01.11
  • Accepted : 2011.03.09
  • Published : 2011.03.30
Download PDF
⟨ Previous Next ⟩

Abstract

In this study, we report the generation and analysis of a total of 1,211 expressed sequence tags (ESTs) from Pinus koraiensis. A cDNA library was generated from the young leaf tissue and a total of 1,211 cDNA were partially sequenced. EST and unigene sequence quality were determined by computational filtering, manual review, and BLAST analyses. In all, 857 ESTs were acquired after the removal of the vector sequence and filtering over a minimum length 50 nucleotides. A total of 411 unigene, consisting of 89 contigs and 322 singletons, was identified after assembling. Also, we identified 77 new microsatellite-containing sequences from the unigenes and classified the structure according to their repeat unit. According to homology search with BLASTX against the NCBI database, 63.1% of ESTs were homologous with known function and 22.2% of ESTs were matched with putative or unknown function. The remaining 14.6% of ESTs showed no significant similarity to any protein sequences found in the public database. Gene ontology (GO) classification showed that the most abundant GO terms were transport, nucleotide binding, plastid, in terms biological process, molecular function and cellular component, respectively. The sequence data will be used to characterize potential roles of new genes in Pinus and provided for the useful tools as a genetic resource.

Keywords

References

  1. Asset G, Staels B, Wolff RL, Bauge E, Madj Z, Fruchart JC, Dallongeville J. 1999. Effects of Pinus pinaster and Pinus koraiensis seed oil supplementation on lipoprotein metabolism in the rat. Lipids 34: 39-44. https://doi.org/10.1007/s11745-999-335-2
  2. Bagchi D, Bagchi M, Stohs SJ, Das DK, Ray SD, Kuszynski CA, Joshi SS, Pruess HG. 2000. Free radicals and grape seed proanthocyanidin extract: Importance in human health and disease prevention. Toxicology 148: 187-197. https://doi.org/10.1016/S0300-483X(00)00210-9
  3. Chang S, Puryear J, Cairney J. 1993. A simple and efficient method for isolating RNA from pine trees. Plant Mol. Biol. Rep. 11(2): 113-116. https://doi.org/10.1007/BF02670468
  4. Choi DS, Kayama M, Jin HO, Lee CH, Izuta T, Koike T. 2006. Growth and photosynthetic responses of two pine species (Pinus koraiensis and Pinus rigida) in a polluted industrial region in Korea. Environmental Pollution 139: 421-432. https://doi.org/10.1016/j.envpol.2005.06.006
  5. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676. https://doi.org/10.1093/bioinformatics/bti610
  6. Durand J, Catherine B, Chancerel E, Frigerio JM, Vendramin G, Sebastiani F, Buonamici A, Gailing O, Koelewijn HP, Villani F, Mattioni C, Cherubini M, Goicoechea PG, Herrn A, Ikaran Z, Caban C, Ueno S, Alberto F, Dumoulin PY, Guichoux E, Daruvar A, Kremer A, Plomion C. 2010. A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study. BMC Genomics 11: 570-582. https://doi.org/10.1186/1471-2164-11-570
  7. Han SS, Hwang BH. 1990. Analysis of amino acid, fatty acid and vitamin in Korean pine(Pinus koraiensis) seed. Jour. Korean For. Soc. 79(4): 345-351.
  8. ISUN. 2001. The ISUN red list categories (Version 3.1). ISUN Species Survival Commission. Gland. Switzerland.
  9. Kantety RV, La Rota M, Matthews DE, Sorrells ME. 2002. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol. Biol. 48: 501-510. https://doi.org/10.1023/A:1014875206165
  10. Li K, Qingwang L, Jian L, Zhang T, Han Z, Gao D, Zheng F. 2007. Antitumor activity of the procyanidins from Pinus koraiensis bark on mice bearing U14 cervical cancer. Yakugaku Zasshi 127: 1145-1151. https://doi.org/10.1248/yakushi.127.1145
  11. Mirov NT. 1967. The Genus Pinus, Ronald, New York.
  12. Noh EW, Lee JS, Choi YI, Han MS, Lee H, Yi YS, Han SU. 2007. Hotspots in chloroplast genome as new tools to study relationship among pines. Korean White Pine (Pinus koraiensis)II: 41-50.
  13. Okayama H, Berg P. 1982. High efficiency cloning of full-length cDNA. Mol. Cell Biol. 2: 161-170. https://doi.org/10.1128/MCB.2.2.161
  14. Temnykh S, Park WD, Ayers N, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch SR. 1999. Mapping and genome organization of microsatellites in rice (Oryza sativa). Theor. Appl. Genet. 100: 697-712.
  15. Vidakovic M. 1991. Conifers: Morphology and Variation, Crafickizavod Hrvatske, Croatia.
  16. William BC. 1966. Geographic distribution on the pines of the world. 32: 5.
  17. Yoon TH. 1987. Fatty acid composition of total lipids from seeds of Pinus koraiensis. J. Korean Soc. Food Nutr. 16(2): 93-97.

Cited by

  1. Investigation of Active Anti-Inflammatory Constituents of Essential Oil from Pinus koraiensis (Sieb. et Zucc.) Wood in LPS-Stimulated RBL-2H3 Cells vol.11, pp.6, 2021, https://doi.org/10.3390/biom11060817