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Construction of a Full-length cDNA Library from Korean Stewartia (Stewartia koreana Nakai) and Characterization of EST Dataset  

Im, Su-Bin (Department of Horticulture, Chungnam National University)
Kim, Joon-Ki (Department of Horticulture, Chungnam National University)
Choi, Young-In (Department of Horticulture, Chungnam National University)
Choi, Sun-Hee (Department of Horticulture, Chungnam National University)
Kwon, Hye-Jin (Department of Forestry Resources, Chungnam National University)
Song, Ho-Kyung (Department of Forestry Resources, Chungnam National University)
Lim, Yong-Pyo (Department of Horticulture, Chungnam National University)
Publication Information
Horticultural Science & Technology / v.29, no.2, 2011 , pp. 116-122 More about this Journal
Abstract
In this study, we report the generation and analysis of 1,392 expressed sequence tags (ESTs) from Korean Stewartia (Stewartia koreana Nakai). A cDNA library was generated from the young leaf tissue and a total of 1,392 cDNA were partially sequenced. EST and unigene sequence quality were determined by computational filtering, manual review, and BLAST analyses. Finally, 1,301 ESTs were acquired after the removal of the vector sequence and filtering over a minimum length 100 nucleotides. A total of 893 unigene, consisting of 150 contigs and 743 singletons, was identified after assembling. Also, we identified 95 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, 65% of ESTs were homologous with known function and 11.6% of ESTs were matched with putative or unknown function. The remaining 23.2% of ESTs showed no significant similarity to any protein sequences found in the public database. Annotation based searches against multiple databases including wine grape and populus sequences helped to identify putative functions of ESTs and unigenes. 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 Stewartia and provided for the useful tools as a genetic resource.
Keywords
contig; gene ontology; homology; singleton; unigene;
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1 Struve, D.K., B.A. Oleksak, T. Kawahara, and A. Kanazashi. 1999. Germination of Japanese Stewartia seeds: The effects of warm and cold stratification. J. Envt. Horticul. 17:197-202.
2 Temnykh, S., W.D. Park, N. Ayers, S. Cartinhour, N. Hauck, L. Lipovich, Y.G. Cho, T. Ishii, and S.R. McCouch. 1999. Mapping and genome organization of microsatellites in rice (Oryza sativa). Theor. Appl. Genet. 100:697-712.
3 Yang, B.H., S.D. Han, Y.B. Koo, and Y.G. Park. 2006. Genetic variation in the natural populations of Korean Stewartia (Stewartia koreana Nakai) based on I-SSR analysis. Korean J. Plant Res. 19:189-195.
4 Min, B.S., K.H. Bae, Y.H. Kim, H. Miyashiro, M. Hattori, and K. Shimotohno. 1999. Screening of Korean plants against human immunodeficiency virus type 1 protease. Phytother. Res. 13:680-682.   DOI   ScienceOn
5 Okayama, H. and P. Berg. 1982. High efficiency cloning of fulllength cDNA. Mol. Cell Biol. 2:161-170.   DOI
6 Peng, F.Y., K.E. Reida, N. Liaob, J. Schlossera, D. Lijavetzkyc, R. Holtb, J.M.M. Zapaterc, S. Jonesb, M. Marrab, J. Bohlmannd, and S.T. Lund. 2007. Generation of ESTs in Vitis vinifera wine grape (Cabernet Sauvignon) and table grape (Muscat Hamburg) and discovery of new candidate genes with potential roles in berry development. Gene 402:40-50.   DOI
7 Son, S.G., Y.J. Cho, and H.K. Moon. 2004. Effects of BA and NAA on adventitious shoot formation from mature zygotic of Stewartia koreana Nakai. Korean J. Plant. Res. 17:272-277.
8 Prince, L.M. and C.R. Parks. 2001. Phylogenetic relationships of Theaceae inferred from chloroplast DNA sequence data. Am. J. Bot. 88:2309-2320.   DOI   ScienceOn
9 Shim, K.K., B.K. Seo, K.W. Lee, K.W. Cho, and S.C. Shim. 1992. Study on the Korean native Stewartia (Stewartia koreana) I. Study on the native distribution of Korean Stewartia (Stewartia koreana) in Mt. Sobaek. J. Kor. Soc. Hort. Sci. 33:413-424.
10 Shim, K.K., B.K. Seo, K.W. Cho, and S.C. Shim. 1993. Study on the Korean native Stewartia (Stewartia koreana) II. Seed germination and softwood cutting of Korean Stewartia (Stewartia koreana) in Mt. Sobaek. J. Kor. Soc. Hort. Sci. 34:160-166.
11 Spongberg, A.S. and A.J. Fordham. 1975. Stewartias-small trees and shrubs for all seasons. Arnoldia 35:165-180.
12 Stevens, P.F., S. Dressler, and A.L. Weitzman. 2004. Theaceae. In The Families and Genera of Vascular Plants, p. 463-471. VI. Kubitzki, K. (ed.), Springer.
13 Durand, J., B. Catherine, E. Chancerel, J.-M. Frigerio, G. Vendramin, F. Sebastiani, A. Buonamici, O. Gailing, H.-P. Koelewijn, F. Villani, C. Mattioni, M. Cherubini, P. G. Goicoechea, A. Herrán, Z. Ikaran, C. Cabane, S. Ueno, F. Alberto, P.-Y. Dumoulin, E. Guichoux, A. Daruvar, A. Kremer, and C. Plomion. 2010. A fast and cost-effective approach to develop and map ESTSSR markers: oak as a case study. BM Genomics 11:570.   DOI
14 Eom, I.Y., H.H. Kim, S.M. Lee, Y.S. Yi, and J.W. Choi. 2010. Characterization of chemical composition in Poplar wood (Populus deltoids) by suppression of CCoAOMT gene expression. Mokchae Konghak 38:213-222.
15 Han, S.S., S.C. Lo, Y. Choi, J.H. Kim, and S.H. Baek. 2003. Antioxidant activity of crude extract and pure compounds of Acer ginnala Max. Bull Korean Chem. Soc. 25:389-391.   DOI
16 Kwon, H. and H. Song. 2008. Vegetation structures and ecological properties of Sterwartia koreana community. Jour. Korean For. Soc. 97:296-304.
17 ISUN. 2001. The ISUN red list catagoris (Version 3.1). ISUN Species Survival Commission. Gland. Switzerland.
18 Kantety, R.V., M. La Rota, D.E. Matthews, and M.E, Sorrells. 2002. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol. Biol. 48:501-510.   DOI   ScienceOn
19 Kim, Y., H.Y. Min, H.J. Park, E.J. Lee, E.J. Park, H.J. Hwang, C. Jin, Y.S. Lee, and S.K. Lee. 2004. Suppressive effects of nitric oxide production and inducible nitric oxide synthase (NOS) gene expression by Calystegia soldanella methanol extract on lipopolysaccharide-activated RAW 264.7 cells. Eur. J. Cancer Prev. 13:419-424.   DOI   ScienceOn
20 Kwon, H., H., Song, and M. Kim. 2008. Taxonomic review of the Stewartia koreana Nakai ex Rehder (Theaceae). Korean J. PI. Taxon. 38:233-250.   DOI
21 Li, J. 1996. A systematic study on the genera Stewartia and Hartia (Theaceae). Acta Phytotaxonnmica Sinica 34:48-67.
22 Anterola, A.M. and N.G. Lewis. 2002. Trends in lignin modification: a comprehensive analysis of the effects of genetic manipulations/mutations on lignification and vascular intergrity. Phytochemistry 61:221-294.   DOI   ScienceOn
23 Conesa, A., S. Gotz, J.M. Garcia-Gomez, J. Terol, M. Talon, and M. Robles. 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674-3676.   DOI   ScienceOn
24 Chang, C.S., H. Kim, and Y.S. Kim. 2001. Reconstruction of rare and endangered plant species in Korea based on the IUCN red list categories. Korean J. PI. Taxon. 31:107-142.   DOI
25 Chang, S., J. Puryear, and J, Cairney. 1993. A simple and efficient method for isolating RNA from pine trees. Plant Mol. Biol. Rep. 11:113-116.   DOI   ScienceOn
26 Choi, Y.H., S.S. Han, H.O. Lee, and S.H. Baek. 2005. Biological activity of bioactive components from Acer ginnala max. Bull. Korean Chem. Soc. 26:1450-1452.   DOI
27 Dirr, M.A. 1990. Manual of woody landscape plants. 4th. ed. p. 1007. Stipes Publishing company Ilinois.
28 Dirr, M.A. 1991. It's time to bring Stewartia out of the garden closet. Nursery Manager 10:27-30.