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http://dx.doi.org/10.5010/JPB.2009.36.2.130

Structural analysis of expressed sequence tags inimmature seed of Oryza sativa L.  

Yoon, Ung-Han (Genomics Division, National Academy of Agricultural Science, RDA)
Lee, Gang-Seob (Genomics Division, National Academy of Agricultural Science, RDA)
Lee, Jung-Sook (Genomics Division, National Academy of Agricultural Science, RDA)
Hahn, Jang-Ho (Genomics Division, National Academy of Agricultural Science, RDA)
Kim, Chang-Kug (Genomics Division, National Academy of Agricultural Science, RDA)
Kikuch, Shoshi (Genome and Biodiversity Research Division, National Institute of Agrobiological Science)
Satoh, Kouji (Genome and Biodiversity Research Division, National Institute of Agrobiological Science)
Kim, Jin-A (Genomics Division, National Academy of Agricultural Science)
Lee, Jeong-Hwa (Genomics Division, National Academy of Agricultural Science)
Lee, Tae-Ho (Bioscience and Bioinformatics Division, MyongJi University)
Kim, Yong-Hwan (Genomics Division, National Academy of Agricultural Science)
Publication Information
Journal of Plant Biotechnology / v.36, no.2, 2009 , pp. 130-136 More about this Journal
Abstract
Rice (Oryza sativa) is the most important staple crop in Korea. With its small genome size of 389Mb, rice is a model plant for genome research. We analyzed expressed sequence tag (EST) clones from immature seeds of rice (cv. Ilpum) at 20 days after heading. The 25,668 EST clones were clustered by using SeqMan program and 7,509 clones were selected as unique clones. We compared the 7,509 unique genes with KOME database including the 32,127 FL-cDNA in rice. Finally, 4,990 clones were homologous and 2,519 clones non-homologous to FL-cDNA clones. In addition, we mapped the 7,509 cDNA clones by using TIGR rice pseudomolecule version 5. Ultimately, 7,347 clones were matched to be significant clones related to the TIGR rice pseudomolecules, but 162 clones were unmapped. For the clustering of orthologous group genes, we further analyzed the 7,509 EST clones from immature seeds using NCBI clusters of orthologous groups database. Among the clones, 4,968 clones were categorized into information storage and processing, cellular processes and signaling, metabolism and poorly characterized genes, proportioning 799 (14.89%), 1,536 (28.3%), 1,148 (21.2%) and 1,936 (35.7%) clones to the previous four categories, respectively.
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1 Rice Annotation Project. (2008) The Rice Annotation Project Database (RAP-DB). Nucleic Acids Res. 36(Database issue):D1028-33   DOI   ScienceOn
2 Doi K, Hosaka A, Nagata T, Satoh K, Suzuki K, Mauleon R, Mendoza MJ, Bruskiewich R, Kikuchi S. (2008) Development of a novel data mining tool to find cis-elements in rice gene promoter regions. BMC Plant Biol. 8:20   DOI   ScienceOn
3 Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L, Orvis J, Haas B, Wortman J, Buell CR. (2007) The TIGR Rice Genome Annotation Resource: improvements and new features Nucleic Acids Res. 35(Database issue):D883-7   DOI   ScienceOn
4 International Rice Genome Sequencing Project. (2005) The mapbased sequence of the rice genome. Nature. 436: 793-800   DOI   ScienceOn
5 Jung KH, An G, Ronald PC. (2008) Towards a better bowl of rice: assigning function to tens of thousands of rice genes. Nat Rev Genet. 9:91-101   DOI   ScienceOn
6 Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M. (2008) Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet. 40:1023-8   DOI   ScienceOn
7 Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA. (2003). The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 4:41   DOI   ScienceOn
8 Nakamura H, Hakata M, Amano K, Miyao A, Toki N, Kajikawa M, Pang J, Higashi N, Ando S, Toki S, Fujita M, Enju A, Seki M, Nakazawa M, Ichikawa T, Shinozaki K, Matsui M, Nagamura Y, Hirochika H, Ichikawa H. (2007) A genome-wide gain-of function analysis of rice genes using the FOX-hunting system. Plant Mol Biol. 65:357-71   DOI   ScienceOn
9 Paterson AH, Freeling M, Sasaki T. (2005) Grains of knowledge:genomics of model cereals. Genome Res. 215: 1643-50.   DOI   ScienceOn
10 Seki M, Carninci P, Nishiyama Y, Hayashizaki Y, Shinozaki K. (1998) High-efficiency cloning of Arabidopsis full-length cDNA by biotinylated CAP trapper. Plant J. 15:707-20   DOI   ScienceOn
11 Song XJ, Huang W, Shi M, Zhu MZ, Lin HX. (2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet. 39:623-30   DOI   ScienceOn
12 Carninci P, Kvam C, Kitamura A, Ohsumi T, Okazaki Y, Itoh M, Kamiya M, Shibata K, Sasaki N, Izawa M, Muramatsu M, Hayashizaki Y, Schneider C. (1996) High-efficiency full-length cDNA cloning by biotinylated CAP trapper. Genomics. 37:327-36   DOI   ScienceOn
13 Umezawa T, Sakurai T, Totoki Y, Toyoda A, Seki M, Ishiwata A, Akiyama K, Kurotani A, Yoshida T, Mochida K, Kasuga M, Todaka D, Maruyama K, Nakashima K, Enju A, Mizukado S, Ahmed S, Yoshiwara K, Harada K, Tsubokura Y, Hayashi M, Sato S, Anai T, Ishimoto M, Funatsuki H, Teraishi M, Osaki M, Shinano T, Akashi R, Sakaki Y, Yamaguchi-Shinozaki K, Shinozaki K. (2008) Sequencing and analysis of approximately 40,000 soybean cDNA clones from a full-length-enriched cDNA library. DNA Res. 15:333-46   DOI   ScienceOn
14 Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Ishikawa M, Yamada H, Ooka H, Hotta I, Kojima K, Namiki T, Ohneda E, Yahagi W, Suzuki K, Li CJ, Ohtsuki K, Shishiki T; Foundation of Advancement of International Science Genome Sequencing & Analysis Group, Otomo Y, Murakami K, Iida Y, Sugano S, Fujimura T, Suzuki Y, Tsunoda Y, Kurosaki T, Kodama T, Masuda H, Kobayashi M, Xie Q, Lu M, Narikawa R, Sugiyama A, Mizuno K, Yokomizo S, Niikura J, Ikeda R, Ishibiki J, Kawamata M, Yoshimura A, Miura J, Kusumegi T, Oka M, Ryu R, Ueda M, Matsubara K; RIKEN, Kawai J, Carninci P, Adachi J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Hayatsu N, Imotani K, Ishii Y, Itoh M, Kagawa I, Kondo S, Konno H, Miyazaki A, Osato N, Ota Y, Saito R, Sasaki D, Sato K, Shibata K, Shinagawa A, Shiraki T, Yoshino M, Hayashizaki Y, Yasunishi A. (2003) Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science. 301:376-9   DOI   ScienceOn
15 Lu T, Huang X, Zhu C, Huang T, Zhao Q, Xie K, Xiong L, Zhang Q, Han B. (2008) RICD: a rice indica cDNA database resource for rice functional genomics. BMC Plant Biol. 8:118   DOI   ScienceOn
16 Ammiraju JS, Lu F, Sanyal A, Yu Y, Song X, Jiang N, Pontaroli AC, Rambo T, Currie J, Collura K, Talag J, Fan C, Goicoechea JL, Zuccolo A, Chen J, Bennetzen JL, Chen M, Jackson S, Wing RA. (2008) Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. Plant Cell. 20:3191-209   DOI   ScienceOn
17 Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, Arakawa T, Hara A, Fukunishi Y, Konno H, Adachi J, Fukuda S, Aizawa K, Izawa M, Nishi K, Kiyosawa H, Kondo S, Yamanaka I, Saito T, Okazaki Y, Gojobori T, Bono H, Kasukawa T, Saito R, Kadota K, Matsuda H, Ashburner M, Batalov S, Casavant T, Fleischmann W, Gaasterland T, Gissi C, King B, Kochiwa H, Kuehl P, Lewis S, Matsuo Y, NikaidoI, Pesole G, Quackenbush J, Schriml LM, Staubli F, Suzuki R, Tomita M, Wagner L, Washio T, Sakai K, Okido T, Furuno M, Aono H, Baldarelli R, Barsh G, Blake J, Boffelli D, Bojunga N, Carninci P, de Bonaldo MF, Brownstein MJ, Bult C, Fletcher C, Fujita M, Gariboldi M, Gustincich S, Hill D, Hofmann M, Hume DA, Kamiya M, Lee NH, Lyons P, Marchionni L, Mashima J, Mazzarelli J, Mombaerts P, Nordone P, Ring B, Ringwald M, Rodriguez I, Sakamoto N, Sasaki H, Sato K, Schönbach C, Seya T, Shibata Y, Storch KF, Suzuki H, Toyo-oka K, Wang KH, Weitz C, Whittaker C, Wilming L, Wynshaw-Boris A, Yoshida K, Hasegawa Y, Kawaji H, Kohtsuki S, Hayashizaki Y; RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium. (2001) Functional annotation of a full-length mouse cDNA collection. Nature. 409:685-90   DOI   ScienceOn
18 Satoh K, Doi K, Nagata T, Kishimoto N, Suzuki K, Otomo Y, Kawai J, Nakamura M, Hirozane-Kishikawa T, Kanagawa S, Arakawa T, Takahashi-Iida J, Murata M, Ninomiya N, Sasaki D, Fukuda S, Tagami M, Yamagata H, Kurita K, Kamiya K, Yamamoto M, Kikuta A, Bito T, Fujitsuka N, Ito K, Kanamori H, Choi IR, Nagamura Y, Matsumoto T, Murakami K, Matsubara K, Carninci P, Hayashizaki Y, Kikuchi S. (2007) Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray. PLoS ONE. 2(11):e1235   DOI   ScienceOn