Journal of Plant Biotechnology

The Korean Society of Plant Biotechnology (한국식물생명공학회)
권호 표지
DOI QR코드

DOI QR Code

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

벼 미숙종자의 발현유전자 구조특성분석

  • 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)
  • Published : 2009.06.30
Download PDF
⟨ Previous Next ⟩

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.

Keywords

References

  1. 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 https://doi.org/10.1105/tpc.108.063727
  2. 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 https://doi.org/10.1006/geno.1996.0567
  3. 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 https://doi.org/10.1186/1471-2229-8-20
  4. International Rice Genome Sequencing Project. (2005) The mapbased sequence of the rice genome. Nature. 436: 793-800 https://doi.org/10.1038/nature03895
  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 https://doi.org/10.1038/nrg2286
  6. 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 https://doi.org/10.1038/35055500
  7. 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 https://doi.org/10.1126/science.1081288
  8. 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 https://doi.org/10.1186/1471-2229-8-118
  9. 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 https://doi.org/10.1007/s11103-007-9243-y
  10. 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 https://doi.org/10.1093/nar/gkl976
  11. Paterson AH, Freeling M, Sasaki T. (2005) Grains of knowledge:genomics of model cereals. Genome Res. 215: 1643-50. https://doi.org/10.1101/gr.3725905
  12. Rice Annotation Project. (2008) The Rice Annotation Project Database (RAP-DB). Nucleic Acids Res. 36(Database issue):D1028-33 https://doi.org/10.1093/nar/gkm978
  13. 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 https://doi.org/10.1371/journal.pone.0001235
  14. 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 https://doi.org/10.1046/j.1365-313x.1998.00237.x
  15. 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 https://doi.org/10.1038/ng.169
  16. 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 https://doi.org/10.1038/ng2014
  17. 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 https://doi.org/10.1186/1471-2105-4-41
  18. 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 https://doi.org/10.1093/dnares/dsn024

Cited by

  1. Structural and expression analysis of prolamin genes in Oryza sativa L. vol.6, pp.3, 2012, https://doi.org/10.1007/s11816-012-0220-9
  2. Structural and expression analysis of glutelin genes in Oryza sativa L. vol.38, pp.2, 2011, https://doi.org/10.5010/JPB.2011.38.2.176