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Science 18 July 2003:
Vol. 301. no. 5631, pp. 376 - 379
DOI: 10.1126/science.1081288
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Reports

Collection, Mapping, and Annotation of Over 28,000 cDNA Clones from japonica Rice

The Rice Full-Length cDNA Consortium,

National Institute of Agrobiological Sciences Rice Full-Length cDNA Project Team: Shoshi Kikuchi1* Kouji Satoh,1 Toshifumi Nagata,1 Nobuyuki Kawagashira,1 Koji Doi,1 Naoki Kishimoto,1 Junshi Yazaki,1 Masahiro Ishikawa,1 Hitomi Yamada,1 Hisako Ooka,1 Isamu Hotta,1 Keiichi Kojima,2 Takahiro Namiki,2 Eisuke Ohneda,2 Wataru Yahagi,2 Kohji Suzuki,2 Chao Jie Li,2 Kenji Ohtsuki,2 Toru Shishiki,2

Foundation of Advancement of International Science Genome Sequencing & Analysis Group: Yasuhiro Otomo3 Kazuo Murakami,3 Yoshiharu Iida,3 Sumio Sugano,3,4 Tatsuto Fujimura,3,5 Yutaka Suzuki,3,4 Yuki Tsunoda,3 Takashi Kurosaki,3 Takeko Kodama,3 Hiromi Masuda,3 Michie Kobayashi,3 Quihong Xie,3 Min Lu,3 Ryuya Narikawa,3 Akio Sugiyama,3 Kouichi Mizuno,3,5 Satoko Yokomizo,3 Junko Niikura,3 Rieko Ikeda,3 Junya Ishibiki,3 Midori Kawamata,3 Akemi Yoshimura,3 Junichirou Miura,3 Takahiro Kusumegi,3 Mitsuru Oka,3 Risa Ryu,3 Mariko Ueda,3 and Kenichi Matsubara3,6

RIKEN: Jun Kawai7,8 Piero Carninci,7,8 Jun Adachi,7 Katsunori Aizawa,7 Takahiro Arakawa,7 Shiro Fukuda,7 Ayako Hara,7 Wataru Hashidume,7 Norihito Hayatsu,7 Koichi Imotani,7 Yoshiki Ishii,7 Masayoshi Itoh,8 Ikuko Kagawa,7 Shinji Kondo,7 Hedeaki Konno,7 Ai Miyazaki,7 Naoki Osato,7 Yoshimi Ota,7 Rintaro Saito,7 Daisuke Sasaki,7 Kenjiro Sato,8 Kazuhiro Shibata,8 Akira Shinagawa,8 Toshiyuki Shiraki,7 Masayasu Yoshino7 and Yoshihide Hayashizaki7,8

We collected and completely sequenced 28,469 full-length complementary DNA clones from Oryza sativa L. ssp. japonica cv. Nipponbare. Through homology searches of publicly available sequence data, we assigned tentative protein functions to 21,596 clones (75.86%). Mapping of the cDNA clones to genomic DNA revealed that there are 19,000 to 20,500 transcription units in the rice genome. Protein informatics analysis against the InterPro database revealed the existence of proteins presented in rice but not in Arabidopsis. Sixty-four percent of our cDNAs are homologous to Arabidopsis proteins.

1 Department of Molecular Biology, National Institute of Agrobiological Sciences, 2-1-2 Kannon-dai, Tsukuba, Ibaraki 305-8602, Japan. 2 Hitachi Software Engineering Co., Ltd., 6-81, Onoe-cho, Naka-ku, Yokohama 231-0015, Japan. 3 Laboratory of Genome Sequencing & Analysis Group, Foundation of Advancement of International Science (FAIS), 586-9, Akatsuka-Ushigahuchi, Tsukuba, Ibaraki 305-0062, Japan. 4 Department of Virology, Institute of Medical Science, The University of Tokyo, 4-6-1, Shiroganedai, Minatoku, Tokyo 108-8639, Japan. 5 Institute of Agricultural and Forest Engineering, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8577, Japan. 6 Nara Institute of Science and Technology (NAIST), 8916-5, Takayama-cho, Ikoma, Nara 630-0101, Japan. 7 Laboratory for Genome Exploration Research Group (Institute of Physical and Chemical Research, RIKEN), Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. 8 Genome Science Laboratory, RIKEN Wako Main Campus, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan.

* To whom correspondence should be addressed. E-mail: skikuchi{at}nias.affrc.go.jp

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D. Miki, R. Itoh, and K. Shimamoto (2005)
Plant Physiology 138, 1903-1913
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BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes.
J. McDermott, M. Guerquin, Z. Frazier, A. N. Chang, and R. Samudrala (2005)
Nucleic Acids Res. 33, W324-W325
   Abstract »    Full Text »    PDF »
Serial Analysis of Gene Expression Study of a Hybrid Rice Strain (LYP9) and Its Parental Cultivars.
J. Bao, S. Lee, C. Chen, X. Zhang, Y. Zhang, S. Liu, T. Clark, J. Wang, M. Cao, H. Yang, et al. (2005)
Plant Physiology 138, 1216-1231
   Abstract »    Full Text »    PDF »
Using Artificial Selection to Understand Plastic Plant Phenotypes.
H. S. Callahan (2005)
Integr. Comp. Biol. 45, 475-485
   Abstract »    Full Text »    PDF »
A Novel Receptor Kinase Involved in Jasmonate-mediated Wound and Phytochrome Signaling in Maize Coleoptiles.
G. He, Y. Tarui, and M. Iino (2005)
Plant Cell Physiol. 46, 870-883
   Abstract »    Full Text »    PDF »
Gene Expression of ADP-glucose Pyrophosphorylase and Starch Contents in Rice Cultured Cells are Cooperatively Regulated by Sucrose and ABA.
T. Akihiro, K. Mizuno, and T. Fujimura (2005)
Plant Cell Physiol. 46, 937-946
   Abstract »    Full Text »    PDF »


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