Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice: The rice full-length cDNA consortium

Shoshi Kikuchi; Kouji Satoh; Toshifumi Nagata; Nobuyuki Kawagashira; Koji Doi; Naoki Kishimoto; Junshi Yazaki; Masahiro Ishikawa; Hitomi Yamada; Hisako Ooka; Isamu Hotta; Keiichi Kojima; Takahiro Namiki; Eisuke Ohneda; Wataru Yahagi; Kohji Suzuki; Chao Jie Li; Kenji Ohtsuki; Toru Shishiki; Yasuhiro Otomo; Kazuo Murakami; Yoshiharu Iida; Sumio Sugano; Tatsuto Fujimura; Yutaka Suzuki; Yuki Tsunoda; Takashi Kurosaki; Takeko Kodama; Hiromi Masuda; Michie Kobayashi; Quihong Xie; Min Lu; Ryuya Narikawa; Akio Sugiyama; Kouichi Mizuno; Satoko Yokomizo; Junko Niikura; Rieko Ikeda; Junya Ishibiki; Midori Kawamata; Akemi Yoshimura; Junichirou Miura; Takahiro Kusumegi; Mitsuru Oka; Risa Ryu; Mariko Ueda; Kenichi Matsubara; Jun Kawai; Piero Carninci; Jun Adachi; Katsunori Aizawa; Takahiro Arakawa; Shiro Fukuda; Ayako Hara; Wataru Hashidume; Norihito Hayatsu; Koichi Imotani; Yoshiki Ishii; Masayoshi Itoh; Ikuko Kagawa; Shinji Kondo; Hedeaki Konno; Ai Miyazaki; Naoki Osato; Yoshimi Ota; Rintaro Saito; Daisuke Sasaki; Kenjiro Sato; Kazuhiro Shibata; Akira Shinagawa; Toshiyuki Shiraki; Masayasu Yoshino; Yoshihide Hayashizaki

doi:10.1126/science.1081288

Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice: The rice full-length cDNA consortium

Shoshi Kikuchi^*, Kouji Satoh, Toshifumi Nagata, Nobuyuki Kawagashira, Koji Doi, Naoki Kishimoto, Junshi Yazaki, Masahiro Ishikawa, Hitomi Yamada, Hisako Ooka, Isamu Hotta, Keiichi Kojima, Takahiro Namiki, Eisuke Ohneda, Wataru Yahagi, Kohji Suzuki, Chao Jie Li, Kenji Ohtsuki, Toru Shishiki, Yasuhiro OtomoKazuo Murakami, Yoshiharu Iida, Sumio Sugano, Tatsuto Fujimura, Yutaka Suzuki, Yuki Tsunoda, Takashi Kurosaki, Takeko Kodama, Hiromi Masuda, Michie Kobayashi, Quihong Xie, Min Lu, Ryuya Narikawa, Akio Sugiyama, Kouichi Mizuno, Satoko Yokomizo, Junko Niikura, Rieko Ikeda, Junya Ishibiki, Midori Kawamata, Akemi Yoshimura, Junichirou Miura, Takahiro Kusumegi, Mitsuru Oka, Risa Ryu, Mariko Ueda, Kenichi Matsubara, Jun Kawai, Piero Carninci, Jun Adachi, Katsunori Aizawa, Takahiro Arakawa, Shiro Fukuda, Ayako Hara, Wataru Hashidume, Norihito Hayatsu, Koichi Imotani, Yoshiki Ishii, Masayoshi Itoh, Ikuko Kagawa, Shinji Kondo, Hedeaki Konno, Ai Miyazaki, Naoki Osato, Yoshimi Ota, Rintaro Saito, Daisuke Sasaki, Kenjiro Sato, Kazuhiro Shibata, Akira Shinagawa, Toshiyuki Shiraki, Masayasu Yoshino, Yoshihide Hayashizaki

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

737 Citations (Scopus)

Abstract

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.

Original language	English
Pages (from-to)	376-379
Number of pages	4
Journal	Science
Volume	301
Issue number	5631
DOIs	https://doi.org/10.1126/science.1081288
Publication status	Published - 2003 Jul 18
Externally published	Yes

ASJC Scopus subject areas

General

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10.1126/science.1081288

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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, C. J., Ohtsuki, K., Shishiki, T., ... Hayashizaki, Y. (2003). Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice: The rice full-length cDNA consortium. Science, 301(5631), 376-379. https://doi.org/10.1126/science.1081288

Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice : The rice full-length cDNA consortium. / Kikuchi, Shoshi; Satoh, Kouji; Nagata, Toshifumi; Kawagashira, Nobuyuki; Doi, Koji; Kishimoto, Naoki; Yazaki, Junshi; Ishikawa, Masahiro; Yamada, Hitomi; Ooka, Hisako; Hotta, Isamu; Kojima, Keiichi; Namiki, Takahiro; Ohneda, Eisuke; Yahagi, Wataru; Suzuki, Kohji; Li, Chao Jie; Ohtsuki, Kenji; Shishiki, Toru; Otomo, Yasuhiro; Murakami, Kazuo; Iida, Yoshiharu; Sugano, Sumio; Fujimura, Tatsuto; Suzuki, Yutaka; Tsunoda, Yuki; Kurosaki, Takashi; Kodama, Takeko; Masuda, Hiromi; Kobayashi, Michie; Xie, Quihong; Lu, Min; Narikawa, Ryuya; Sugiyama, Akio; Mizuno, Kouichi; Yokomizo, Satoko; Niikura, Junko; Ikeda, Rieko; Ishibiki, Junya; Kawamata, Midori; Yoshimura, Akemi; Miura, Junichirou; Kusumegi, Takahiro; Oka, Mitsuru; Ryu, Risa; Ueda, Mariko; Matsubara, Kenichi; Kawai, Jun; Carninci, Piero; Adachi, Jun; Aizawa, Katsunori; Arakawa, Takahiro; Fukuda, Shiro; Hara, Ayako; Hashidume, Wataru; Hayatsu, Norihito; Imotani, Koichi; Ishii, Yoshiki; Itoh, Masayoshi; Kagawa, Ikuko; Kondo, Shinji; Konno, Hedeaki; Miyazaki, Ai; Osato, Naoki; Ota, Yoshimi; Saito, Rintaro; Sasaki, Daisuke; Sato, Kenjiro; Shibata, Kazuhiro; Shinagawa, Akira; Shiraki, Toshiyuki; Yoshino, Masayasu; Hayashizaki, Yoshihide.

In: Science, Vol. 301, No. 5631, 18.07.2003, p. 376-379.

Research output: Contribution to journal › Article › peer-review

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, 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, Kawai, J, Carninci, P, Adachi, J, Aizawa, K, Arakawa, T, Fukuda, S, Hara, A, Hashidume, 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 2003, 'Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice: The rice full-length cDNA consortium', Science, vol. 301, no. 5631, pp. 376-379. https://doi.org/10.1126/science.1081288

Kikuchi, Shoshi ; Satoh, Kouji ; Nagata, Toshifumi ; Kawagashira, Nobuyuki ; Doi, Koji ; Kishimoto, Naoki ; Yazaki, Junshi ; Ishikawa, Masahiro ; Yamada, Hitomi ; Ooka, Hisako ; Hotta, Isamu ; Kojima, Keiichi ; Namiki, Takahiro ; Ohneda, Eisuke ; Yahagi, Wataru ; Suzuki, Kohji ; Li, Chao Jie ; Ohtsuki, Kenji ; Shishiki, Toru ; Otomo, Yasuhiro ; Murakami, Kazuo ; Iida, Yoshiharu ; Sugano, Sumio ; Fujimura, Tatsuto ; Suzuki, Yutaka ; Tsunoda, Yuki ; Kurosaki, Takashi ; Kodama, Takeko ; Masuda, Hiromi ; Kobayashi, Michie ; Xie, Quihong ; Lu, Min ; Narikawa, Ryuya ; Sugiyama, Akio ; Mizuno, Kouichi ; Yokomizo, Satoko ; Niikura, Junko ; Ikeda, Rieko ; Ishibiki, Junya ; Kawamata, Midori ; Yoshimura, Akemi ; Miura, Junichirou ; Kusumegi, Takahiro ; Oka, Mitsuru ; Ryu, Risa ; Ueda, Mariko ; Matsubara, Kenichi ; Kawai, Jun ; Carninci, Piero ; Adachi, Jun ; Aizawa, Katsunori ; Arakawa, Takahiro ; Fukuda, Shiro ; Hara, Ayako ; Hashidume, Wataru ; Hayatsu, Norihito ; Imotani, Koichi ; Ishii, Yoshiki ; Itoh, Masayoshi ; Kagawa, Ikuko ; Kondo, Shinji ; Konno, Hedeaki ; Miyazaki, Ai ; Osato, Naoki ; Ota, Yoshimi ; Saito, Rintaro ; Sasaki, Daisuke ; Sato, Kenjiro ; Shibata, Kazuhiro ; Shinagawa, Akira ; Shiraki, Toshiyuki ; Yoshino, Masayasu ; Hayashizaki, Yoshihide. / Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice : The rice full-length cDNA consortium. In: Science. 2003 ; Vol. 301, No. 5631. pp. 376-379.

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abstract = "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.",

author = "Shoshi Kikuchi and Kouji Satoh and Toshifumi Nagata and Nobuyuki Kawagashira and Koji Doi and Naoki Kishimoto and Junshi Yazaki and Masahiro Ishikawa and Hitomi Yamada and Hisako Ooka and Isamu Hotta and Keiichi Kojima and Takahiro Namiki and Eisuke Ohneda and Wataru Yahagi and Kohji Suzuki and Li, {Chao Jie} and Kenji Ohtsuki and Toru Shishiki and Yasuhiro Otomo and Kazuo Murakami and Yoshiharu Iida and Sumio Sugano and Tatsuto Fujimura and Yutaka Suzuki and Yuki Tsunoda and Takashi Kurosaki and Takeko Kodama and Hiromi Masuda and Michie Kobayashi and Quihong Xie and Min Lu and Ryuya Narikawa and Akio Sugiyama and Kouichi Mizuno and Satoko Yokomizo and Junko Niikura and Rieko Ikeda and Junya Ishibiki and Midori Kawamata and Akemi Yoshimura and Junichirou Miura and Takahiro Kusumegi and Mitsuru Oka and Risa Ryu and Mariko Ueda and Kenichi Matsubara and Jun Kawai and Piero Carninci and Jun Adachi and Katsunori Aizawa and Takahiro Arakawa and Shiro Fukuda and Ayako Hara and Wataru Hashidume and Norihito Hayatsu and Koichi Imotani and Yoshiki Ishii and Masayoshi Itoh and Ikuko Kagawa and Shinji Kondo and Hedeaki Konno and Ai Miyazaki and Naoki Osato and Yoshimi Ota and Rintaro Saito and Daisuke Sasaki and Kenjiro Sato and Kazuhiro Shibata and Akira Shinagawa and Toshiyuki Shiraki and Masayasu Yoshino and Yoshihide Hayashizaki",

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AU - Kawagashira, Nobuyuki

AU - Doi, Koji

AU - Kishimoto, Naoki

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AU - Iida, Yoshiharu

AU - Sugano, Sumio

AU - Fujimura, Tatsuto

AU - Suzuki, Yutaka

AU - Tsunoda, Yuki

AU - Kurosaki, Takashi

AU - Kodama, Takeko

AU - Masuda, Hiromi

AU - Kobayashi, Michie

AU - Xie, Quihong

AU - Lu, Min

AU - Narikawa, Ryuya

AU - Sugiyama, Akio

AU - Mizuno, Kouichi

AU - Yokomizo, Satoko

AU - Niikura, Junko

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AU - Kusumegi, Takahiro

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AU - Ueda, Mariko

AU - Matsubara, Kenichi

AU - Kawai, Jun

AU - Carninci, Piero

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AU - Fukuda, Shiro

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AU - Ota, Yoshimi

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Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice: The rice full-length cDNA consortium

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