The map-based sequence of the rice genome

Takashi Matsumoto, Jianzhong Wu, Hiroyuki Kanamori, Yuichi Katayose, Masaki Fujisawa, Nobukazu Namiki, Hiroshi Mizuno, Kimiko Yamamoto, Baltazar A. Antonio, Tomoya Baba, Katsumi Sakata, Yoshiaki Nagamura, Hiroyoshi Aoki, Koji Arikawa, Kohei Arita, Takahito Bito, Yoshino Chiden, Nahoko Fujitsuka, Rie Fukunaka, Masao HamadaChizuko Harada, Akiko Hayashi, Saori Hijishita, Mikiko Honda, Satomi Hosokawa, Yoko Ichikawa, Atsuko Idonuma, Masumi Iijima, Michiko Ikeda, Maiko Ikeno, Kazue Ito, Sachie Ito, Tomoko Ito, Yuichi Ito, Yukiyo Ito, Aki Iwabuchi, Kozue Kamiya, Wataru Karasawa, Kanako Kurita, Satoshi Katagiri, Ari Kikuta, Harumi Kobayashi, Noriko Kobayashi, Kayo MacHita, Tomoko Maehara, Masatoshi Masukawa, Tatsumi Mizubayashi, Yoshiyuki Mukai, Hideki Nagasaki, Yuko Nagata, Shinji Naito, Marina Nakashima, Yuko Nakama, Yumi Nakamichi, Mari Nakamura, Ayano Meguro, Manami Negishi, Isamu Ohta, Tomoya Ohta, Masako Okamoto, Nozomi Ono, Shoko Saji, Miyuki Sakaguchi, Kumiko Sakai, Michie Shibata, Takanori Shimokawa, Jianyu Song, Yuka Takazaki, Kimihiro Terasawa, Mika Tsugane, Kumiko Tsuji, Shigenori Ueda, Kazunori Waki, Harumi Yamagata, Mayu Yamamoto, Shinichi Yamamoto, Hiroko Yamane, Shoji Yoshiki, Rie Yoshihara, Kazuko Yukawa, Huisun Zhong, Masahiro Yano, Takuji Sasaki, Qiaoping Yuan, Shu Ouyang, Jia Liu, Kristine M. Jones, Kristen Gansberger, Kelly Moffat, Jessica Hill, Jayati Bera, Douglas Fadrosh, Shaohua Jin, Shivani Johri, Mary Kim, Larry Overton, Matthew Reardon, Tamara Tsitrin, Hue Vuong, Bruce Weaver, Anne Ciecko, Luke Tallon, Jacqueline Jackson, Grace Pai, Susan Van Aken, Terry Utterback, Steve Reidmuller, Tamara Feldblyum, Joseph Hsiao, Victoria Zismann, Stacey Iobst, Aymeric R. De Vazeille, C. Robin Buell, Kai Ying, Ying Li, Tingting Lu, Yuchen Huang, Qiang Zhao, Qi Feng, Lei Zhang, Jingjie Zhu, Qijun Weng, Jie Mu, Yiqi Lu, Danlin Fan, Yilei Liu, Jianping Guan, Yujun Zhang, Shuliang Yu, Xiaohui Liu, Yu Zhang, Guofan Hong, Bin Han, Nathalie Choisne, Nadia Demange, Gisela Orjeda, Sylvie Samain, Laurence Cattolico, Eric Pelletier, Arnaud Couloux, Beatrice Segurens, Patrick Wincker, Angelique D'Hont, Claude Scarpelli, Jean Weissenbach, Marcel Salanoubat, Francis Quetier, Yeisoo Yu, Hye Ran Kim, Teri Rambo, Jennifer Currie, Kristi Collura, Meizhong Luo, Tae Jin Yang, Jetty S S Ammiraju, Friedrich Engler, Carol Soderlund, Rod A. Wing, Lance E. Palmer, Melissa De La Bastide, Lori Spiegel, Lidia Nascimento, Theresa Zutavern, Andrew O'Shaughnessy, Sujit Dike, Neilay Dedhia, Raymond Preston, Vivekanand Balija, W. Richard McCombie, Teh Yuan Chow, Hong Hwa Chen, Mei Chu Chung, Ching San Chen, Jei Fu Shaw, Hong Pang Wu, Kwang Jen Hsiao, Ya Ting Chao, Mu Kuei Chu, Chia Hsiung Cheng, Ai Ling Hour, Pei Fang Lee, Shu Jen Lin, Yao Cheng Lin, John Yu Liou, Shu Mei Liu, Yue Ie Hsing, S. Raghuvanshi, A. Mohanty, A. K. Bharti, A. Gaur, V. Gupta, D. Kumar, V. Ravi, S. Vij, A. Kapur, Parul Khurana, Paramjit Khurana, J. P. Khurana, A. K. Tyagi, K. Gaikwad, A. Singh, V. Dalal, S. Srivastava, A. Dixit, A. K. Pal, I. A. Ghazi, M. Yadav, A. Pandit, A. Bhargava, K. Sureshbabu, K. Batra, T. R. Sharma, T. Mohapatra, N. K. Singh, Joachim Messing, Amy Bronzino Nelson, Galina Fuks, Steve Kavchok, Gladys Keizer, Eric Linton Victor Llaca, Rentao Song, Bahattin Tanyolac, Steve Young, Kim Ho, Jang Ho Hahn, G. Sangsakoo, A. Vanavichit, Luiz Anderson Teixeira De Mattos, Paulo Dejalma Zimmer, Gaspar Malone, Odir Dellagostin, Antonio Costa De Oliveira, Michael Bevan, Ian Bancroft, Pat Minx, Holly Cordum, Richard Wilson, Zhukuan Cheng, Weiwei Jin, Jiming Jiang, Sally Ann Leong, Hisakazu Iwama, Takashi Gojobori, Takeshi Itoh, Yoshihito Niimura, Yasuyuki Fujii, Takuya Habara, Hiroaki Sakai, Yoshiharu Sato, Greg Wilson, Kiran Kumar, Susan McCouch, Nikoleta Juretic, Douglas Hoen, Stephen Wright, Richard Bruskiewich, Thomas Bureau, Akio Miyao, Hirohiko Hirochika, Tomotaro Nishikawa, Koh Ichi Kadowaki, Masahiro Sugiura, Benjamin Burr

Research output: Contribution to journalArticle

2632 Citations (Scopus)

Abstract

Rice, one of the world's most important food plants, has important syntenic relationships with the other cereal species and is a model plant for the grasses. Here we present a map-based, finished quality sequence that covers 95% of the 389Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 nontransposable- element-related protein-coding genes were identified, of which 71% had a putative homologue in Arabidopsis. In a reciprocal analysis, 90% of the Arabidopsis proteins had a putative homologue in the predicted rice proteome. Twenty-nine per cent of the 37,544 predicted genes appear in clustered gene families. The number and classes of transposable elements found in the rice genome are consistent with the expansion of syntenic regions in the maize and sorghum genomes. We find evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes. The map-based sequence has proven useful for the identification of genes underlying agronomic traits. The additional single-nucleotide polymorphisms and simple sequence repeats identified in our study should accelerate improvements in rice production.

Original languageEnglish
Pages (from-to)793-800
Number of pages8
JournalNature
Volume436
Issue number7052
DOIs
Publication statusPublished - Aug 11 2005
Externally publishedYes

ASJC Scopus subject areas

  • General

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    Matsumoto, T., Wu, J., Kanamori, H., Katayose, Y., Fujisawa, M., Namiki, N., Mizuno, H., Yamamoto, K., Antonio, B. A., Baba, T., Sakata, K., Nagamura, Y., Aoki, H., Arikawa, K., Arita, K., Bito, T., Chiden, Y., Fujitsuka, N., Fukunaka, R., ... Burr, B. (2005). The map-based sequence of the rice genome. Nature, 436(7052), 793-800. https://doi.org/10.1038/nature03895