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

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2685 Scopus citations

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
StatePublished - 11 Aug 2005

Bibliographical note

Funding Information:
Acknowledgements Work at the RGP was supported by the Ministry of Agriculture, Forestry and Fisheries of Japan. Work at TIGR was supported by grants to C.R.B. from the USDA Cooperative State Research, Education and Extension Service–National Research Initiative, the National Science Foundation and the US Department of Energy. Work at the NCGR was supported by the Chinese Ministry of Science and Technology, the Chinese Academy of Sciences, the Shanghai Municipal Commission of Science and Technology, and the National Natural Science Foundation of China. Work at Genoscope was supported by le Ministère de la Recherche, France. Funding for the work at the AGI and AGCoL was provided by grants to R.A.W. and C.S. from the USDA Cooperative State Research, Education and Extension Service–National Research Initiative, the National Science Foundation, the US Department of Energy and the Rockefeller Foundation. Work at CSHL was supported by grants from the USDA Cooperative State Research, Education and Extension Service–National Research Initiative and from the National Science Foundation. Work at the ASPGC was supported by Academia Sinica, National Science Council, Council of Agriculture, and Institute of Botany, Academia Sinica. The IIRGS acknowledges the Department of Biotechnology, Government of India, for financial assistance and the Indian Council of Agricultural Research, New Delhi, for support. Work at Rice Gene Discovery was supported by BIOTECH and the Princess Sirindhorn’s Plant Germplasm Conservation Initiative Program. Work at PGIR was supported by Rutgers University. The BRIGI was supported by Coordenac¸ão de Aperfeic¸oamento de Pessoal de Nível Superior (CAPES), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Financiadora de Estudos e Projetos - Ministério de Ciência e Tecnologia (FINEP-MCT), Fundac¸ão de Amparo a Pesquisa do Rio Grande do Sul (FAPERGS) and Universidade Federal de Pelotas (UFPel). Work at McGill and York Universities was supported by the National Science and Engineering Research Council of Canada and the Canadian International Development Agency. Funding for H.H. at the National Institute of Agrobiological Sciences was from the Ministry of Agriculture, Forestry, and Fisheries of Japan, and the Program for Promotion of Basic Research Activities for Innovative Biosciences. Funding at Brookhaven National Laboratory was from The Rockefeller Foundation and the Office of Basic Energy Science of the United States Department of Energy. We would like to thank G. Barry and S. Goff for their help in negotiating agreements that permitted the sharing of materials and sequence with the IRGSP. We also acknowledge the work of G. Barry, S. Goff and their colleagues in facilitating the transfer of sequence information and supporting data.

Copyright:
Copyright 2014 Elsevier B.V., All rights reserved.

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