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 Hamada; Chizuko 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

doi:10.1038/nature03895

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 journal › Article › peer-review

3140 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 language	English (US)
Pages (from-to)	793-800
Number of pages	8
Journal	Nature
Volume	436
Issue number	7052
DOIs	https://doi.org/10.1038/nature03895
State	Published - Aug 11 2005

ASJC Scopus subject areas

General

Access to Document

10.1038/nature03895

Cite this

Matsumoto, T, Wu, J, Kanamori, H, Katayose, Y, Fujisawa, M, Namiki, N, Mizuno, H, Yamamoto, K, Antonio, BA, Baba, T, Sakata, K, Nagamura, Y, Aoki, H, Arikawa, K, Arita, K, Bito, T, Chiden, Y, Fujitsuka, N, Fukunaka, R, Hamada, M, Harada, C, Hayashi, A, Hijishita, S, Honda, M, Hosokawa, S, Ichikawa, Y, Idonuma, A, Iijima, M, Ikeda, M, Ikeno, M, Ito, K, Ito, S, Ito, T, Ito, Y, Ito, Y, Iwabuchi, A, Kamiya, K, Karasawa, W, Kurita, K, Katagiri, S, Kikuta, A, Kobayashi, H, Kobayashi, N, MacHita, K, Maehara, T, Masukawa, M, Mizubayashi, T, Mukai, Y, Nagasaki, H, Nagata, Y, Naito, S, Nakashima, M, Nakama, Y, Nakamichi, Y, Nakamura, M, Meguro, A, Negishi, M, Ohta, I, Ohta, T, Okamoto, M, Ono, N, Saji, S, Sakaguchi, M, Sakai, K, Shibata, M, Shimokawa, T, Song, J, Takazaki, Y, Terasawa, K, Tsugane, M, Tsuji, K, Ueda, S, Waki, K, Yamagata, H, Yamamoto, M, Yamamoto, S, Yamane, H, Yoshiki, S, Yoshihara, R, Yukawa, K, Zhong, H, Yano, M, Sasaki, T, Yuan, Q, Ouyang, S, Liu, J, Jones, KM, Gansberger, K, Moffat, K, Hill, J, Bera, J, Fadrosh, D, Jin, S, Johri, S, Kim, M, Overton, L, Reardon, M, Tsitrin, T, Vuong, H, Weaver, B, Ciecko, A, Tallon, L, Jackson, J, Pai, G, Van Aken, S, Utterback, T, Reidmuller, S, Feldblyum, T, Hsiao, J, Zismann, V, Iobst, S, De Vazeille, AR, Buell, CR, Ying, K, Li, Y, Lu, T, Huang, Y, Zhao, Q, Feng, Q, Zhang, L, Zhu, J, Weng, Q, Mu, J, Lu, Y, Fan, D, Liu, Y, Guan, J, Zhang, Y, Yu, S, Liu, X, Zhang, Y, Hong, G, Han, B, Choisne, N, Demange, N, Orjeda, G, Samain, S, Cattolico, L, Pelletier, E, Couloux, A, Segurens, B, Wincker, P, D'Hont, A, Scarpelli, C, Weissenbach, J, Salanoubat, M, Quetier, F, Yu, Y, Kim, HR, Rambo, T, Currie, J, Collura, K, Luo, M, Yang, TJ, Ammiraju, JSS, Engler, F, Soderlund, C, Wing, RA, Palmer, LE, De La Bastide, M, Spiegel, L, Nascimento, L, Zutavern, T, O'Shaughnessy, A, Dike, S, Dedhia, N, Preston, R, Balija, V, McCombie, WR, Chow, TY, Chen, HH, Chung, MC, Chen, CS, Shaw, JF, Wu, HP, Hsiao, KJ, Chao, YT, Chu, MK, Cheng, CH, Hour, AL, Lee, PF, Lin, SJ, Lin, YC, Liou, JY, Liu, SM, Hsing, YI, Raghuvanshi, S, Mohanty, A, Bharti, AK, Gaur, A, Gupta, V, Kumar, D, Ravi, V, Vij, S, Kapur, A, Khurana, P, Khurana, P, Khurana, JP, Tyagi, AK, Gaikwad, K, Singh, A, Dalal, V, Srivastava, S, Dixit, A, Pal, AK, Ghazi, IA, Yadav, M, Pandit, A, Bhargava, A, Sureshbabu, K, Batra, K, Sharma, TR, Mohapatra, T, Singh, NK, Messing, J, Nelson, AB, Fuks, G, Kavchok, S, Keizer, G, Llaca, ELV, Song, R, Tanyolac, B, Young, S, Ho, K, Hahn, JH, Sangsakoo, G, Vanavichit, A, De Mattos, LAT, Zimmer, PD, Malone, G, Dellagostin, O, De Oliveira, AC, Bevan, M, Bancroft, I, Minx, P, Cordum, H, Wilson, R, Cheng, Z, Jin, W, Jiang, J, Leong, SA, Iwama, H, Gojobori, T, Itoh, T, Niimura, Y, Fujii, Y, Habara, T, Sakai, H, Sato, Y, Wilson, G, Kumar, K, McCouch, S, Juretic, N, Hoen, D, Wright, S, Bruskiewich, R, Bureau, T, Miyao, A, Hirochika, H, Nishikawa, T, Kadowaki, KI, Sugiura, M & Burr, B 2005, 'The map-based sequence of the rice genome', Nature, vol. 436, no. 7052, pp. 793-800. https://doi.org/10.1038/nature03895

@article{b18abf858f83437db90eb226d966b08a,

title = "The map-based sequence of the rice genome",

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.",

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

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 Minist{\`e}re 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{\textquoteright}s Plant Germplasm Conservation Initiative Program. Work at PGIR was supported by Rutgers University. The BRIGI was supported by Coordenac¸{\~a}o de Aperfeic¸oamento de Pessoal de N{\'i}vel Superior (CAPES), Conselho Nacional de Desenvolvimento Cient{\'i}fico e Tecnol{\'o}gico (CNPq), Financiadora de Estudos e Projetos - Minist{\'e}rio de Ci{\^e}ncia e Tecnologia (FINEP-MCT), Fundac¸{\~a}o 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.",

year = "2005",

month = aug,

day = "11",

doi = "10.1038/nature03895",

language = "English (US)",

volume = "436",

pages = "793--800",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Publishing Group",

number = "7052",

}

TY - JOUR

T1 - The map-based sequence of the rice genome

AU - Matsumoto, Takashi

AU - Wu, Jianzhong

AU - Kanamori, Hiroyuki

AU - Katayose, Yuichi

AU - Fujisawa, Masaki

AU - Namiki, Nobukazu

AU - Mizuno, Hiroshi

AU - Yamamoto, Kimiko

AU - Antonio, Baltazar A.

AU - Baba, Tomoya

AU - Sakata, Katsumi

AU - Nagamura, Yoshiaki

AU - Aoki, Hiroyoshi

AU - Arikawa, Koji

AU - Arita, Kohei

AU - Bito, Takahito

AU - Chiden, Yoshino

AU - Fujitsuka, Nahoko

AU - Fukunaka, Rie

AU - Hamada, Masao

AU - Harada, Chizuko

AU - Hayashi, Akiko

AU - Hijishita, Saori

AU - Honda, Mikiko

AU - Hosokawa, Satomi

AU - Ichikawa, Yoko

AU - Idonuma, Atsuko

AU - Iijima, Masumi

AU - Ikeda, Michiko

AU - Ikeno, Maiko

AU - Ito, Kazue

AU - Ito, Sachie

AU - Ito, Tomoko

AU - Ito, Yuichi

AU - Ito, Yukiyo

AU - Iwabuchi, Aki

AU - Kamiya, Kozue

AU - Karasawa, Wataru

AU - Kurita, Kanako

AU - Katagiri, Satoshi

AU - Kikuta, Ari

AU - Kobayashi, Harumi

AU - Kobayashi, Noriko

AU - MacHita, Kayo

AU - Maehara, Tomoko

AU - Masukawa, Masatoshi

AU - Mizubayashi, Tatsumi

AU - Mukai, Yoshiyuki

AU - Nagasaki, Hideki

AU - Nagata, Yuko

AU - Naito, Shinji

AU - Nakashima, Marina

AU - Nakama, Yuko

AU - Nakamichi, Yumi

AU - Nakamura, Mari

AU - Meguro, Ayano

AU - Negishi, Manami

AU - Ohta, Isamu

AU - Ohta, Tomoya

AU - Okamoto, Masako

AU - Ono, Nozomi

AU - Saji, Shoko

AU - Sakaguchi, Miyuki

AU - Sakai, Kumiko

AU - Shibata, Michie

AU - Shimokawa, Takanori

AU - Song, Jianyu

AU - Takazaki, Yuka

AU - Terasawa, Kimihiro

AU - Tsugane, Mika

AU - Tsuji, Kumiko

AU - Ueda, Shigenori

AU - Waki, Kazunori

AU - Yamagata, Harumi

AU - Yamamoto, Mayu

AU - Yamamoto, Shinichi

AU - Yamane, Hiroko

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N1 - 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.

PY - 2005/8/11

Y1 - 2005/8/11

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84907150192&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84907150192&partnerID=8YFLogxK

U2 - 10.1038/nature03895

DO - 10.1038/nature03895

M3 - Article

AN - SCOPUS:84907150192

SN - 0028-0836

VL - 436

SP - 793

EP - 800

JO - Nature

JF - Nature

IS - 7052

ER -

The map-based sequence of the rice genome

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