The genome sequence and structure of rice chromosome 1

Takuji Sasaki; Takashi Matsumoto; Kimiko Yamamoto; Katsumi Sakata; Tomoya Baba; Yuichi Katayose; Jianzhong Wu; Yoshihito Niimura; Zhukuan Cheng; Yoshiaki Nagamura; Baltazar A. Antonio; Hiroyuki Kanamori; Satomi Hosokawa; Masatoshi Masukawa; Koji Arikawa; Yoshino Chiden; Mika Hayashi; Masako Okamoto; Tsuyu Ando; Hiroyoshi Aoki; Kohei Arita; Masao Hamada; Chizuko Harada; Saori Hijishita; Mikiko Honda; Yoko Ichikawa; Atsuko Idonuma; Masumi Iijlma; Michiko Ikeda; Maiko Ikeno; Sachle Ito; Tomoko Ito; Yuichi Ito; Yukiyo Ito; Aki Iwabuchi; Kozue Kamiya; Wataru Karasawa; Satoshi Katagiri; Ari Kikuta; Noriko Kobayashi; Izumi Kono; Kayo Machita; Tomoko Maehara; Hiroshi Mizuno; Tatsumi Mizubayashi; Yoshiyuki Mukai; Hideki Nagasaki; Marina Nakashima; Yuko Nakama; Yumi Nakamichi; Mari Nakamura; Nobukazu Namiki; Manami Negishi; Isamu Ohta; Nozomi Ono; Shoko Saji; Kumiko Sakai; Michie Shibata; Takanori Shimokawa; Ayahiko Shomura; Jianyu Song; Yuka Takazaki; Kimihiro Terasawa; Kumiko Tsuji; Kazunori Waki; Harumi Yamagata; Hiroko Yamane; Shoji Yoshiki; Rie Yoshihara; Kazuko Yukawa; Huisun Zhong; Hisakazu Iwama; Toshinori Endo; Hidetaka Ito; Jang Ho Hahn; Ho Il Kim; Moo Young Eun; Masahiro Yano; Jiming Jiang; Takashi Gojobori

doi:10.1038/nature01184

The genome sequence and structure of rice chromosome 1

Takuji Sasaki^*, Takashi Matsumoto, Kimiko Yamamoto, Katsumi Sakata, Tomoya Baba, Yuichi Katayose, Jianzhong Wu, Yoshihito Niimura, Zhukuan Cheng, Yoshiaki Nagamura, Baltazar A. Antonio, Hiroyuki Kanamori, Satomi Hosokawa, Masatoshi Masukawa, Koji Arikawa, Yoshino Chiden, Mika Hayashi, Masako Okamoto, Tsuyu Ando, Hiroyoshi AokiKohei Arita, Masao Hamada, Chizuko Harada, Saori Hijishita, Mikiko Honda, Yoko Ichikawa, Atsuko Idonuma, Masumi Iijlma, Michiko Ikeda, Maiko Ikeno, Sachle Ito, Tomoko Ito, Yuichi Ito, Yukiyo Ito, Aki Iwabuchi, Kozue Kamiya, Wataru Karasawa, Satoshi Katagiri, Ari Kikuta, Noriko Kobayashi, Izumi Kono, Kayo Machita, Tomoko Maehara, Hiroshi Mizuno, Tatsumi Mizubayashi, Yoshiyuki Mukai, Hideki Nagasaki, Marina Nakashima, Yuko Nakama, Yumi Nakamichi, Mari Nakamura, Nobukazu Namiki, Manami Negishi, Isamu Ohta, Nozomi Ono, Shoko Saji, Kumiko Sakai, Michie Shibata, Takanori Shimokawa, Ayahiko Shomura, Jianyu Song, Yuka Takazaki, Kimihiro Terasawa, Kumiko Tsuji, Kazunori Waki, Harumi Yamagata, Hiroko Yamane, Shoji Yoshiki, Rie Yoshihara, Kazuko Yukawa, Huisun Zhong, Hisakazu Iwama, Toshinori Endo, Hidetaka Ito, Jang Ho Hahn, Ho Il Kim, Moo Young Eun, Masahiro Yano, Jiming Jiang, Takashi Gojobori

^*Corresponding author for this work

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

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Abstract

The rice species Oryza sativa is considered to be a model plant because of its small genome size, extensive genetic map, relative ease of transformation and synteny with other cereal crops^1-4. Here we report the essentially complete sequence of chromosome 1, the longest chromosome in the rice genome. We summarize characteristics of the chromosome structure and the biological insight gained from the sequence. The analysis of 43.3 megabases (Mb) of non-overlapping sequence reveals 6,756 protein coding genes, of which 3,161 show homology to proteins of Arabidopsis thaliana, another model plant. About 30% (2,073) of the genes have been functionally categorized. Rice chromosome 1 is (G + C)-rich, especially in its coding regions, and is characterized by several gene families that are dispersed or arranged in tandem repeats. Comparison with a draft sequences⁵ indicates the importance of a high-quality finished sequence.

Original language	English (US)
Pages (from-to)	312-316
Number of pages	5
Journal	NATURE
Volume	420
Issue number	6913
DOIs	https://doi.org/10.1038/nature01184
State	Published - Nov 21 2002
Externally published	Yes

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Sasaki, T., Matsumoto, T., Yamamoto, K., Sakata, K., Baba, T., Katayose, Y., Wu, J., Niimura, Y., Cheng, Z., Nagamura, Y., Antonio, B. A., Kanamori, H., Hosokawa, S., Masukawa, M., Arikawa, K., Chiden, Y., Hayashi, M., Okamoto, M., Ando, T., ... Gojobori, T. (2002). The genome sequence and structure of rice chromosome 1. NATURE, 420(6913), 312-316. https://doi.org/10.1038/nature01184

@article{078969f1e02b455daff802b788a07778,

title = "The genome sequence and structure of rice chromosome 1",

abstract = "The rice species Oryza sativa is considered to be a model plant because of its small genome size, extensive genetic map, relative ease of transformation and synteny with other cereal crops1-4. Here we report the essentially complete sequence of chromosome 1, the longest chromosome in the rice genome. We summarize characteristics of the chromosome structure and the biological insight gained from the sequence. The analysis of 43.3 megabases (Mb) of non-overlapping sequence reveals 6,756 protein coding genes, of which 3,161 show homology to proteins of Arabidopsis thaliana, another model plant. About 30% (2,073) of the genes have been functionally categorized. Rice chromosome 1 is (G + C)-rich, especially in its coding regions, and is characterized by several gene families that are dispersed or arranged in tandem repeats. Comparison with a draft sequences5 indicates the importance of a high-quality finished sequence.",

author = "Takuji Sasaki and Takashi Matsumoto and Kimiko Yamamoto and Katsumi Sakata and Tomoya Baba and Yuichi Katayose and Jianzhong Wu and Yoshihito Niimura and Zhukuan Cheng and Yoshiaki Nagamura and Antonio, {Baltazar A.} and Hiroyuki Kanamori and Satomi Hosokawa and Masatoshi Masukawa and Koji Arikawa and Yoshino Chiden and Mika Hayashi and Masako Okamoto and Tsuyu Ando and Hiroyoshi Aoki and Kohei Arita and Masao Hamada and Chizuko Harada and Saori Hijishita and Mikiko Honda and Yoko Ichikawa and Atsuko Idonuma and Masumi Iijlma and Michiko Ikeda and Maiko Ikeno and Sachle Ito and Tomoko Ito and Yuichi Ito and Yukiyo Ito and Aki Iwabuchi and Kozue Kamiya and Wataru Karasawa and Satoshi Katagiri and Ari Kikuta and Noriko Kobayashi and Izumi Kono and Kayo Machita and Tomoko Maehara and Hiroshi Mizuno and Tatsumi Mizubayashi and Yoshiyuki Mukai and Hideki Nagasaki and Marina Nakashima and Yuko Nakama and Yumi Nakamichi and Mari Nakamura and Nobukazu Namiki and Manami Negishi and Isamu Ohta and Nozomi Ono and Shoko Saji and Kumiko Sakai and Michie Shibata and Takanori Shimokawa and Ayahiko Shomura and Jianyu Song and Yuka Takazaki and Kimihiro Terasawa and Kumiko Tsuji and Kazunori Waki and Harumi Yamagata and Hiroko Yamane and Shoji Yoshiki and Rie Yoshihara and Kazuko Yukawa and Huisun Zhong and Hisakazu Iwama and Toshinori Endo and Hidetaka Ito and Hahn, {Jang Ho} and Kim, {Ho Il} and Eun, {Moo Young} and Masahiro Yano and Jiming Jiang and Takashi Gojobori",

note = "Funding Information: Acknowledgements We thank M. Ramos for help in preparing the manuscript; and R. Prum for critical comments on the manuscript. Figure 1b is modified from ref. 1. This work is supported by grants from the National Institute of Arthritis and Musculoskeletal and Skin Diseases, USA, and the National Science Foundation to C.-M.C., and a National Cancer Institute grant to R.B.W.",

year = "2002",

month = nov,

day = "21",

doi = "10.1038/nature01184",

language = "English (US)",

volume = "420",

pages = "312--316",

journal = "NATURE",

issn = "0028-0836",

publisher = "Nature Research",

number = "6913",

}

Sasaki, T, Matsumoto, T, Yamamoto, K, Sakata, K, Baba, T, Katayose, Y, Wu, J, Niimura, Y, Cheng, Z, Nagamura, Y, Antonio, BA, Kanamori, H, Hosokawa, S, Masukawa, M, Arikawa, K, Chiden, Y, Hayashi, M, Okamoto, M, Ando, T, Aoki, H, Arita, K, Hamada, M, Harada, C, Hijishita, S, Honda, M, Ichikawa, Y, Idonuma, A, Iijlma, M, Ikeda, M, Ikeno, M, Ito, S, Ito, T, Ito, Y, Ito, Y, Iwabuchi, A, Kamiya, K, Karasawa, W, Katagiri, S, Kikuta, A, Kobayashi, N, Kono, I, Machita, K, Maehara, T, Mizuno, H, Mizubayashi, T, Mukai, Y, Nagasaki, H, Nakashima, M, Nakama, Y, Nakamichi, Y, Nakamura, M, Namiki, N, Negishi, M, Ohta, I, Ono, N, Saji, S, Sakai, K, Shibata, M, Shimokawa, T, Shomura, A, Song, J, Takazaki, Y, Terasawa, K, Tsuji, K, Waki, K, Yamagata, H, Yamane, H, Yoshiki, S, Yoshihara, R, Yukawa, K, Zhong, H, Iwama, H, Endo, T, Ito, H, Hahn, JH, Kim, HI, Eun, MY, Yano, M, Jiang, J & Gojobori, T 2002, 'The genome sequence and structure of rice chromosome 1', NATURE, vol. 420, no. 6913, pp. 312-316. https://doi.org/10.1038/nature01184

TY - JOUR

T1 - The genome sequence and structure of rice chromosome 1

AU - Sasaki, Takuji

AU - Matsumoto, Takashi

AU - Yamamoto, Kimiko

AU - Sakata, Katsumi

AU - Baba, Tomoya

AU - Katayose, Yuichi

AU - Wu, Jianzhong

AU - Niimura, Yoshihito

AU - Cheng, Zhukuan

AU - Nagamura, Yoshiaki

AU - Antonio, Baltazar A.

AU - Kanamori, Hiroyuki

AU - Hosokawa, Satomi

AU - Masukawa, Masatoshi

AU - Arikawa, Koji

AU - Chiden, Yoshino

AU - Hayashi, Mika

AU - Okamoto, Masako

AU - Ando, Tsuyu

AU - Aoki, Hiroyoshi

AU - Arita, Kohei

AU - Hamada, Masao

AU - Harada, Chizuko

AU - Hijishita, Saori

AU - Honda, Mikiko

AU - Ichikawa, Yoko

AU - Idonuma, Atsuko

AU - Iijlma, Masumi

AU - Ikeda, Michiko

AU - Ikeno, Maiko

AU - Ito, Sachle

AU - Ito, Tomoko

AU - Ito, Yuichi

AU - Ito, Yukiyo

AU - Iwabuchi, Aki

AU - Kamiya, Kozue

AU - Karasawa, Wataru

AU - Katagiri, Satoshi

AU - Kikuta, Ari

AU - Kobayashi, Noriko

AU - Kono, Izumi

AU - Machita, Kayo

AU - Maehara, Tomoko

AU - Mizuno, Hiroshi

AU - Mizubayashi, Tatsumi

AU - Mukai, Yoshiyuki

AU - Nagasaki, Hideki

AU - Nakashima, Marina

AU - Nakama, Yuko

AU - Nakamichi, Yumi

AU - Nakamura, Mari

AU - Namiki, Nobukazu

AU - Negishi, Manami

AU - Ohta, Isamu

AU - Ono, Nozomi

AU - Saji, Shoko

AU - Sakai, Kumiko

AU - Shibata, Michie

AU - Shimokawa, Takanori

AU - Shomura, Ayahiko

AU - Song, Jianyu

AU - Takazaki, Yuka

AU - Terasawa, Kimihiro

AU - Tsuji, Kumiko

AU - Waki, Kazunori

AU - Yamagata, Harumi

AU - Yamane, Hiroko

AU - Yoshiki, Shoji

AU - Yoshihara, Rie

AU - Yukawa, Kazuko

AU - Zhong, Huisun

AU - Iwama, Hisakazu

AU - Endo, Toshinori

AU - Ito, Hidetaka

AU - Hahn, Jang Ho

AU - Kim, Ho Il

AU - Eun, Moo Young

AU - Yano, Masahiro

AU - Jiang, Jiming

AU - Gojobori, Takashi

N1 - Funding Information: Acknowledgements We thank M. Ramos for help in preparing the manuscript; and R. Prum for critical comments on the manuscript. Figure 1b is modified from ref. 1. This work is supported by grants from the National Institute of Arthritis and Musculoskeletal and Skin Diseases, USA, and the National Science Foundation to C.-M.C., and a National Cancer Institute grant to R.B.W.

PY - 2002/11/21

Y1 - 2002/11/21

N2 - The rice species Oryza sativa is considered to be a model plant because of its small genome size, extensive genetic map, relative ease of transformation and synteny with other cereal crops1-4. Here we report the essentially complete sequence of chromosome 1, the longest chromosome in the rice genome. We summarize characteristics of the chromosome structure and the biological insight gained from the sequence. The analysis of 43.3 megabases (Mb) of non-overlapping sequence reveals 6,756 protein coding genes, of which 3,161 show homology to proteins of Arabidopsis thaliana, another model plant. About 30% (2,073) of the genes have been functionally categorized. Rice chromosome 1 is (G + C)-rich, especially in its coding regions, and is characterized by several gene families that are dispersed or arranged in tandem repeats. Comparison with a draft sequences5 indicates the importance of a high-quality finished sequence.

AB - The rice species Oryza sativa is considered to be a model plant because of its small genome size, extensive genetic map, relative ease of transformation and synteny with other cereal crops1-4. Here we report the essentially complete sequence of chromosome 1, the longest chromosome in the rice genome. We summarize characteristics of the chromosome structure and the biological insight gained from the sequence. The analysis of 43.3 megabases (Mb) of non-overlapping sequence reveals 6,756 protein coding genes, of which 3,161 show homology to proteins of Arabidopsis thaliana, another model plant. About 30% (2,073) of the genes have been functionally categorized. Rice chromosome 1 is (G + C)-rich, especially in its coding regions, and is characterized by several gene families that are dispersed or arranged in tandem repeats. Comparison with a draft sequences5 indicates the importance of a high-quality finished sequence.

UR - http://www.scopus.com/inward/record.url?scp=0037153190&partnerID=8YFLogxK

U2 - 10.1038/nature01184

DO - 10.1038/nature01184

M3 - Article

C2 - 12447438

AN - SCOPUS:0037153190

SN - 0028-0836

VL - 420

SP - 312

EP - 316

JO - NATURE

JF - NATURE

IS - 6913

ER -

The genome sequence and structure of rice chromosome 1

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