Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.
We present here the annotation of the complete genome of riceOryza sativaL. ssp.japonicacultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 pos...
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Cold Spring Harbor Laboratory
2007
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/166506 |
| _version_ | 1855540030613749760 |
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| author | Itoh, Takeshi Tanaka, Tsuyoshi Barrero, Roberto A. Yamasaki, Chisato Fujii, Yasuyuki Hilton, Phillip B. Antonio, Baltazar A. Aono, Hideo Apweiler, Rolf Bruskiewich, Richard Bureau, Thomas Burr, Frances Costa de Oliveira, Antonio Fuks, Galina Habara, Takuya Haberer, Georg Han, Bin Harada, Erimi Hiraki, Aiko T. Hirochika, Hirohiko Hoen, Douglas Hokari, Hiroki Hosokawa, Satomi Hsing, Yue Ikawa, Hiroshi Ikeo, Kazuho Imanishi, Tadashi Ito, Yukiyo Jaiswal, Pankaj Kanno, Masako Kawahara, Yoshihiro Kawamura, Toshiyuki Kawashima, Hiroaki Khurana, Jitendra P. Kikuchi, Shoshi Komatsu, Setsuko Koyanagi, Kanako O. Kubooka, Hiromi Lieberherr, Damien Lin, Yao-Cheng Lonsdale, David Matsumoto, Takashi Matsuya, Akihiro McCombie, W. Richard Messing, Joachim Miyao, Akio Mulder, Nicola Nagamura, Yoshiaki Nam, Jongmin Namiki, Nobukazu Numa, Hisataka Nurimoto, Shin O’Donovan, Claire Ohyanagi, Hajime Okido, Toshihisa OOta, Satoshi Osato, Naoki Palmer, Lance E. Quetier, Francis Raghuvanshi, Saurabh Saichi, Naomi Sakai, Hiroaki Sakai, Yasumichi Sakata, Katsumi Sakurai, Tetsuya Sato, Fumihiko Sato, Yoshiharu Schoof, Heiko Seki, Motoaki Shibata, Michie Shimizu, Yuji Shinozaki, Kazuo Shinso, Yuji Singh, Nagendra K. Smith-White, Brian Takeda, Jun-ichi Tanino, Motohiko Tatusova, Tatiana Thongjuea, Supat Todokoro, Fusano Tsugane, Mika Tyagi, Akhilesh K. Vanavichit, Apichart Wang, Aihui Wing, Rod A. Yamaguchi, Kaori Yamamoto, Mayu Yamamoto, Naoyuki Yu, Yeisoo Zhang, Hao Zhao, Qiang Higo, Kenichi Burr, Benjamin Gojobori, Takashi Sasaki, Takuji |
| author_browse | Antonio, Baltazar A. Aono, Hideo Apweiler, Rolf Barrero, Roberto A. Bruskiewich, Richard Bureau, Thomas Burr, Benjamin Burr, Frances Costa de Oliveira, Antonio Fujii, Yasuyuki Fuks, Galina Gojobori, Takashi Habara, Takuya Haberer, Georg Han, Bin Harada, Erimi Higo, Kenichi Hilton, Phillip B. Hiraki, Aiko T. Hirochika, Hirohiko Hoen, Douglas Hokari, Hiroki Hosokawa, Satomi Hsing, Yue Ikawa, Hiroshi Ikeo, Kazuho Imanishi, Tadashi Ito, Yukiyo Itoh, Takeshi Jaiswal, Pankaj Kanno, Masako Kawahara, Yoshihiro Kawamura, Toshiyuki Kawashima, Hiroaki Khurana, Jitendra P. Kikuchi, Shoshi Komatsu, Setsuko Koyanagi, Kanako O. Kubooka, Hiromi Lieberherr, Damien Lin, Yao-Cheng Lonsdale, David Matsumoto, Takashi Matsuya, Akihiro McCombie, W. Richard Messing, Joachim Miyao, Akio Mulder, Nicola Nagamura, Yoshiaki Nam, Jongmin Namiki, Nobukazu Numa, Hisataka Nurimoto, Shin OOta, Satoshi Ohyanagi, Hajime Okido, Toshihisa Osato, Naoki O’Donovan, Claire Palmer, Lance E. Quetier, Francis Raghuvanshi, Saurabh Saichi, Naomi Sakai, Hiroaki Sakai, Yasumichi Sakata, Katsumi Sakurai, Tetsuya Sasaki, Takuji Sato, Fumihiko Sato, Yoshiharu Schoof, Heiko Seki, Motoaki Shibata, Michie Shimizu, Yuji Shinozaki, Kazuo Shinso, Yuji Singh, Nagendra K. Smith-White, Brian Takeda, Jun-ichi Tanaka, Tsuyoshi Tanino, Motohiko Tatusova, Tatiana Thongjuea, Supat Todokoro, Fusano Tsugane, Mika Tyagi, Akhilesh K. Vanavichit, Apichart Wang, Aihui Wing, Rod A. Yamaguchi, Kaori Yamamoto, Mayu Yamamoto, Naoyuki Yamasaki, Chisato Yu, Yeisoo Zhang, Hao Zhao, Qiang |
| author_facet | Itoh, Takeshi Tanaka, Tsuyoshi Barrero, Roberto A. Yamasaki, Chisato Fujii, Yasuyuki Hilton, Phillip B. Antonio, Baltazar A. Aono, Hideo Apweiler, Rolf Bruskiewich, Richard Bureau, Thomas Burr, Frances Costa de Oliveira, Antonio Fuks, Galina Habara, Takuya Haberer, Georg Han, Bin Harada, Erimi Hiraki, Aiko T. Hirochika, Hirohiko Hoen, Douglas Hokari, Hiroki Hosokawa, Satomi Hsing, Yue Ikawa, Hiroshi Ikeo, Kazuho Imanishi, Tadashi Ito, Yukiyo Jaiswal, Pankaj Kanno, Masako Kawahara, Yoshihiro Kawamura, Toshiyuki Kawashima, Hiroaki Khurana, Jitendra P. Kikuchi, Shoshi Komatsu, Setsuko Koyanagi, Kanako O. Kubooka, Hiromi Lieberherr, Damien Lin, Yao-Cheng Lonsdale, David Matsumoto, Takashi Matsuya, Akihiro McCombie, W. Richard Messing, Joachim Miyao, Akio Mulder, Nicola Nagamura, Yoshiaki Nam, Jongmin Namiki, Nobukazu Numa, Hisataka Nurimoto, Shin O’Donovan, Claire Ohyanagi, Hajime Okido, Toshihisa OOta, Satoshi Osato, Naoki Palmer, Lance E. Quetier, Francis Raghuvanshi, Saurabh Saichi, Naomi Sakai, Hiroaki Sakai, Yasumichi Sakata, Katsumi Sakurai, Tetsuya Sato, Fumihiko Sato, Yoshiharu Schoof, Heiko Seki, Motoaki Shibata, Michie Shimizu, Yuji Shinozaki, Kazuo Shinso, Yuji Singh, Nagendra K. Smith-White, Brian Takeda, Jun-ichi Tanino, Motohiko Tatusova, Tatiana Thongjuea, Supat Todokoro, Fusano Tsugane, Mika Tyagi, Akhilesh K. Vanavichit, Apichart Wang, Aihui Wing, Rod A. Yamaguchi, Kaori Yamamoto, Mayu Yamamoto, Naoyuki Yu, Yeisoo Zhang, Hao Zhao, Qiang Higo, Kenichi Burr, Benjamin Gojobori, Takashi Sasaki, Takuji |
| author_sort | Itoh, Takeshi |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | We present here the annotation of the complete genome of riceOryza sativaL. ssp.japonicacultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is ∼32,000, which is smaller than previous estimates. We conducted comparative analyses between rice andArabidopsis thalianaand found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene. |
| format | Journal Article |
| id | CGSpace166506 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2007 |
| publishDateRange | 2007 |
| publishDateSort | 2007 |
| publisher | Cold Spring Harbor Laboratory |
| publisherStr | Cold Spring Harbor Laboratory |
| record_format | dspace |
| spelling | CGSpace1665062024-12-19T14:13:37Z Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Itoh, Takeshi Tanaka, Tsuyoshi Barrero, Roberto A. Yamasaki, Chisato Fujii, Yasuyuki Hilton, Phillip B. Antonio, Baltazar A. Aono, Hideo Apweiler, Rolf Bruskiewich, Richard Bureau, Thomas Burr, Frances Costa de Oliveira, Antonio Fuks, Galina Habara, Takuya Haberer, Georg Han, Bin Harada, Erimi Hiraki, Aiko T. Hirochika, Hirohiko Hoen, Douglas Hokari, Hiroki Hosokawa, Satomi Hsing, Yue Ikawa, Hiroshi Ikeo, Kazuho Imanishi, Tadashi Ito, Yukiyo Jaiswal, Pankaj Kanno, Masako Kawahara, Yoshihiro Kawamura, Toshiyuki Kawashima, Hiroaki Khurana, Jitendra P. Kikuchi, Shoshi Komatsu, Setsuko Koyanagi, Kanako O. Kubooka, Hiromi Lieberherr, Damien Lin, Yao-Cheng Lonsdale, David Matsumoto, Takashi Matsuya, Akihiro McCombie, W. Richard Messing, Joachim Miyao, Akio Mulder, Nicola Nagamura, Yoshiaki Nam, Jongmin Namiki, Nobukazu Numa, Hisataka Nurimoto, Shin O’Donovan, Claire Ohyanagi, Hajime Okido, Toshihisa OOta, Satoshi Osato, Naoki Palmer, Lance E. Quetier, Francis Raghuvanshi, Saurabh Saichi, Naomi Sakai, Hiroaki Sakai, Yasumichi Sakata, Katsumi Sakurai, Tetsuya Sato, Fumihiko Sato, Yoshiharu Schoof, Heiko Seki, Motoaki Shibata, Michie Shimizu, Yuji Shinozaki, Kazuo Shinso, Yuji Singh, Nagendra K. Smith-White, Brian Takeda, Jun-ichi Tanino, Motohiko Tatusova, Tatiana Thongjuea, Supat Todokoro, Fusano Tsugane, Mika Tyagi, Akhilesh K. Vanavichit, Apichart Wang, Aihui Wing, Rod A. Yamaguchi, Kaori Yamamoto, Mayu Yamamoto, Naoyuki Yu, Yeisoo Zhang, Hao Zhao, Qiang Higo, Kenichi Burr, Benjamin Gojobori, Takashi Sasaki, Takuji amino acid sequences complementary dna genes genomes genome analysis loci nucleotide sequences translation We present here the annotation of the complete genome of riceOryza sativaL. ssp.japonicacultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is ∼32,000, which is smaller than previous estimates. We conducted comparative analyses between rice andArabidopsis thalianaand found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene. 2007-02 2024-12-19T12:56:21Z 2024-12-19T12:56:21Z Journal Article https://hdl.handle.net/10568/166506 en Cold Spring Harbor Laboratory Itoh, Takeshi; Tanaka, Tsuyoshi; Barrero, Roberto A.; Yamasaki, Chisato; Fujii, Yasuyuki; Hilton, Phillip B.; Antonio, Baltazar A.; Aono, Hideo; Apweiler, Rolf; Bruskiewich, Richard; Bureau, Thomas; Burr, Frances; Costa de Oliveira, Antonio; Fuks, Galina; Habara, Takuya; Haberer, Georg; Han, Bin; Harada, Erimi; Hiraki, Aiko T.; Hirochika, Hirohiko; Hoen, Douglas; Hokari, Hiroki; Hosokawa, Satomi; Hsing, Yue; Ikawa, Hiroshi; Ikeo, Kazuho; Imanishi, Tadashi; Ito, Yukiyo; Jaiswal, Pankaj; Kanno, Masako; Kawahara, Yoshihiro; Kawamura, Toshiyuki; Kawashima, Hiroaki; Khurana, Jitendra P.; Kikuchi, Shoshi; Komatsu, Setsuko; Koyanagi, Kanako O.; Kubooka, Hiromi; Lieberherr, Damien; Lin, Yao-Cheng; Lonsdale, David; Matsumoto, Takashi; Matsuya, Akihiro; McCombie, W. Richard; Messing, Joachim; Miyao, Akio; Mulder, Nicola; Nagamura, Yoshiaki; Nam, Jongmin; Namiki, Nobukazu; Numa, Hisataka; Nurimoto, Shin; O’Donovan, Claire; Ohyanagi, Hajime; Okido, Toshihisa; OOta, Satoshi; Osato, Naoki; Palmer, Lance E.; Quetier, Francis; Raghuvanshi, Saurabh; Saichi, Naomi; Sakai, Hiroaki; Sakai, Yasumichi; Sakata, Katsumi; Sakurai, Tetsuya; Sato, Fumihiko; Sato, Yoshiharu; Schoof, Heiko; Seki, Motoaki; Shibata, Michie; Shimizu, Yuji; Shinozaki, Kazuo; Shinso, Yuji; Singh, Nagendra K.; Smith-White, Brian; Takeda, Jun-ichi; Tanino, Motohiko; Tatusova, Tatiana; Thongjuea, Supat; Todokoro, Fusano; Tsugane, Mika; Tyagi, Akhilesh K.; Vanavichit, Apichart; Wang, Aihui; Wing, Rod A.; Yamaguchi, Kaori; Yamamoto, Mayu; Yamamoto, Naoyuki; Yu, Yeisoo; Zhang, Hao; Zhao, Qiang; Higo, Kenichi; Burr, Benjamin; Gojobori, Takashi; Sasaki, Takuji and. 2007. Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res., Volume 17 no. 2 p. 175-183 |
| spellingShingle | amino acid sequences complementary dna genes genomes genome analysis loci nucleotide sequences translation Itoh, Takeshi Tanaka, Tsuyoshi Barrero, Roberto A. Yamasaki, Chisato Fujii, Yasuyuki Hilton, Phillip B. Antonio, Baltazar A. Aono, Hideo Apweiler, Rolf Bruskiewich, Richard Bureau, Thomas Burr, Frances Costa de Oliveira, Antonio Fuks, Galina Habara, Takuya Haberer, Georg Han, Bin Harada, Erimi Hiraki, Aiko T. Hirochika, Hirohiko Hoen, Douglas Hokari, Hiroki Hosokawa, Satomi Hsing, Yue Ikawa, Hiroshi Ikeo, Kazuho Imanishi, Tadashi Ito, Yukiyo Jaiswal, Pankaj Kanno, Masako Kawahara, Yoshihiro Kawamura, Toshiyuki Kawashima, Hiroaki Khurana, Jitendra P. Kikuchi, Shoshi Komatsu, Setsuko Koyanagi, Kanako O. Kubooka, Hiromi Lieberherr, Damien Lin, Yao-Cheng Lonsdale, David Matsumoto, Takashi Matsuya, Akihiro McCombie, W. Richard Messing, Joachim Miyao, Akio Mulder, Nicola Nagamura, Yoshiaki Nam, Jongmin Namiki, Nobukazu Numa, Hisataka Nurimoto, Shin O’Donovan, Claire Ohyanagi, Hajime Okido, Toshihisa OOta, Satoshi Osato, Naoki Palmer, Lance E. Quetier, Francis Raghuvanshi, Saurabh Saichi, Naomi Sakai, Hiroaki Sakai, Yasumichi Sakata, Katsumi Sakurai, Tetsuya Sato, Fumihiko Sato, Yoshiharu Schoof, Heiko Seki, Motoaki Shibata, Michie Shimizu, Yuji Shinozaki, Kazuo Shinso, Yuji Singh, Nagendra K. Smith-White, Brian Takeda, Jun-ichi Tanino, Motohiko Tatusova, Tatiana Thongjuea, Supat Todokoro, Fusano Tsugane, Mika Tyagi, Akhilesh K. Vanavichit, Apichart Wang, Aihui Wing, Rod A. Yamaguchi, Kaori Yamamoto, Mayu Yamamoto, Naoyuki Yu, Yeisoo Zhang, Hao Zhao, Qiang Higo, Kenichi Burr, Benjamin Gojobori, Takashi Sasaki, Takuji Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. |
| title | Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. |
| title_full | Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. |
| title_fullStr | Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. |
| title_full_unstemmed | Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. |
| title_short | Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. |
| title_sort | curated genome annotation of oryza sativa ssp japonica and comparative genome analysis with arabidopsis thaliana |
| topic | amino acid sequences complementary dna genes genomes genome analysis loci nucleotide sequences translation |
| url | https://hdl.handle.net/10568/166506 |
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curatedgenomeannotationoforyzasativasspjaponicaandcomparativegenomeanalysiswitharabidopsisthaliana AT zhanghao curatedgenomeannotationoforyzasativasspjaponicaandcomparativegenomeanalysiswitharabidopsisthaliana AT zhaoqiang curatedgenomeannotationoforyzasativasspjaponicaandcomparativegenomeanalysiswitharabidopsisthaliana AT higokenichi curatedgenomeannotationoforyzasativasspjaponicaandcomparativegenomeanalysiswitharabidopsisthaliana AT burrbenjamin curatedgenomeannotationoforyzasativasspjaponicaandcomparativegenomeanalysiswitharabidopsisthaliana AT gojoboritakashi curatedgenomeannotationoforyzasativasspjaponicaandcomparativegenomeanalysiswitharabidopsisthaliana AT sasakitakuji curatedgenomeannotationoforyzasativasspjaponicaandcomparativegenomeanalysiswitharabidopsisthaliana |