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Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

Itoh, Takeshi and Tanaka, Tsuyoshi and Barrero, Roberto A. and Yamasaki, Chisato and Fujii, Yasuyuki and Hilton, Phillip B. and Antonio, Baltazar A. and Aono, Hideo and Apweiler, Rolf and Bruskiewich, Richard and Bureau, Thomas and Burr, Frances and Costa de Oliveira, Antonio and Fuks, Galina and Habara, Takuya and Haberer, Georg and Han, Bin and Harada, Erimi and Hiraki, Aiko T. and Hirochika, Hirohiko and Hoen, Douglas and Hokari, Hiroki and Hosokawa, Satomi and Hsing, Yue and Ikawa, Hiroshi and Ikeo, Kazuho and Imanishi, Tadashi and Ito, Yukiyo and Jaiswal, Pankaj and Kanno, Masako and Kawahara, Yosihiro and Kawamura, Toshiyuki and Kawashima, Hiroaki and Khurana, Jitendra P. and Kikuchi, Shoshi and Komatsu, Setsuko and Koyanagi, Kanako O. and Kubooka, Hiromi and McCombie, W. Richard and Messing, Joachim and Miyao, Akio and Mulder, Nicola and Nagamura, Yoshiaki and Nam, Jongmin and Namiki, Nobukazu and Numa, Hisataka and Nurimoto, Shin and O'Donovan, Claire and Ohyanagi, Hajimi and Liberherr, Damien and Lin, Yao-Cheng and Lonsdale, David and Matsumoto, Takashi and Matsuya, Akihiro and Okido, Toshihisa and OOta, Satoshi and Osato, Naoki and Palmer, Lance E. and Quetier, Francis and Raghuvanshi, Surabh and Saichi, Naomi and Sakai, Hiroaki and Sakai, Yasumichi and Sakata, Katsumi and Sakurai, Tetsuya and Sato, Fumihiko and Sato, Yoshiharu and Schoof, Heiko and Seki, Motoaki and Shibata, Katsumi and Shibata, Michie and Shimizu, Yuji and Shinozaki, Kazuo and Shinso, Yuji and Singh, Nagendra K. and Smith-White, Brian and Takeda, Jun-ichi and Tanino, Motohiko and Tatusova, Tatiana and Thongjuea, Supat and Todokoro, Fusano and Tsugane, Mika and Tyagi, Akhilesh K. and Vanavichit, Apichart and Wang, Aihui and Wing, Rod A. and Yamaguchi, Kaori and Yamamoto, Mayu and Yamamoto, Naoyuki and Yu, Yeisoo and Zhang, Hao and Zhao, Qiang and Higo, Kenichi and Burr, Benjamin and Gojobori, Takashi and Saski, Takuji (2007) Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Research, 17 (2). pp. 175-183. ISSN 1088-9051. http://resolver.caltech.edu/CaltechAUTHORS:ITOgr07

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Abstract

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar 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 and Arabidopsis thaliana and 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.


Item Type:Article
Additional Information:© 2007 by Cold Spring Harbor Laboratory Press. Freely available online through the Genome Research Open Access option. The Authors acknowledge that six months after the full-issue publication date, the Article will be distributed under a Creative Commons CC-BY-NC License (Attribution-NonCommercial 4.0 International License, http://creativecommons.org/licenses/by-nc/4.0/). Received May 17, 2006; accepted in revised form October 31, 2006. Published online before print January 8, 2007, 10.1101/gr.5509507 We are grateful to C. Robin Buell, Hisakazu Iwama, Satoshi Fukuchi, Craig Gough, Kumiko Suzuki, Junko Sugiyama, Emiko Saito, Masato Kawabata, Chikatada Satoh, Shigetoyo Furukawa, Satoshi Nobushima, Ryo Aono, Tomohiro Endo, and Michitoshi Nagamochi for their support. We thank all the participants of the First Rice Annotation Project Meeting (RAP1). We also thank the Computer Center for Agriculture, Forestry and Fisheries Research for assisting RAP1. This work was supported by a grant from the Special Coordination Funds for Promoting Science and Technology of the Ministry of Education, Culture, Sports, Science and Technology of Japan. [Supplemental material is available online at www.genome.org.]
Issue or Number:2
Record Number:CaltechAUTHORS:ITOgr07
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:ITOgr07
Alternative URL:http://dx.doi.org/10.1101/gr.5509507
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:8690
Collection:CaltechAUTHORS
Deposited By: Archive Administrator
Deposited On:05 Sep 2007
Last Modified:22 May 2017 16:58

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