Curated genome annotation ofOryza sativassp.japonicaand comparative genome analysis withArabidopsis thaliana
Authors: 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 ,   for the Rice Annotation Project
Published: January 2007

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.