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

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dc.creatorItoh, Takeshi
dc.creatorTanaka, Tsuyoshi
dc.creatorBarrero, Roberto A.
dc.creatorYamasaki, Chisato
dc.creatorFujii, Yasuyuki
dc.creatorHilton, Phillip B.
dc.creatorAntonio, Baltazar A.
dc.creatorAono, Hideo
dc.creatorApweiler, Rolf
dc.creatorBruskiewich, Richard
dc.creatorBureau, Thomas
dc.creatorBurr, Frances
dc.creatorCosta de Oliveira, Antonio
dc.creatorFuks, Galina
dc.creatorHabara, Takuya
dc.creatorHaberer, Georg
dc.creatorHan, Bin
dc.creatorHarada, Erimi
dc.creatorHiraki, Aiko T.
dc.creatorHirochika, Hirohiko
dc.creatorHoen, Douglas
dc.creatorHokari, Hiroki
dc.creatorHosokawa, Satomi
dc.creatorHsing, Yue
dc.creatorIkawa, Hiroshi
dc.creatorIkeo, Kazuho
dc.creatorImanishi, Tadashi
dc.creatorIto, Yukiyo
dc.creatorJaiswal, Pankaj
dc.creatorKanno, Masako
dc.creatorKawahara, Yoshihiro
dc.creatorKawamura, Toshiyuki
dc.creatorKawashima, Hiroaki
dc.creatorKhurana, Jitendra P.
dc.creatorKikuchi, Shoshi
dc.creatorKomatsu, Setsuko
dc.creatorKoyanagi, Kanako O.
dc.creatorKubooka, Hiromi
dc.creatorLieberherr, Damien
dc.creatorLin, Yao-Cheng
dc.creatorLonsdale, David
dc.creatorMatsumoto, Takashi
dc.creatorMatsuya, Akihiro
dc.creatorMcCombie, W. Richard
dc.creatorMessing, Joachim
dc.creatorMiyao, Akio
dc.creatorMulder, Nicola
dc.creatorNagamura, Yoshiaki
dc.creatorNam, Jongmin
dc.creatorNamiki, Nobukazu
dc.creatorNuma, Hisataka
dc.creatorNurimoto, Shin
dc.creatorO’Donovan, Claire
dc.creatorOhyanagi, Hajime
dc.creatorOkido, Toshihisa
dc.creatorOOta, Satoshi
dc.creatorOsato, Naoki
dc.creatorPalmer, Lance E.
dc.creatorQuetier, Francis
dc.creatorRaghuvanshi, Saurabh
dc.creatorSaichi, Naomi
dc.creatorSakai, Hiroaki
dc.creatorSakai, Yasumichi
dc.creatorSakata, Katsumi
dc.creatorSakurai, Tetsuya
dc.creatorSato, Fumihiko
dc.creatorSato, Yoshiharu
dc.creatorSchoof, Heiko
dc.creatorSeki, Motoaki
dc.creatorShibata, Michie
dc.creatorShimizu, Yuji
dc.creatorShinozaki, Kazuo
dc.creatorShinso, Yuji
dc.creatorSingh, Nagendra K.
dc.creatorSmith-White, Brian
dc.creatorTakeda, Jun-ichi
dc.creatorTanino, Motohiko
dc.creatorTatusova, Tatiana
dc.creatorThongjuea, Supat
dc.creatorTodokoro, Fusano
dc.creatorTsugane, Mika
dc.creatorTyagi, Akhilesh K.
dc.creatorVanavichit, Apichart
dc.creatorWang, Aihui
dc.creatorWing, Rod A.
dc.creatorYamaguchi, Kaori
dc.creatorYamamoto, Mayu
dc.creatorYamamoto, Naoyuki
dc.creatorYu, Yeisoo
dc.creatorZhang, Hao
dc.creatorZhao, Qiang
dc.creatorHigo, Kenichi
dc.creatorBurr, Benjamin
dc.creatorGojobori, Takashi
dc.creatorSasaki, Takuji
dc.date2007-02
dc.date2024-12-19T12:56:21Z
dc.date2024-12-19T12:56:21Z
dc.date.accessioned2026-06-27T04:15:14Z
dc.descriptionWe 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.
dc.identifierhttps://hdl.handle.net/10568/166506
dc.identifier.urihttp://hdl.handle.net/123456789/26673
dc.languageen
dc.publisherCold Spring Harbor Laboratory
dc.sourceItoh, 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
dc.subjectamino acid sequences
dc.subjectcomplementary dna
dc.subjectgenes
dc.subjectgenomes
dc.subjectgenome analysis
dc.subjectloci
dc.subjectnucleotide sequences
dc.subjecttranslation
dc.titleCurated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.
dc.typeJournal Article

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Instituto Internacional de Investigación del Arroz (IRRI)