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

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cg.identifier.doihttps://doi.org/10.1101/gr.5509507en
cg.issn1088-9051en
cg.issue2en
cg.journalGenome Researchen
cg.volume17en
dc.contributor.authorItoh, Takeshien
dc.contributor.authorTanaka, Tsuyoshien
dc.contributor.authorBarrero, Roberto A.en
dc.contributor.authorYamasaki, Chisatoen
dc.contributor.authorFujii, Yasuyukien
dc.contributor.authorHilton, Phillip B.en
dc.contributor.authorAntonio, Baltazar A.en
dc.contributor.authorAono, Hideoen
dc.contributor.authorApweiler, Rolfen
dc.contributor.authorBruskiewich, Richarden
dc.contributor.authorBureau, Thomasen
dc.contributor.authorBurr, Francesen
dc.contributor.authorCosta de Oliveira, Antonioen
dc.contributor.authorFuks, Galinaen
dc.contributor.authorHabara, Takuyaen
dc.contributor.authorHaberer, Georgen
dc.contributor.authorHan, Binen
dc.contributor.authorHarada, Erimien
dc.contributor.authorHiraki, Aiko T.en
dc.contributor.authorHirochika, Hirohikoen
dc.contributor.authorHoen, Douglasen
dc.contributor.authorHokari, Hirokien
dc.contributor.authorHosokawa, Satomien
dc.contributor.authorHsing, Yueen
dc.contributor.authorIkawa, Hiroshien
dc.contributor.authorIkeo, Kazuhoen
dc.contributor.authorImanishi, Tadashien
dc.contributor.authorIto, Yukiyoen
dc.contributor.authorJaiswal, Pankajen
dc.contributor.authorKanno, Masakoen
dc.contributor.authorKawahara, Yoshihiroen
dc.contributor.authorKawamura, Toshiyukien
dc.contributor.authorKawashima, Hiroakien
dc.contributor.authorKhurana, Jitendra P.en
dc.contributor.authorKikuchi, Shoshien
dc.contributor.authorKomatsu, Setsukoen
dc.contributor.authorKoyanagi, Kanako O.en
dc.contributor.authorKubooka, Hiromien
dc.contributor.authorLieberherr, Damienen
dc.contributor.authorLin, Yao-Chengen
dc.contributor.authorLonsdale, Daviden
dc.contributor.authorMatsumoto, Takashien
dc.contributor.authorMatsuya, Akihiroen
dc.contributor.authorMcCombie, W. Richarden
dc.contributor.authorMessing, Joachimen
dc.contributor.authorMiyao, Akioen
dc.contributor.authorMulder, Nicolaen
dc.contributor.authorNagamura, Yoshiakien
dc.contributor.authorNam, Jongminen
dc.contributor.authorNamiki, Nobukazuen
dc.contributor.authorNuma, Hisatakaen
dc.contributor.authorNurimoto, Shinen
dc.contributor.authorO’Donovan, Claireen
dc.contributor.authorOhyanagi, Hajimeen
dc.contributor.authorOkido, Toshihisaen
dc.contributor.authorOOta, Satoshien
dc.contributor.authorOsato, Naokien
dc.contributor.authorPalmer, Lance E.en
dc.contributor.authorQuetier, Francisen
dc.contributor.authorRaghuvanshi, Saurabhen
dc.contributor.authorSaichi, Naomien
dc.contributor.authorSakai, Hiroakien
dc.contributor.authorSakai, Yasumichien
dc.contributor.authorSakata, Katsumien
dc.contributor.authorSakurai, Tetsuyaen
dc.contributor.authorSato, Fumihikoen
dc.contributor.authorSato, Yoshiharuen
dc.contributor.authorSchoof, Heikoen
dc.contributor.authorSeki, Motoakien
dc.contributor.authorShibata, Michieen
dc.contributor.authorShimizu, Yujien
dc.contributor.authorShinozaki, Kazuoen
dc.contributor.authorShinso, Yujien
dc.contributor.authorSingh, Nagendra K.en
dc.contributor.authorSmith-White, Brianen
dc.contributor.authorTakeda, Jun-ichien
dc.contributor.authorTanino, Motohikoen
dc.contributor.authorTatusova, Tatianaen
dc.contributor.authorThongjuea, Supaten
dc.contributor.authorTodokoro, Fusanoen
dc.contributor.authorTsugane, Mikaen
dc.contributor.authorTyagi, Akhilesh K.en
dc.contributor.authorVanavichit, Apicharten
dc.contributor.authorWang, Aihuien
dc.contributor.authorWing, Rod A.en
dc.contributor.authorYamaguchi, Kaorien
dc.contributor.authorYamamoto, Mayuen
dc.contributor.authorYamamoto, Naoyukien
dc.contributor.authorYu, Yeisooen
dc.contributor.authorZhang, Haoen
dc.contributor.authorZhao, Qiangen
dc.contributor.authorHigo, Kenichien
dc.contributor.authorBurr, Benjaminen
dc.contributor.authorGojobori, Takashien
dc.contributor.authorSasaki, Takujien
dc.date.accessioned2024-12-19T12:56:21Zen
dc.date.available2024-12-19T12:56:21Zen
dc.identifier.urihttps://hdl.handle.net/10568/166506
dc.titleCurated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.en
dcterms.abstractWe 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.en
dcterms.available2007-01-08
dcterms.bibliographicCitationItoh, 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. 175-183en
dcterms.extentpp. 175-183en
dcterms.issued2007-02
dcterms.languageen
dcterms.publisherCold Spring Harbor Laboratoryen
dcterms.subjectamino acid sequencesen
dcterms.subjectcomplementary dnaen
dcterms.subjectgenesen
dcterms.subjectgenomesen
dcterms.subjectgenome analysisen
dcterms.subjectlocien
dcterms.subjectnucleotide sequencesen
dcterms.subjecttranslationen
dcterms.typeJournal Article

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