title: Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.
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 approximately 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.
authors.affiliation: Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.
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authors.lastname: Itoh
authors.forename: Tsuyoshi
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authors.forename: Roberto A
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authors.lastname: Barrero
authors.forename: Chisato
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authors.lastname: Yamasaki
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authors.lastname: Fujii
authors.forename: Phillip B
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authors.forename: Baltazar A
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authors.lastname: Burr
authors.forename: Antonio
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authors.lastname: Costa de Oliveira
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authors.lastname: Fuks
authors.forename: Takuya
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authors.lastname: Habara
authors.forename: Georg
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authors.lastname: Haberer
authors.forename: Bin
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authors.forename: Erimi
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authors.forename: Aiko T
authors.initials: AT
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authors.forename: Hirohiko
authors.initials: H
authors.lastname: Hirochika
authors.forename: Douglas
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authors.lastname: Hoen
authors.forename: Hiroki
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authors.lastname: Hokari
authors.forename: Satomi
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authors.lastname: Hosokawa
authors.forename: Yue-ie
authors.initials: YI
authors.lastname: Hsing
authors.forename: Hiroshi
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authors.lastname: Ikawa
authors.forename: Kazuho
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authors.lastname: Ikeo
authors.forename: Tadashi
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authors.lastname: Imanishi
authors.forename: Yukiyo
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authors.lastname: Ito
authors.forename: Pankaj
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authors.lastname: Jaiswal
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authors.lastname: Kawamura
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Kawashima
authors.forename: Jitendra P
authors.initials: JP
authors.lastname: Khurana
authors.forename: Shoshi
authors.initials: S
authors.lastname: Kikuchi
authors.forename: Setsuko
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authors.lastname: Komatsu
authors.forename: Kanako O
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authors.forename: Hiromi
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authors.forename: Damien
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authors.lastname: Lieberherr
authors.forename: Yao-Cheng
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authors.lastname: Lin
authors.forename: David
authors.initials: D
authors.lastname: Lonsdale
authors.forename: Takashi
authors.initials: T
authors.lastname: Matsumoto
authors.forename: Akihiro
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authors.forename: Joachim
authors.initials: J
authors.lastname: Messing
authors.forename: Akio
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authors.lastname: Miyao
authors.forename: Nicola
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authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Nagamura
authors.forename: Jongmin
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authors.forename: Hisataka
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authors.lastname: Numa
authors.forename: Shin
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authors.lastname: Nurimoto
authors.forename: Claire
authors.initials: C
authors.lastname: O'Donovan
authors.forename: Hajime
authors.initials: H
authors.lastname: Ohyanagi
authors.forename: Toshihisa
authors.initials: T
authors.lastname: Okido
authors.forename: Satoshi
authors.initials: S
authors.lastname: Oota
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authors.initials: N
authors.lastname: Osato
authors.forename: Lance E
authors.initials: LE
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authors.forename: Francis
authors.initials: F
authors.lastname: Quetier
authors.forename: Saurabh
authors.initials: S
authors.lastname: Raghuvanshi
authors.forename: Naomi
authors.initials: N
authors.lastname: Saichi
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Sakai
authors.forename: Yasumichi
authors.initials: Y
authors.lastname: Sakai
authors.forename: Katsumi
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authors.lastname: Sakata
authors.forename: Tetsuya
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authors.lastname: Sakurai
authors.forename: Fumihiko
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authors.lastname: Sato
authors.forename: Yoshiharu
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authors.forename: Heiko
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authors.lastname: Schoof
authors.forename: Motoaki
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authors.lastname: Seki
authors.forename: Michie
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authors.lastname: Shimizu
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authors.forename: Nagendra K
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authors.lastname: Smith-White
authors.forename: Jun-ichi
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authors.forename: Supat
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authors.lastname: Yamaguchi
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authors.lastname: Yamamoto
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authors.initials: N
authors.lastname: Yamamoto
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authors.lastname: Zhang
authors.forename: Qiang
authors.initials: Q
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authors.forename: Kenichi
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authors.lastname: Higo
authors.forename: Benjamin
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authors.lastname: Burr
authors.forename: Takashi
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authors.lastname: Gojobori
authors.forename: Takuji
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authors.lastname: Sasaki
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D003062:Codon / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D030562:Databases, Protein; D019143:Evolution, Molecular; D014644:Genetic Variation; D018745:Genome, Plant; D016254:Mutagenesis, Insertional; D016366:Open Reading Frames; D012275:Oryza / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D013045:Species Specificity
chemical_list: D029681:Arabidopsis Proteins; D003062:Codon; D018076:DNA, Complementary; D018744:DNA, Plant; D010940:Plant Proteins; D012333:RNA, Messenger; D018749:RNA, Plant; D012343:RNA, Transfer