Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.
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.
Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.
Itoh
Takeshi
T
Tanaka
Tsuyoshi
T
Barrero
Roberto A
RA
Yamasaki
Chisato
C
Fujii
Yasuyuki
Y
Hilton
Phillip B
PB
Antonio
Baltazar A
BA
Aono
Hideo
H
Apweiler
Rolf
R
Bruskiewich
Richard
R
Bureau
Thomas
T
Burr
Frances
F
Costa de Oliveira
Antonio
A
Fuks
Galina
G
Habara
Takuya
T
Haberer
Georg
G
Han
Bin
B
Harada
Erimi
E
Hiraki
Aiko T
AT
Hirochika
Hirohiko
H
Hoen
Douglas
D
Hokari
Hiroki
H
Hosokawa
Satomi
S
Hsing
Yue-ie
YI
Ikawa
Hiroshi
H
Ikeo
Kazuho
K
Imanishi
Tadashi
T
Ito
Yukiyo
Y
Jaiswal
Pankaj
P
Kanno
Masako
M
Kawahara
Yoshihiro
Y
Kawamura
Toshiyuki
T
Kawashima
Hiroaki
H
Khurana
Jitendra P
JP
Kikuchi
Shoshi
S
Komatsu
Setsuko
S
Koyanagi
Kanako O
KO
Kubooka
Hiromi
H
Lieberherr
Damien
D
Lin
Yao-Cheng
YC
Lonsdale
David
D
Matsumoto
Takashi
T
Matsuya
Akihiro
A
McCombie
W Richard
WR
Messing
Joachim
J
Miyao
Akio
A
Mulder
Nicola
N
Nagamura
Yoshiaki
Y
Nam
Jongmin
J
Namiki
Nobukazu
N
Numa
Hisataka
H
Nurimoto
Shin
S
O'Donovan
Claire
C
Ohyanagi
Hajime
H
Okido
Toshihisa
T
Oota
Satoshi
S
Osato
Naoki
N
Palmer
Lance E
LE
Quetier
Francis
F
Raghuvanshi
Saurabh
S
Saichi
Naomi
N
Sakai
Hiroaki
H
Sakai
Yasumichi
Y
Sakata
Katsumi
K
Sakurai
Tetsuya
T
Sato
Fumihiko
F
Sato
Yoshiharu
Y
Schoof
Heiko
H
Seki
Motoaki
M
Shibata
Michie
M
Shimizu
Yuji
Y
Shinozaki
Kazuo
K
Shinso
Yuji
Y
Singh
Nagendra K
NK
Smith-White
Brian
B
Takeda
Jun-ichi
J
Tanino
Motohiko
M
Tatusova
Tatiana
T
Thongjuea
Supat
S
Todokoro
Fusano
F
Tsugane
Mika
M
Tyagi
Akhilesh K
AK
Vanavichit
Apichart
A
Wang
Aihui
A
Wing
Rod A
RA
Yamaguchi
Kaori
K
Yamamoto
Mayu
M
Yamamoto
Naoyuki
N
Yu
Yeisoo
Y
Zhang
Hao
H
Zhao
Qiang
Q
Higo
Kenichi
K
Burr
Benjamin
B
Gojobori
Takashi
T
Sasaki
Takuji
T
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
D029681:Arabidopsis Proteins; D003062:Codon; D018076:DNA, Complementary; D018744:DNA, Plant; D010940:Plant Proteins; D012333:RNA, Messenger; D018749:RNA, Plant; D012343:RNA, Transfer