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

T. Itoh; T. Tanaka; R.A. Barrero; C. Yamasaki; Y. Fujii; P.B. Hilton; B.A. Antonio; H. Aono; R. Apweiler; R. Bruskiewich; T. Bureau; F. Burr; A. Costa de Oliveira; G. Fuks; T. Habara; G. Haberer; B. Han; E. Harada; A.T. Hiraki; H. Hirochika; D. Hoen; H. Hokari; S. Hosokawa; Y. Hsing; H. Ikawa; K. Ikeo; T. Imanishi; Y. Ito; P. Jaiswal; M. Kanno; Y. Kawahara; T. Kawamura; H. Kawashima; J.P. Khurana; S. Kikuchi; S. Komatsu; K.O. Koyanagi; H. Kubooka; D. Lieberherr; Y-C Lin; D. Lonsdale; T. Matsumoto; A. Matsuya; W.R. McCombie; J. Messing; A. Miyao; N. Mulder; Y. Nagamura; J. Nam; N. Namiki; H. Numa; S. Nurimoto; C. O'Donovan; H. Ohyanagi; T. Okido; S. OOta; N. Osato; L.E. Palmer; F. Quetier; S. Raghuvanshi; N. Saichi; H. Sakai; Y. Sakai; K. Sakata; T. Sakurai; F. Sato; Y. Sato; H. Schoof; M. Seki; M. Shibata; Y. Shimizu; K. Shinozaki; Y. Shinso; N.K. Singh; B. Smith-White; J.-i. Takeda; M. Tanino; T. Tatusova; S. Thongjuea; F. Todokoro; M. Tsugane; A.K. Tyagi; A. Vanavichit; A. Wang; R.A. Wing; K. Yamaguchi; M. Yamamoto; N. Yamamoto; Y. Yu; H. Zhang; Q. Zhao; K. Higo; B. Burr; T. Gojobori; T. Sasaki

doi:10.1101/gr.5509507

Back

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

Journal article

Open access

Peer reviewed

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

T. Itoh, T. Tanaka, R.A. Barrero, C. Yamasaki, Y. Fujii, P.B. Hilton, B.A. Antonio, H. Aono, R. Apweiler, R. Bruskiewich, …

Genome Research, Vol.17(2), pp.175-183

2007

DOI: https://doi.org/10.1101/gr.5509507

Files and links (2)

pdf

curated_genome_annotation.pdfDownload View

Published (Version of Record) Open Access

url

Link to Published Version *Subscription may be requiredView

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 ∼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.

Details

Title: Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana
Authors/Creators: T. Itoh (Author/Creator)
T. Tanaka (Author/Creator)
R.A. Barrero (Author/Creator)
C. Yamasaki (Author/Creator)
Y. Fujii (Author/Creator)
P.B. Hilton (Author/Creator)
B.A. Antonio (Author/Creator)
H. Aono (Author/Creator)
R. Apweiler (Author/Creator)
R. Bruskiewich (Author/Creator)
T. Bureau (Author/Creator)
F. Burr (Author/Creator)
A. Costa de Oliveira (Author/Creator)
G. Fuks (Author/Creator)
T. Habara (Author/Creator)
G. Haberer (Author/Creator)
B. Han (Author/Creator)
E. Harada (Author/Creator)
A.T. Hiraki (Author/Creator)
H. Hirochika (Author/Creator)
D. Hoen (Author/Creator)
H. Hokari (Author/Creator)
S. Hosokawa (Author/Creator)
Y. Hsing (Author/Creator)
H. Ikawa (Author/Creator)
K. Ikeo (Author/Creator)
T. Imanishi (Author/Creator)
Y. Ito (Author/Creator)
P. Jaiswal (Author/Creator)
M. Kanno (Author/Creator)
Y. Kawahara (Author/Creator)
T. Kawamura (Author/Creator)
H. Kawashima (Author/Creator)
J.P. Khurana (Author/Creator)
S. Kikuchi (Author/Creator)
S. Komatsu (Author/Creator)
K.O. Koyanagi (Author/Creator)
H. Kubooka (Author/Creator)
D. Lieberherr (Author/Creator)
Y-C Lin (Author/Creator)
D. Lonsdale (Author/Creator)
T. Matsumoto (Author/Creator)
A. Matsuya (Author/Creator)
W.R. McCombie (Author/Creator)
J. Messing (Author/Creator)
A. Miyao (Author/Creator)
N. Mulder (Author/Creator)
Y. Nagamura (Author/Creator)
J. Nam (Author/Creator)
N. Namiki (Author/Creator)
H. Numa (Author/Creator)
S. Nurimoto (Author/Creator)
C. O'Donovan (Author/Creator)
H. Ohyanagi (Author/Creator)
T. Okido (Author/Creator)
S. OOta (Author/Creator)
N. Osato (Author/Creator)
L.E. Palmer (Author/Creator)
F. Quetier (Author/Creator)
S. Raghuvanshi (Author/Creator)
N. Saichi (Author/Creator)
H. Sakai (Author/Creator)
Y. Sakai (Author/Creator)
K. Sakata (Author/Creator)
T. Sakurai (Author/Creator)
F. Sato (Author/Creator)
Y. Sato (Author/Creator)
H. Schoof (Author/Creator)
M. Seki (Author/Creator)
M. Shibata (Author/Creator)
Y. Shimizu (Author/Creator)
K. Shinozaki (Author/Creator)
Y. Shinso (Author/Creator)
N.K. Singh (Author/Creator)
B. Smith-White (Author/Creator)
J.-i. Takeda (Author/Creator)
M. Tanino (Author/Creator)
T. Tatusova (Author/Creator)
S. Thongjuea (Author/Creator)
F. Todokoro (Author/Creator)
M. Tsugane (Author/Creator)
A.K. Tyagi (Author/Creator)
A. Vanavichit (Author/Creator)
A. Wang (Author/Creator)
R.A. Wing (Author/Creator)
K. Yamaguchi (Author/Creator)
M. Yamamoto (Author/Creator)
N. Yamamoto (Author/Creator)
Y. Yu (Author/Creator)
H. Zhang (Author/Creator)
Q. Zhao (Author/Creator)
K. Higo (Author/Creator)
B. Burr (Author/Creator)
T. Gojobori (Author/Creator)
T. Sasaki (Author/Creator)
Publication Details: Genome Research, Vol.17(2), pp.175-183
Publisher: Cold Spring Harbor Laboratory Press.
Identifiers: 991005543675507891
Copyright: ©2007 by Cold Spring Harbor Laboratory Press.
Murdoch Affiliation: Murdoch University
Language: English
Resource Type: Journal article

UN Sustainable Development Goals (SDGs)

This output has contributed to the advancement of the following goals:

Source: InCites

Metrics

212 File views/ downloads

75 Record Views

169 Times Cited - Web of Science

InCites Highlights

These are selected metrics from InCites Benchmarking & Analytics tool, related to this output

Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.96 QTL
Web Of Science research areas: Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Genetics & Heredity
ESI research areas: Molecular Biology & Genetics