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Published February 2007 | Version Published + Supplemental Material
Journal Article Open

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

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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.

Additional Information

© 2007 by Cold Spring Harbor Laboratory Press. Freely available online through the Genome Research Open Access option. The Authors acknowledge that six months after the full-issue publication date, the Article will be distributed under a Creative Commons CC-BY-NC License (Attribution-NonCommercial 4.0 International License, http://creativecommons.org/licenses/by-nc/4.0/). Received May 17, 2006; accepted in revised form October 31, 2006. Published online before print January 8, 2007, 10.1101/gr.5509507 We are grateful to C. Robin Buell, Hisakazu Iwama, Satoshi Fukuchi, Craig Gough, Kumiko Suzuki, Junko Sugiyama, Emiko Saito, Masato Kawabata, Chikatada Satoh, Shigetoyo Furukawa, Satoshi Nobushima, Ryo Aono, Tomohiro Endo, and Michitoshi Nagamochi for their support. We thank all the participants of the First Rice Annotation Project Meeting (RAP1). We also thank the Computer Center for Agriculture, Forestry and Fisheries Research for assisting RAP1. This work was supported by a grant from the Special Coordination Funds for Promoting Science and Technology of the Ministry of Education, Culture, Sports, Science and Technology of Japan. [Supplemental material is available online at www.genome.org.]

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8690
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CaltechAUTHORS:ITOgr07

Dates

Created
2007-09-05
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Updated
2021-11-08
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