Itoh, T., Tanaka, T., Barrero, R. A., Yamasaki, C., Fujii, Y., Hilton, P. B., Antonio, B. A., Aono, H., Apweiler, R., Bruskiewich, R., Bureau, T., Burr, F., De Oliveira, A. C., Fuks, G., Habara, T., Haberer, G., Han, B., Harada, E., Hiraki, A. T., Hirochika, H., Hoen, D., Hokari, H., Hosokawa, S., Hsing, Y. I., Ikawa, H., Ikeo, K., Imanishi, T., Ito, Y., Jaiswal, P., Kanno, M., Kawahara, Y., Kawamura, T., Kawashima, H., Khurana, J. P., Kikuchi, S., Komatsu, S., Koyanagi, K. O., Kubooka, H., Lieberherr, D., Lin, Y. C., Lonsdale, D., Matsumoto, T., Matsuya, A., McCombie, W. R., Messing, J., Miyao, A., Mulder, N., Nagamura, Y., Nam, J., Namiki, N., Numa, H., Nurimoto, S., O'Donovan, C., Ohyanagi, H., Okido, T., Oota, S., Osato, N., Palmer, L. E., Quetier, F., Raghuvanshi, S., Saichi, N., Sakai, H., Sakai, Y., Sakata, K., Sakurai, T., Sato, F., Sato, Y., Schoof, H., Seki, M., Shibata, M., Shimizu, Y., Shinozaki, K., Shinso, Y., Singh, N. K., Smith-White, B., Takeda, J. I., Tanino, M., Tatusova, T., Thongjuea, S., Todokoro, F., Tsugane, M., Tyagi, A. K., Vanavichit, A., Wang, A., Wing, R. A., Yamaguchi, K., Yamamoto, M., Yamamoto, N., Yu, Y., Zhang, H., Zhao, Q., Higo, K., Burr, B., Gojobori, T., Sasaki, T. (2007) Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana: The Rice Annotation Project. Genome Research, 17 (2). pp. 175-183. ISSN 10889051 (ISSN)
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. ©2007 by Cold Spring Harbor Laboratory Press.
| Item Type: | Paper |
|---|---|
| Uncontrolled Keywords: | complementary DNA RNA amino acid sequence Arabidopsis article comparative study DNA sequence evolution gene duplication gene function gene locus genomics nonhuman plant genetics priority journal protein analysis protein domain protein function rice validation process Arabidopsis Proteins Codon Databases, Protein DNA, Complementary DNA, Plant Evolution, Molecular Genome, Plant Mutagenesis, Insertional Open Reading Frames Oryza sativa Plant Proteins RNA, Messenger RNA, Plant RNA, Transfer Species Specificity Variation (Genetics) Arabidopsis thaliana Japonica |
| Subjects: | organism description > plant > Arabidopsis bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes > genome annotation organism description > plant organism description > plant > rice |
| CSHL Authors: | |
| Communities: | CSHL labs > McCombie lab |
| Depositing User: | Matt Covey |
| Date: | 2007 |
| Date Deposited: | 25 Apr 2013 18:56 |
| Last Modified: | 25 Apr 2013 18:56 |
| PMCID: | PMC1781349 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/28206 |
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