ArticleGenome research2007
Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
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91 citing papers in PubMed.
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- Molecular Dating of the Emergence of Anaerobic Rumen Fungi and the Impact of Laterally Acquired Genes.mSystems · 2019Article
- Involving community in genes and pathway curation.Database : the journal of biological databases and curation · 2019Article
- METHimpute: imputation-guided construction of complete methylomes from WGBS data.BMC genomics · 2018Article
- The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies.The Plant cell · 2017Article
- Updated Rice Kinase Database RKD 2.0: enabling transcriptome and functional analysis of rice kinase genes.Rice (New York, N.Y.) · 2016Article
- Rice Improvement Through Genome-Based Functional Analysis and Molecular Breeding in India.Rice (New York, N.Y.) · 2016Article
- Myriad Triple-Helix-Forming Structures in the Transposable Element RNAs of Plants and Fungi.Cell reports · 2016Article
- OryzaGenome: Genome Diversity Database of Wild Oryza Species.Plant & cell physiology · 2016Article
- Metabolome-genome-wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism.The Plant journal : for cell and molecular biology · 2015Article
- Plant-PrAS: a database of physicochemical and structural properties and novel functional regions in plant proteomes.Plant & cell physiology · 2015Article
- Genes controlling root development in rice.Rice (New York, N.Y.) · 2014Article
- Association mapping of brassinosteroid candidate genes and plant architecture in a diverse panel of Sorghum bicolor.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2014Article
- Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements.BMC bioinformatics · 2014Article
31 more citing papers are in PubMed but not listed here.
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96 authors.
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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 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.
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