Abstract
Sequencing and computational annotation revealed several features, including high gene numbers1,2,3,4,5,6, unusual composition of the predicted genes1,7 and a large number of genes lacking homology to known genes8,9, that distinguish the rice (Oryza sativa) genome from that of other fully sequenced model species. We report here a full-genome transcription analysis of the indica rice subspecies using high-density oligonucleotide tiling microarrays. Our results provided expression data support for the existence of 35,970 (81.9%) annotated gene models and identified 5,464 unique transcribed intergenic regions that share similar compositional properties with the annotated exons and have significant homology to other plant proteins. Elucidating and mapping of all transcribed regions revealed an association between global transcription and cytological chromosome features, and an overall similarity of transcriptional activity between duplicated segments of the genome. Collectively, our results provide the first whole-genome transcription map useful for further understanding the rice genome.
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References
Yu, J. et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296, 79–92 (2002).
Goff, S.A. et al. A draft sequence of the rice genome (Oryza sativa L. ssp japonica). Science 296, 92–100 (2002).
Yu, J. et al. The genomes of Oryza sativa: a history of duplications. PLoS Biol. 3, e38 (2005).
Sasaki, T. et al. The genome sequence and structure of rice chromosome 1. Nature 420, 312–316 (2002).
Feng, Q. et al. Sequence and analysis of rice chromosome 4. Nature 420, 316–320 (2002).
Rice Chromosome 10 Sequencing Consortium. In-depth view of structure, activity, and evolution of rice Chromosome 10. Science 300, 1566–1569 (2003).
Wong, G.K. et al. Compositional gradients in Gramineae genes. Genome Res. 12, 851–856 (2002).
Bennetzen, J.L., Coleman, C., Liu, R., Ma, J. & Ramakrishna, W. Consistent over-estimation of gene number in complex plant genomes. Curr. Opin. Plant Biol. 7, 732–736 (2004).
Jabbari, K., Cruveiller, S., Clay, O., Le Saux, J. & Bernardi, G. The new genes of rice: a closer look. Trends Plant Sci. 9, 281–285 (2004).
Nuwaysir, E.F. et al. Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res. 12, 1749–1755 (2002).
Stolc, V. et al. A gene expression map for the euchromatic genome of Drosophila melanogaster. Science 306, 655–660 (2004).
Bertone, P. et al. Global identification of human transcribed sequences with genome tiling arrays. Science 306, 2242–2246 (2004).
Li, L. et al. Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture. Genome Biol. 6, R52 (2005).
Yamada, K. et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302, 842–846 (2003).
Kikuchi, S. et al. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 300, 1566–1569 (2003).
Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant. Arabidopsis thaliana. Nature 408, 796–815 (2000).
Bedell, J.A. et al. Sorghum genome sequencing by methylation filtration. PLoS Biol. 3, e1 (2005).
Kapranov, P. et al. Large-scale transcriptional activity in chromosomes 21 and 22. Science 296, 916–919 (2002).
Kampa, D. et al. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res. 14, 331–342 (2004).
Cheng, J. et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308, 1149–1154 (2005).
Rinn, J.L. et al. The transcriptional activity of human Chromosome 22. Genes Dev. 17, 529–540 (2003).
Messing, J. et al. Sequence composition and genome organization of maize. Proc. Natl. Acad. Sci. USA 101, 14349–14354 (2004).
Temnykh, S. et al. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 11, 1441–1452 (2001).
Li, C. et al. Sequence variations of simple sequence repeats on chromosome-4 in two subspecies of the Asian cultivated rice. Theor. Appl. Genet. 108, 392–400 (2004).
Nagaki, K. et al. Sequencing of a rice centromere uncovers active genes. Nat. Genet. 36, 138–145 (2004).
International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431, 931–945 (2004).
She, X. et al. Shotgun sequence assembly and recent segmental duplications within the human genome. Nature 431, 927–930 (2004).
Jiao, Y. et al. A tiling microarray expression analysis of rice chromosome 4 suggests a chromosomal level regulation of transcription. Plant Cell 17, 1641–1657 (2005).
Cheng, Z. et al. Toward a cytological characterization of the rice genome. Genome Res. 11, 2133–2141 (2001).
Kent, W.J. BLAT-the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002).
Acknowledgements
The collaborative indica rice tiling microarray project in China was supported by the 863 rice functional genomics program from the Ministry of Science and Technology of China and by the National Institute of Biological Sciences at Beijing. The rice tiling microarray project at Yale University was supported by a grant from the US National Science Foundation Plant Genome Program.
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Supplementary information
Supplementary Fig. 1
Hybridization rate (HR) distribution in exons and introns of full-length cDNA supported (CG) gene models. (PDF 708 kb)
Supplementary Fig. 2
Transcription analysis of the 12 indica chromosomes. (PDF 353 kb)
Supplementary Fig. 3
Structural properties of different indica gene models. (PDF 245 kb)
Supplementary Fig. 4
Compositional property of the six groups if indica gene models. (PDF 466 kb)
Supplementary Fig. 5
Distribution of signal probes along the 12 indica chromosomes. (PDF 975 kb)
Supplementary Fig. 6
Cytological image of the 12 indica chromosomes. (PDF 1043 kb)
Supplementary Table 1
Transcriptional analysis of duplicated segments in the indica genome. (PDF 45 kb)
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Li, L., Wang, X., Stolc, V. et al. Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet 38, 124–129 (2006). https://doi.org/10.1038/ng1704
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DOI: https://doi.org/10.1038/ng1704
