Nature Genetics 38, 124 - 129 (2006)
Published online: 20 December 2005; | doi:10.1038/ng1704
Genome-wide transcription analyses in rice using tiling microarraysLei Li1, 2, 9, Xiangfeng Wang1, 3, 4, 9, Viktor Stolc2, 5, 9, Xueyong Li2, 6, Dongfen Zhang7, Ning Su2, Waraporn Tongprasit8, Songgang Li3, Zhukuan Cheng7, Jun Wang4
& Xing Wang Deng2, 31
National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China. 2
Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA. 3
Peking-Yale Joint Research Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, China. 4
Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China. 5
Genome Research Facility, NASA Ames Research Center, MS 239-11, Moffett Field, California 94035, USA. 6
National Center for Crop Design, China Bioway Biotech Group Co., LTD, Beijing 100085, China. 7
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China. 8
Eloret Corporation, Sunnyvale, California 94087, USA. 9
These authors contributed equally to this work.
Correspondence should be addressed to Xing Wang Deng xingwang.deng@yale.edu 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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