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Letter

A microarray analysis of the rice transcriptome and its comparison to Arabidopsis

¹ Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871 and National Institute of Biological Sciences, Zhongguancun Biological Science Park, Beijing 102206, People's Republic of China ² Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, Connecticut 06520, USA ³ Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing 101300, People's Republic of China ⁴ James D. Watson Institute of Genome Sciences of Zhejiang University, Hangzhou 310008, People's Republic of China ⁵ Laboratory of Molecular Cell Biology, Hebei Normal University, Shijiazhuang, Hebei 050016, People's Republic of China ⁶ National Hybrid Rice Research and Development Center, Changsha 410125, People's Republic of China ⁷ Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut 06520, USA ⁸ The Institute of Human Genetics, University of Aarhus, DK-8000 Aarhus C, Denmark ⁹ University of Washington Genome Center, Department of Medicine, University of Washington, Seattle, Washington 98195, USA

Arabidopsis and rice are the only two model plants whose finished phase genome sequence has been completed. Here we report the construction of an oligomer microarray based on the presently known and predicted gene models in the rice genome. This microarray was used to analyze the transcriptional activity of the gene models in representative rice organ types. Expression of 86% of the 41,754 known and predicted gene models was detected. A significant fraction of these expressed gene models are organized into chromosomal regions, about 100 kb in length, that exhibit a coexpression pattern. Compared with similar genome-wide surveys of the Arabidopsis transcriptome, our results indicate that similar proportions of the two genomes are expressed in their corresponding organ types. A large percentage of the rice gene models that lack significant Arabidopsis homologs are expressed. Furthermore, the expression patterns of rice and Arabidopsis best-matched homologous genes in distinct functional groups indicate dramatic differences in their degree of conservation between the two species. Thus, this initial comparative analysis reveals some basic similarities and differences between the Arabidopsis and rice transcriptomes.

¹¹ Corresponding authors.
E-mail xingwang.deng{at}yale.edu; fax (203) 432-5726.
E-mail Wangjian{at}genomics.org.cn; fax 86-010-80498676.

[Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to GEO under accession no. GSE2691.]

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.3657405.

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