Plant Cell Advance Online Publication
Published on November 11, 2005; 10.1105/tpc.105.035840
Received July 7, 2005
Returned for revision September 24, 2005
Accepted October 7, 2005
Conservation and Divergence of Light-Regulated Genome Expression Patterns during Seedling Development in Rice and Arabidopsis
Yuling Jiao 1, Ligeng Ma 2, Elizabeth Strickland 1, and Xing Wang Deng 1*
1 Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8014
2 Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8014; Peking-Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, China; National Institute of Biological Sciences, Beijing 102206, China
* To whom correspondence should be addressed. E-mail: xingwang.deng{at}yale.edu.
Genome-wide 70-mer oligonucleotide microarrays of rice (Oryza sativa) and Arabidopsis thaliana were used to profile genome expression changes during light-regulated seedling development. We estimate that the expression of  20% of the genome in both rice and Arabidopsis seedlings is regulated by white light. Qualitatively similar expression profiles from seedlings grown under different light qualities were observed in both species; however, a quantitatively weaker effect on genome expression was observed in rice. Most metabolic pathways exhibited qualitatively similar light regulation in both species with a few species-specific differences. Global comparison of expression profiles between rice and Arabidopsis reciprocal best-matched gene pairs revealed a higher correlation of genome expression patterns in constant light than in darkness, suggesting that the genome expression profile of photomorphogenesis is more conserved. Transcription factor gene expression under constant light exposure was poorly conserved between the two species, implying a faster-evolving rate of transcription factor gene expression in light-grown plants. Organ-specific expression profiles during seedling photomorphogenesis provide genome-level evidence for divergent light effects in different higher plant organs. Finally, overrepresentation of specific promoter motifs in root- and leaf-specific light-regulated genes in both species suggests that these cis-elements are important for gene expression responses to light.
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