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GENOME ANALYSIS

Genome-Wide Analysis of Basic/Helix-Loop-Helix Transcription Factor Family in Rice and Arabidopsis^1,[W]

Shanghai Jiao Tong University-Shanghai Institutes for Biological Sciences-Pennsylvania State University Joint Center for Life Sciences, Key Laboratory of Microbial Metabolism, Ministry of Education, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China, 200240 (X.L., H.J., Z.Y., W.L., H.M., D.Z.); School of Life Science, Shanghai University, Shanghai, People's Republic of China, 200444 (X.D., Y.T., J.G., J.Y., J.W.); School of Life Science, Xiamen University, Xiamen, People's Republic of China, 361005 (X.L., L.C.); Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China, 200032 (H.M., D.Z.); and Department of Biology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802 (Y.S., H.M.)

The basic/helix-loop-helix (bHLH) transcription factors and their homologs form a large family in plant and animal genomes. They are known to play important roles in the specification of tissue types in animals. On the other hand, few plant bHLH proteins have been studied functionally. Recent completion of whole genome sequences of model plants Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) allows genome-wide analysis and comparison of the bHLH family in flowering plants. We have identified 167 bHLH genes in the rice genome, and their phylogenetic analysis indicates that they form well-supported clades, which are defined as subfamilies. In addition, sequence analysis of potential DNA-binding activity, the sequence motifs outside the bHLH domain, and the conservation of intron/exon structural patterns further support the evolutionary relationships among these proteins. The genome distribution of rice bHLH genes strongly supports the hypothesis that genome-wide and tandem duplication contributed to the expansion of the bHLH gene family, consistent with the birth-and-death theory of gene family evolution. Bioinformatics analysis suggests that rice bHLH proteins can potentially participate in a variety of combinatorial interactions, endowing them with the capacity to regulate a multitude of transcriptional programs. In addition, similar expression patterns suggest functional conservation between some rice bHLH genes and their close Arabidopsis homologs.

² These authors contributed equally to the paper.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Dabing Zhang (zhangdb{at}sjtu.edu.cn).

^[W] The online version of this article contains Web-only data.

www.plantphysiol.org/cgi/doi/10.1104/pp.106.080580.

^* Corresponding author; e-mail zhangdb{at}sjtu.edu.cn; fax 86–21–34204869.

Received March 16, 2006; returned for revision May 16, 2006; accepted May 20, 2006.