| The basic/helix-loop-helix (bHLH) transcription factors and their homologs form a large family in plant and animal genomes and play important roles in the specification of tissue type in animals. However, few plant bHLH proteins have been studied functionally. Recent whole genome sequences of model plants Arabidopsis thaliana and Orysa sativa allow genome-wide analysis and comparison of the bHLH family in flowering plants. We have identified 165 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 finding of motifs outside the bHLH domain, the conservation of intron/exon structural patterns further support the evolutionary and potential functional relationships among these proteins. The genome distribution of rice bHLH genes strongly supported the hypothesis that genome duplication(s) contributed to the expansion of the bHLH gene family. Furthermore, phylogenetic studies of both rice and Arabidopsis bHLH genes estimate that 66 bHLH genes were present in the most recent common ancestor of monocots and eudicots, represented by rice and Arabidopsis, respectively. Also, this analysis also provides strong support for the"birth-and-death"theory of gene family evolution. Bioinformatic 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 support functional conservation between some rice bHLH genes and their close Arabidopsis homologs.
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