The completion of whole genome sequence of rice (Oryza sativa) has significantly accelerated functional genomics studies. Despite this progress, rate of gene function annotation is very low compared with the total number of genes estimated in the rice genome. One limitation to progress is the presence of functional redundancy among members of the same rice gene family, which covers 51.6 % of all non-transposable element-encoding genes. There remain a significant portion or rice genes that are not functionally redundant, as reflected in the recovery of loss-of-function mutants.
Transcription factors (TFs) are proteins which control the transcription of genetic information from DNA to mRNA by binding to specific DNA sequences. TFs are found in all living organisms, indicating their essential roles in the regulation of gene expression. TFs also play many key roles in plant developmental processes and the responses to environmental challenges. Transcriptional control of diverse cellular events mediated by normal growth and external stress conditions is regulated by coordinated action of TF family members or a combinatorial interaction of genes from multiple families. Since rice has increasing significance as a model crop, molecular genetics and genomics in rice have been intensively undergoing.The rice genome encodes 2,377 TF genes classified into 80 families.
To provide a systematic view of rice TFs, we have constructed a phylogenomic database, RTFDB that integrates multiple data types available in public databases including the structural features, orthologous relationships, availability of mutants and gene expression patterns for each TF family in a phylogenomic context. The integrating heatmap of the expression profiles to the phylogenic tree is effective in estimating the functional redundancy or dominancy among closely linked members in the same family.