Transcription factors in rice: a genome-wide comparative analysis between monocots and eudicots

It is not known how representative the Arabidopsis thaliana complement of transcription factors (TFs) is of other plants. The availability of rice (Oryza sativa) genome sequences makes possible a comparative analysis of TFs between monocots and eudicots, the two major monophyletic groups of angiosperms. Here, we identified 1611 TF genes that belong to 37 gene families in rice, comparable to the 1510 in Arabidopsis. Several gene subfamilies, but no families, were found to be lineage-specific. Phylogenetic analyses indicated that nearly half of the TF genes form clear orthologous pairs or groups, which were derived from 383 ancestral genes in the common ancestor of rice and Arabidopsis. Investigating gene duplication mechanisms revealed twelve pairs of large intragenomic duplicated blocks, which account for more than 40% of the rice genome. About 60% of the duplicated TF genes have been retained on duplicated segments. Functional conservation and diversification of TFs across monocot and eudicot lineages are discussed.