Molecular evolution of the duplicated TFIIAγ genes in Oryzeae and its relatives

Background: Gene duplication provides raw genetic materials for evolutionary novelty and adaptation. The evolutionary fate of duplicated transcription factor genes is less studied although transcription factor gene plays important roles in many biological processes. TFIIA gamma is a small subunit of TFIIA that is one of general transcription factors required by RNA polymerase II. Previous studies identified two TFIIA gamma-like genes in rice genome and found that these genes either conferred resistance to rice bacterial blight or could be induced by pathogen invasion, raising the question as to their functional divergence and evolutionary fates after gene duplication. Results: We reconstructed the evolutionary history of the TFIIA gamma genes from main lineages of angiosperms and demonstrated that two TFIIA gamma genes (TFIIA gamma 1 and TFIIA gamma 5) arose from a whole genome duplication that happened in the common ancestor of grasses. Likelihood-based analyses with branch, codon, and branch-site models showed no evidence of positive selection but a signature of relaxed selective constraint after the TFIIA gamma duplication. In particular, we found that the nonsynonymous/synonymous rate ratio (omega = d(N)/d(S)) of the TFIIA gamma 1 sequences was two times higher than that of TFIIA gamma 5 sequences, indicating highly asymmetric rates of protein evolution in rice tribe and its relatives, with an accelerated rate of TFIIA gamma 1 gene. Our expression data and EST database search further indicated that after whole genome duplication, the expression of TFIIA gamma 1 gene was significantly reduced while TFIIA gamma 5 remained constitutively expressed and maintained the ancestral role as a subunit of the TFIIA complex. Conclusion: The evolutionary fate of TFIIA gamma duplicates is not consistent with the neofunctionalization model that predicts that one of the duplicated genes acquires a new function because of positive Darwinian selection. Instead, we suggest that subfunctionalization might be involved in TFIIA gamma evolution in grasses. The fact that both TFIIA gamma 1 and TFIIA gamma 5 genes were effectively involved in response to biotic or abiotic factors might be explained by either Dykhuizen-Hartl effect or buffering hypothesis.