Gene duplication and co-evolution of G1/S transcription factor specificity in fungi are essential for optimizing cell fitness
(A) Conservation of G1/S TF from  and the expansion of the gene expression network (number of genes expressed during G1/S from [1, 6]). (B) Evolutionary history of the G1/S transcription factors that bind DNA (Res, Swi4, Mbp1, outlined in black) in Dikarya. Our work is focused on the evolution of DNA-binding specificity and, thus, our analysis did not include the co-regulator (Swi6, Cdc10). Species used in our study are highlighted in bold. Consensus DNA-binding motifs for each DNA-binding protein (S. cerevisiae Swi4 and Mbp1) were obtained from JASPAR (ID shown) or reconstructed from promoter regions (1000bp upstream) of previously published target genes [4, 6] with MEME (C. albicans MCB, S. pombe MCB1 and MCB2). Maximum likelihood phylogenetic tree (RAxML, LG substitution matrix) is shown. Thick branches indicate a highly supported branch. Orange dots: RAxML RBS ≥ 70%, Blue dots: PhyML SH-aLRT ≥ 80%, Red dots: PhyML a la Bayes aLRT ≥ 90%. Details of MEME and phylogenetic analysis are in Materials & Methods.