Fig. 2.

Evolution of the regulatory mechanisms in the highly conserved module of ribosomal proteins. Phylogenetic cis-profile of the RP module. A schematic phylogenetic tree (branches are not drawn to scale) representing the known phylogeny (14) of the 17 analyzed species is shown, together with the sequence logos of the main cis-elements enriched in each module's promoters, grouped into three distinct types (colored boxes): RAP1 (orange), IFHL (blue), and Homol-D (red). The total number of genes in each POM is shown in parentheses, and the number of genes that contain each motif is indicated as well. Although the RP module is phenotypically extremely conserved, the phylogenetic cis-profile reveals a gradual switch from a Homol-D-dominated mechanism to a RAP1-controlled one, beginning before the speciation of A. gossypii. Concomitantly, the IFHL site underwent gradual sequence divergence and possible dimerization or domain duplication of the corresponding transcription factor.