Comparative genomics and regulatory evolution: Conservation and function of the Chs and Apetala3 promoters

DNA sequence variations of chalcone synthase (Chs) and Apetala3 gene promot ers from 22 cruciferous plant species were analyzed to identify putative co nserved regulatory elements. Our comparative approach confirmed the existen ce of numerous conserved sequences which may act as regulatory elements in both investigated promoters. To confirm the correct identification of a wel l-conserved UV-Light-responsive promoter region, a subset of Chs promoter f ragments were tested in Arabidopsis thaliana protoplasts. All promoters dis played similar light responsivenesses, indicating the general functional re levance of the conserved regulatory element. In addition to known regulator y elements, other highly conserved regions were detected which are likely t o be of functional importance. Phylogenetic trees based on DNA sequences fr om both promoters (gene trees) were compared with the hypothesized phylogen etic relationships (species trees) of these taxa. The data derived from bot h promoter sequences were congruent with the phylogenies obtained from codi ng regions of other nuclear genes and from chloroplast DNA sequences. This indicates that promoter sequence evolution generally is reflective of speci es phylogeny. Our study also demonstrates the great value of comparative ge nomics and phylogenetics as a basis for functional analysis of promoter act ion and gene regulation.