Ancestral and derived attributes of the dlx gene repertoire, cluster structure and expression patterns in an African cichlid fish

In this study, we characterized the dlx genes of an African cichlid fish, Astatotilapia burtoni, to provide a baseline to later allow cross-species comparison within Cichlidae. We identified seven dlx paralogs (dlx1a, -2a, -4a, -3b, -4b, -5a and -6a), whose orthologies were validated with molecular phylogenetic trees. The intergenic regions of three dlx gene clusters (dlx1a-2a, dlx3b-4b, and dlx5a-6a) were amplified with long PCR. Intensive cross-species comparison revealed a number of conserved non-coding elements (CNEs) that are shared with other percomorph fishes. This analysis highlighted additional lineage-specific gains/losses of CNEs in different teleost fish lineages and a novel CNE that had previously not been identified. Our gene expression analyses revealed overlapping but distinct expression of dlx orthologs in the developing brain and pharyngeal arches. Notably, four of the seven A. burtoni dlx genes, dlx2a, dlx3b, dlx4a and dlx5a, were expressed in the developing pharyngeal teeth.This comparative study of the dlx genes of A. burtoni has deepened our knowledge of the diversity of the Dlx gene family, in terms of gene repertoire, expression patterns and non-coding elements. We have identified possible cichlid lineage-specific changes, including losses of a subset of dlx expression domains in the pharyngeal teeth, which will be the targets of future functional studies.Cichlid fishes are amongst the premier models of evolution, as they have undergone rapid adaptive radiation to fill a multitude of ecological niches. This has been made possible, in part, by their striking diversity of jaw and tooth morphologies [1-5]. It has been hypothesized that one of the central factors that has permitted the cichlids' dramatic trophic radiation is their unique pharyngeal jaw apparatus, or 'throat jaws' [6,7]. These modified gill arches have taken on the role of food processing, freeing up the oral jaws for more specialized forms of food acquisition such as algal scrapi