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Background  Cichlid fishes have undergone rapid, expansive evolutionary radiations that are manifested in the diversification of their trophic morphologies, tooth patterning and coloration. Understanding the molecular mechanisms that underlie the cichlids' unique patterns of evolution requires a thorough examination of genes that pattern the neural crest, from which these diverse phenotypes are derived. Among those genes, the homeobox-containing  Dlx  gene family is of particular interest since it is involved in the patterning of the brain, jaws and teeth.    Results  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.    Conclusion  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.

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