Abstract
Background hes genes are chordate homologs of Drosophila genes, hairy and enhancer of split, which encode a basic helix-loop-helix (bHLH) transcriptional repressor with a WRPW motif. Various developmental functions of hes genes, including early embryogenesis and neurogenesis, have been elucidated in vertebrates. However, their orthologous relationships remain unclear partly because of less conservation of relatively short amino acid sequences, less conserved synteny, and species-specific gene duplication. This results in complicated gene names in vertebrates, which are not consistent in orthologs. In a previous study, we revealed that Xenopus frogs have two clusters of hes5, named “the hes5.1 cluster” and “the hes5.3 cluster.” The origin has not yet been revealed. Results Here, we elucidated the orthologous and paralogous relationships of all hes genes of human, mouse, chicken, gecko, zebrafish, medaka, coelacanth, spotted gar, elephant shark, and Xenopus frogs (X. tropicalis and X. laevis) by phylogenic and synteny analysis. Any clusters of hes5 were not found in amniotes, whereas duplicated hes5 clusters in teleost were found although not as many genes as Xenopus. In addition, hes5 cluster-like structure was found in the elephant shark genome, but not found in cyclostomata. Conclusion These data suggest that the hes5 cluster existed in the gnathostome ancestor, but was lost in amniotes.