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Background  Basic helix-loop-helix and homeodomain transcription factors have been shown to specify all different neuronal cell subtypes composing the vertebrate retina. The appearance of gene paralogs of such retina-specific transcription factors in lower vertebrates, with differently evolved function and/or conserved non-coding elements, might provide an important source for the generation of neuronal diversity within the vertebrate retinal architecture. In line with this hypothesis, we investigated the evolution of the homeobox Barhl family of transcription factors,  barhl1  and  barhl2 , in the teleost and tetrapod lineages. In tetrapod  barhl2 , but not  barhl1 , is expressed in the retina and is important for amacrine cell specification. Zebrafish has three  barhl  paralogs:  barhl1.1, barhl1.2  and  barhl2 , but their precise spatio-temporal retinal expression, as well as their function is yet unknown.    Results  Here we performed a meticulous expression pattern comparison of all known  barhl  fish paralogs and described a novel  barhl  paralog in medaka. Our detailed analysis of zebrafish  barhl  gene expression in wild type and mutant retinas revealed that only  barhl1.2  and  barhl2  are present in the retina. We also showed that these two paralogs are expressed in distinct neuronal lineages and are differently regulated by Atoh7, a key retinal-specific transcription factor. Finally, we found that the two retained medaka fish  barhl  paralogs,  barhl1  and  barhl2 , are both expressed in the retina, in a pattern reminiscent of zebrafish  barhl1.2  and  barhl2  respectively. By performing phylogenetic and synteny analysis, we provide evidence that  barhl  retinal expression domain is an ancestral feature, probably lost in tetrapods due to functional redundancy.    Conclusions  Functional differences among retained paralogs of key retina-specific transcription factors between teleosts and tetrapods might provide important clues for understanding their potential impact on the generation of retinal neuronal diversity. Intriguingly, within teleosts, retention of zebrafish  barhl1.2  and its medaka ortholog  barhl1  appears to correlate with the acquisition of distinct signalling mechanisms by the two genes within distinct retinal cell lineages. Our findings provide a starting point for the study of  barhl  gene evolution in relation to the generation of cell diversity in the vertebrate retina.

Evolutionary relationships and diversification of barhl genes within retinal cell lineages