Sequencing of Pax6 Loci from the Elephant Shark Reveals a Family of Pax6 Genes in Vertebrate Genomes,Forged by Ancient Duplications and Divergences

Pax6 is a developmental control gene essential for eye development throughout the animal kingdom. in addition,pax6 plays key roles in other parts of the cns,olfactory system,and pancreas. in mammals a single pax6 gene encoding multiple isoforms delivers these pleiotropic functions. here we provide evidence that the genomes of many other vertebrate species contain multiple pax6 loci. we sequenced pax6-containing bacs from the cartilaginous elephant shark (callorhinchus milii) and found two distinct pax6 loci. pax6.1 is highly similar to mammalian pax6,while pax6.2 encodes a paired-less pax6. using synteny relationships,we identify homologs of this novel paired-less pax6.2 gene in lizard and in frog,as well as in zebrafish and in other teleosts. in zebrafish two full-length pax6 duplicates were known previously,originating from the fish-specific genome duplication (fsgd) and expressed in divergent patterns due to paralog-specific loss of cis-elements. we show that teleosts other than zebrafish also maintain duplicate full-length pax6 loci,but differences in gene and regulatory domain structure suggest that these pax6 paralogs originate from a more ancient duplication event and are hence renamed as pax6.3. sequence comparisons between mammalian and elephant shark pax6.1 loci highlight the presence of short- and long-range conserved noncoding elements (cnes). functional analysis demonstrates the ancient role of long-range enhancers for pax6 transcription. we show that the paired-less pax6.2 ortholog in zebrafish is expressed specifically in the developing retina. transgenic analysis of elephant shark and zebrafish pax6.2 cnes with homology to the mouse nre/pα internal promoter revealed highly specific retinal expression. finally,morpholino depletion of zebrafish pax6.2 resulted in a small eye phenotype,supporting a role in retinal development. in summary,our study reveals that the pleiotropic functions of pax6 in vertebrates are served by a divergent family of pax6 genes,forged by ancient duplication events and by independent,lineage-specific gene losses. © 2013 ravi et al.