| Summary: | Hox genes are developmental regulatory genes that function to pattern the cranial nerves that are derived from the rhombomeres (r) during vertebrate embryonic development. Hoxb3, in particular, has been shown to be expressed in r5-7 in several tetrapod species, including mouse (Mus musculus). A whole genome duplication has occurred prior to the radiation of teleost fishes, and several teleost species have retained both duplicate Hoxb3 genes, hoxb3a and hoxb3b. Hoxb3a has been shown to be expressed in r4-7 and hoxb3b solely in r4. While functional genomic analyses have identified several cis-regulatory elements (CREs) that direct Hoxb3 in the hindbrain of tetrapods, very little is known regarding the CREs for hoxb3a or hoxb3b of teleosts. We used several software programs, including VISTA and CLUSTAL, to identify conserved CREs upstream of hoxb3a in teleost fishes from which the expression patterns of this gene have been documented, including zebrafish (Danio rerio), Atlantic salmon (Salmo salar), Japanese medaka (Oryzias latipes), Japanese pufferfish (Takifugu rubripes), and Nile tilapia (Oreochromis niloticus). We observed the presence of several putative CREs that have been shown to regulate Hox gene expression in the rhombomeres for all teleost species that were analyzed. However, we found that the species that have branched earlier during teleost evolution, zebrafish and salmon, show higher sequence conservation with vertebrates whose ancestors predate the teleost-specific genome duplication, such as spotted gar (Lepisosteus oculatus). By contrast, the more derived species, medaka, pufferfish, and tilapia, are synapomorphic for putatively functional genomic DNA sequences that are divergent from those of zebrafish, salmon, and vertebrates that are descendent from ancestors that predate the teleost-specific genome duplication. Our preliminary analyses suggest the occurrence of a structural mutation event in the genomic DNA upstream of hoxb3a in the ancestor of medaka, pufferfish, and tilapia but which has maintained hoxb3a expression in r4-7.
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