Genome-wide analysis of Sox genes in Medaka (Oryzias latipes) and their expression pattern in embryonic development

Genes of the Sox family encode evolutionarily conserved high-mobility group box containing transcription factors, which play key roles in various events of developmental contexts. In this study, we identified 15 sox genes by searching for the high-mobility group domain in the medaka genome and by polymerase chain reaction using primers designed from the results obtained from homology protein alignment. All medaka sox genes except a novel sox gene, Olsox32, are encoded in 5 groups as follows: 4 sox genes in group B; 3 sox genes in group D and F, respectively; 2 sox genes in group C and E, respectively, while no sox genes were found in groups A, G, H, I, and J. The medaka Olsox32 does not fall within any of the previously defined groups A-J. Here we have assigned it to a new group K. Together with the Sox protein sequences of other species, the phylogenetic relationship was analyzed and compared. Our findings point to recent sox gene loss, duplication and divergence occurring during the evolution of tetrapod and teleost lineages. The expression pattern shows that sox genes play a variety of roles in the early embryonic development of medaka.