Supplementary Material for: Genome-Wide Analysis of <i>Sox</i> Genes in Medaka <i>(Oryzias latipes)</i> and Their Expression Pattern in Embryonic Development

2011-06-29T00:00:00Z (GMT) by Cui J. Shen X. Zhao H. Nagahama Y.
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 <i>sox</i> 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 <i>sox</i> genes except a novel <i>sox</i> gene, <i>Olsox32</i>, are encoded in 5 groups as follows: 4 <i>sox</i> genes in group B; 3 <i>sox</i> genes in group D and F, respectively; 2 <i>sox</i> genes in group C and E, respectively, while no <i>sox</i> genes were found in groups A, G, H, I, and J. The medaka <i>Olsox32</i> 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 <i>sox</i> gene loss, duplication and divergence occurring during the evolution of tetrapod and teleost lineages. The expression pattern shows that <i>sox</i> genes play a variety of roles in the early embryonic development of medaka.

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