Supplementary Material for: The Forkhead Gene Family in Medaka: Expression Patterns and Gene Evolution

Using the genome sequence of the medaka, <i>Oryzias latipes</i>, we examined the genomic complement of Fox genes in this organism to gain insight into the evolutionary relationships and expression patterns of this gene family. We identified 31 Fox genes by searching for Forkhead domains in the medaka genome and by polymerase chain reaction (PCR) using primers designed from protein alignments. All the medaka Fox genes are encoded in 18 subclasses as follows: 5 Fox genes in subclass D; 3 Fox genes in subclass O; 2 Fox genes in each of subclass A, B, E, F, G, I, P, and Q, respectively; 1 Fox gene in each of subclass C, H, J, K, M, N, and R. The gene structures and general features are also discussed. In addition, we examined the expression patterns of some of these genes in different adult tissues and during embryonic development in medaka using quantitative PCR and in situ hybridization. The present study shows that Forkhead transcription factors play an important role during early embryonic development in medaka, and the results will enhance our knowledge in terms of Fox family evolution in different taxa.