Abstract:Sox genes are developmental regulators characterized by the presence of an HMG (high mobility group) DNA-binding domain, and they exist extensively in animal bodies in nature. Members of the Sox gene family have been shown to be conserved during evolution and play crucial roles in a wide variety of developmental processes, including growth and development, hemopoiesis, the development and formation of the nervous system, especially, sex determination and differentiation. Genome resources are growing faster and faster, and it provides a platform for the study gene families by scanning whole genomic sequences. We study Sox genes in Cynoglossus semilaevis by using bioinformatics analysis on the standard of whole genome. A total of 23 Sox genes were identified systematically from C. semilaevis and classified into 7 subfamilies which had not been reported yet. They are subfamily B1, B2, C, D, E, F and K, each of these groups may have distinct and specific functions. Sequence analysis of conserved domain of Sox genes in C. semilaevis shows that, all of members in the family contain 9 amino acid residues (RPMNAFMVW) as a highly conserved motif except CseSox32. On the other hand, the motif in Sox32 is identical in all specie as RPLNAF. Research on the highly conserved HMG box in C. semilaevis causes the discovery of these Sox genes, and phylogenetic analysis supports the classification of subfamily. To date, about 10 and 40 Sox genes have been identified in invertebrates and vertebrates separately. The phylogenetic analysis also suggests that the groups of Sox genes might be extended in the process of evolution. Subfamilies have got convergence between different species, and got otherness inside one of these species. Gene location results show that these 23 Sox genes were distributed randomly on 15 chromosomes, and we do not find gene cluster. The analysis of gene structure divides all of the Sox genes into two categories, evaluation on the basis of the exon numbers of the gene are less or more than two. The expression profiles of C. semilaevis Sox genes show a characteristic of different kinds of gonad and metamorphosis specific, and it indicated Sox genes may play key roles during sex determination, gonad differentiation and early development in C. semilaevis. To sum up the above, we enhance understanding of Sox genes in C. semilaevis with bioinformatics analysis, such as system evolution, gene structure, chromosomal location and gene expression patterns. Our results suggest that bioinformatics analysis may contribute to further functional verification of gene family and be good for genome resources mining and utilization.
