Isolation and sequence analysis of Sox genes in the red crucian carp (Carassius carassius, red variety)

Zheng, J; Long, L; Hu, J; Zhou, J; Wu, D

Isolation and sequence analysis of Sox genes in the red crucian carp (Carassius carassius, red variety)

2008

Zheng, J | Long, L | Hu, J | Zhou, J | Wu, D

Sox genes encode a family of transcription factors, which are characterized by the conserved HMG domain and are involved in a diverse range of developmental processes. Using degenerate primer PCR, seven different sequences encoding the HMG domains of Sox1, Sox9 and Sox11b were cloned and sequenced from genomic DNA in the red crucian carp (Carassius carassius, red variety). In the case of Sox1 and Sox11b, we found evidence of gene duplication. In the phylogenetic tree, two paralogs of Sox11b (Sox11b1 and Sox11b2) fit within the clade of Sox11, especially in the Sox11 b subfamily, not in the Sox11a subfamily. Three Sox1 sequences (Sox1-1, Sox1-2, and Sox1-3), which shared the same amino acid sequence, were identified in the red crucian carp. At the nucleotide level, Sox1-1 shared the highest sequence similarity to the zebrafish Sox1a, and Sox1-2 and Sox1-3 showed the highest similarity to the zebrafish Sox1b. The phylogenetic tree clearly demonstrated that the red crucian carp Sox1-1 clustered together with the zebrafish Sox1a, and the red crucian carp Sox1-2 and Sox1-3, with the zebrafish Sox1b. The result suggested that the red crucian carp Sox1-1, Sox1-2 and Sox1-3 resulted from duplication of the Sox1 gene rather than polymorphisms of the same gene.

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