Study Of Sox Genes In The Red Crucian Carp (Carassius Auratus Red Variety)

Objective The study was designed to further understand the evolution of Sox genes in fish and to understand the origin of red crucian carp by calculating the divergence time of red crucian carp and zebrafish.Methods Genomic DNA from the red crucian carp was used as the template for PCR amplification using two pairs of degenerate primers designed on the basis of the amino acid sequences of the vertebrates HMG domains. PCR products were subcloned and sequenced. And then the sequences obtained were analyzed by homology comparisons and phylogenetic trees.Results (1) Nine nucleotide sequences encoding the Sox HMG domains were cloned and sequenced from genomic DNA in the red crucian carp, which were designated Sox1-1, Sox1-2, Sox1-3, Sox4-1, Sox4-2, Sox9, Sox11b1-1, Sox11b1-2 and Sox11b2, respectively. (2) Sox1-1, Sox1-2 and Sox1-3 shared the same amino acid sequences. However, at the nucleotide level, the red crucian carp Sox1-1 shared the highest sequence identity with the zebrafish Sox1a (96.1%), whereas the Sox1-2 and Sox1-3 shared the highest identities with the zebrafish Sox1b (95.1% and 95.5%, respectively). The phylogenetic tree analysis demonstrated that the red crucian carp Sox1-1 cluster together with the zebrafish Sox1a, and the red crucian carp Sox1-2 and Sox1-3 cluster with the zebrafish Sox1b. (3) The similarity between the amino acid sequences of Sox4-1 and Sox4-2 was 98.1%. Both of the red crucian carp Sox4-1 and Sox4-2 showed the highest identity with the mouse Sox4, 88.9% and 90.1%, respectively. (4) Sox11b1-1 and Sox11b1-2 encoded the same amino acid sequences. The phylogenetic tree based on the amino acid sequences indicated that the red crucian carp Sox11b1 and Sox11b2 were clustered together with the zebrafish Sox11b and were apart from the zebrafish Sox11a. (5) Phylogenetic tree of the teleostei Sox1, Sox9 and Sox11 nucleotide sequences indicated that the duplication of Sox1, Sox9 and Sox11 occurred before the divergence of red crucian carp, zebrafish, pufferfish, sea bass and Amphilophus citrinellum. (5) Using the Sox1, Sox9 and Sox11 genes as the molecular clock marker, the red crucian carp (belong to the genus Carassius, family Cyprininae, order Cypriniformes) and zebrafish (belong to the genus Danio, family Cyprininae, order Cypriniformes) diverged approximatedly 80 million years ago.Conclusions (1) Sox1, Sox4 and Sox11b genes have been duplicated in the red crucian carp. This is the first report of two paralogous genes of Sox11b in any fish. (2) Gene duplication, loss and divergence of Sox11 may occur during the evolution of some species of the fish lineage. (3) The results further support the theory of"the duplication of fish Sox genes occurring before the divergence of the teleostei". (3) Red crucian carp (belong to the genus Carassius, family Cyprininae, order Cypriniformes) and zebrafish (belong to the genus Danio, family Cyprininae, order Cypriniformes) diverged approximatedly 80 million years ago. Objective The study was designed to investigate expression patterns of duplicated Sox1 and Sox11b genes in different tissues of the red crucian carp.Methods The expression patterns of Sox1 and Sox11b in 13 adult tissues of the red crucian carp (including the liver, kidney, spleen, heart, fat, telencephalon, midbrain, hypothalamus, cerebellum, medulla oblongata, muscle, ovary and testis) were analyzed by RT-PCR technique. Parts of PCR products were subcloned and sequenced.Results (1) No expressions of Sox1-1, Sox1-2/Sox1-3 and Sox11b were observed in the adult fat, muscle, ovary and testis of red crucian carp. (2) Sox1-1 and Sox1-2/Sox1-3 were expressed unequally in the liver, kidney, spleen, heart and brains (telencephalon, midbrain, hypothalamus, cerebellum, medulla oblongata), and high amount of transcripts were detected in the brains. (3) In the liver, kidney, spleen, heart, telencephalon, midbrain and medulla oblongata, transcripts of Sox11b1-1, Sox11b1-2 and Sox11b2 were detected. However, transcripts of Sox11b1-1 and Sox11b1-2 genes were detected in the hypothalamus and cerebellum, where no transcripts of Sox11b2 were detected.Conclusions (1) The Sox1 and Sox11b genes have tissue-specific expression patterns in the red crucian carp. (2) The red crucain carp Sox1 may play an important role in the nervous system. (3) The duplicates of Sox11b (Sox11b1-1, Sox11b1-2 and Sox11b2) have similar but distinct expression patterns in the red crucian carp lineage.