Organization and Expression Analysis of 5S and 45S Ribosomal DNA Clusters in Autotetraploid Fish Derived From Carassius Auratus Red Var. (♀) × Megalobrama Amblycephala (♂)

Abstract

Background: Autotetraploid fish (4n = 200, RRRR) (abbreviated as 4nRR) are derived from whole genome duplication of red crucian carp (2n = 100, RR) (abbreviated as RCC). rDNA is often used to study molecular evolution of repeated sequences because it has high copy rate and special conserved coding regions in genomes. In this study, we determined the sequences (5S, ITS1-5.8S-ITS2 region), structure, methylation level (NTS and IGS), and expression level (5S and 18S) of 5S and 45S rRNA genes in 4nRR and RCC in order to elucidate the effects of autotetraploidization on ribosomal DNA (rDNA) in fish. Results: Results showed that there was high sequence similarity of 5S, 5.8S and ITS1 region between 4nRR and RCC. This study also identified two different types of ITS2 region in 4nRR and predicted the secondary structure. It turns out that both secondary structures are functional. Compared with the diploid ancestor of RCC, there was no significant difference in NTS (5S) methylation level, but the expression level of 5S rRNA was lower in 4nRR, indicating that methylation had little effect on the expression level in 4nRR. IGS (45S) was hypermethylated in 4nRR compared to RCC, but the expression of 18S gene were no significantly different from that in RCC, indicating that methylation regulation affected gene expression in 4nRR. Conclusion: These results demonstrate the effects of related structure and expression of autotetraploidization on rDNA. In addition, this study provides reference for studying the effect of autopolyploid on the evolution of species.