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Background  Autotetraploid  Carassius auratus  (4 n  = 200, RRRR) (abbreviated as 4 n RR) is derived from whole genome duplication of  Carassius auratus  red var. (2 n  = 100, RR) (abbreviated as RCC). Ribosome DNA (rDNA) is often used to study molecular evolution of repeated sequences because it has high copy number and special conserved coding regions in genomes. In this study, we analysed the sequences (5S, ITS1-5.8S-ITS2 region), structure, methylation level (NTS and IGS), and expression level (5S and 18S) of 5S and 45S ribosomal RNA (rRNA) genes in 4 n RR and RCC in order to elucidate the effects of autotetraploidization on rDNA in fish.    Results  Results showed that there was high sequence similarity of 5S, 5.8S and ITS1 region between 4 n RR and RCC. This study also identified two different types of ITS2 region in 4 n RR and predicted the secondary structure of ITS2. It turns out that both secondary structures are functional. Compared with RCC, there was no significant difference in NTS (5S rRNA) methylation level, but the expression level of 5S rRNA was lower in 4 n RR, indicating that methylation had little effect on the expression level in 4 n RR. IGS (45S rRNA) was hypermethylated in 4 n RR compared to RCC, but the expression of 18S rRNA gene was no significantly different from that in RCC, indicating that methylation regulation affected gene expression in 4nRR.    Conclusion  The above studies initially revealed the effects of autotetraploidization on the structure and function of 5S and 45S rRNA in  Carassius auratus , and provided a theoretical support for the systematic study of the evolution pattern and characteristics of rDNA in vertebrates.

Organization and expression analysis of 5S and 45S ribosomal DNA clusters in autotetraploid Carassius auratus