State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
BMC Ecol Evol. 2021 Nov 5;21(1):201. doi: 10.1186/s12862-021-01918-2.
Autotetraploid Carassius auratus (4n = 200, RRRR) (abbreviated as 4nRR) is derived from whole genome duplication of Carassius auratus red var. (2n = 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 4nRR and RCC in order to elucidate the effects of autotetraploidization on rDNA in fish.
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 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 4nRR, indicating that methylation had little effect on the expression level in 4nRR. IGS (45S rRNA) was hypermethylated in 4nRR 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.
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.
四倍体金鱼（4n = 200，RRRR）（简称 4nRR）是由金鱼红变种（2n = 100，RR）（简称 RCC）的全基因组复制而来。核糖体 DNA（rDNA）通常用于研究重复序列的分子进化，因为它在基因组中具有高拷贝数和特殊的保守编码区。在这项研究中，我们分析了 4nRR 和 RCC 中 5S 和 45S 核糖体 RNA（rRNA）基因的序列（5S、ITS1-5.8S-ITS2 区）、结构、甲基化水平（NTS 和 IGS）和表达水平（5S 和 18S），以阐明鱼类中同源四倍化对 rDNA 的影响。
结果表明，4nRR 和 RCC 中 5S、5.8S 和 ITS1 区具有高度的序列相似性。本研究还在 4nRR 中鉴定出两种不同类型的 ITS2 区，并预测了 ITS2 的二级结构。事实证明，这两种二级结构都是功能性的。与 RCC 相比，5S rRNA 的 NTS（5S rRNA）甲基化水平没有显著差异，但 4nRR 中 5S rRNA 的表达水平较低，表明甲基化对 4nRR 中的表达水平影响不大。与 RCC 相比，4nRR 中的 IGS（45S rRNA）过度甲基化，但 18S rRNA 基因的表达与 RCC 没有显著差异，表明甲基化调控影响了 4nRR 中的基因表达。
上述研究初步揭示了同源四倍化对金鱼 5S 和 45S rRNA 结构和功能的影响，为脊椎动物 rDNA 进化模式和特征的系统研究提供了理论支持。
