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

Abstract Background 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...

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Autores principales:	Chun Zhao, Yuxin Zhang, Huan Qin, Chongqing Wang, Xu Huang, Li Yang, Tingting Yu, Xidan Xu, Xiang Luo, Qinbo Qin, Shaojun Liu
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Autotetraploid Ribosomal DNA Methylation Polyploidy Ecology QH540-549.5 Evolution QH359-425
Acceso en línea:	https://doaj.org/article/8787f39b57bc44b89788a1da432fb1c9
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spelling	oai:doaj.org-article:8787f39b57bc44b89788a1da432fb1c92021-11-07T12:04:24ZOrganization and expression analysis of 5S and 45S ribosomal DNA clusters in autotetraploid Carassius auratus10.1186/s12862-021-01918-22730-7182https://doaj.org/article/8787f39b57bc44b89788a1da432fb1c92021-11-01T00:00:00Zhttps://doi.org/10.1186/s12862-021-01918-2https://doaj.org/toc/2730-7182Abstract Background 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 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. 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.Chun ZhaoYuxin ZhangHuan QinChongqing WangXu HuangLi YangTingting YuXidan XuXiang LuoQinbo QinShaojun LiuBMCarticleAutotetraploidRibosomal DNAMethylationPolyploidyEcologyQH540-549.5EvolutionQH359-425ENBMC Ecology and Evolution, Vol 21, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Autotetraploid Ribosomal DNA Methylation Polyploidy Ecology QH540-549.5 Evolution QH359-425
spellingShingle	Autotetraploid Ribosomal DNA Methylation Polyploidy Ecology QH540-549.5 Evolution QH359-425 Chun Zhao Yuxin Zhang Huan Qin Chongqing Wang Xu Huang Li Yang Tingting Yu Xidan Xu Xiang Luo Qinbo Qin Shaojun Liu Organization and expression analysis of 5S and 45S ribosomal DNA clusters in autotetraploid Carassius auratus
description	Abstract Background 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 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. 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.
format	article
author	Chun Zhao Yuxin Zhang Huan Qin Chongqing Wang Xu Huang Li Yang Tingting Yu Xidan Xu Xiang Luo Qinbo Qin Shaojun Liu
author_facet	Chun Zhao Yuxin Zhang Huan Qin Chongqing Wang Xu Huang Li Yang Tingting Yu Xidan Xu Xiang Luo Qinbo Qin Shaojun Liu
author_sort	Chun Zhao
title	Organization and expression analysis of 5S and 45S ribosomal DNA clusters in autotetraploid Carassius auratus
title_short	Organization and expression analysis of 5S and 45S ribosomal DNA clusters in autotetraploid Carassius auratus
title_full	Organization and expression analysis of 5S and 45S ribosomal DNA clusters in autotetraploid Carassius auratus
title_fullStr	Organization and expression analysis of 5S and 45S ribosomal DNA clusters in autotetraploid Carassius auratus
title_full_unstemmed	Organization and expression analysis of 5S and 45S ribosomal DNA clusters in autotetraploid Carassius auratus
title_sort	organization and expression analysis of 5s and 45s ribosomal dna clusters in autotetraploid carassius auratus
publisher	BMC
publishDate	2021
url	https://doaj.org/article/8787f39b57bc44b89788a1da432fb1c9
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_version_	1718443559041892352

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

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