Nucleolar Dominance in a Tetraploidy Hybrid Lineage Derived From Carassius auratus red var. () × Megalobrama amblycephala ()

Cao, Lingfeng; Qin, Qinbo; Xiao, Qiu; Yin, HongTing; Wen, Jia; Liu, Qiwen; Huang, Xu; Huo, Yangyang; Tao, Min; Zhang, Chun; Luo, Kun; Liu, Shaojun

doi:10.3389/fgene.2018.00386

Cited by 12 publications

(9 citation statements)

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“…It is characteristic of some plant and animal distant hybrids and represents an example of a non-mammalian maternal imprinting of 45S rDNA [19,20]. Among animals it has been so far evidenced in details in intra-generic hybrids of Xenopus [20,21], in inter-generic hybrids of cyprinid fish [22,23] and in two lines of mouse-human somatic hybrids, where the human ribosomal genes were repressed, and only mouse ribosomal genes were expressed [24]. In the species Drosophila melanogaster , a special example of allelic inactivation resembling nucleolar dominance exists [25].…”

Section: The Nucleolus Forming 45s Rdnamentioning

confidence: 99%

Integrative rDNAomics—Importance of the Oldest Repetitive Fraction of the Eukaryote Genome

Symonová

2019

Genes

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Nuclear ribosomal RNA (rRNA) genes represent the oldest repetitive fraction universal to all eukaryotic genomes. Their deeply anchored universality and omnipresence during eukaryotic evolution reflects in multiple roles and functions reaching far beyond ribosomal synthesis. Merely the copy number of non-transcribed rRNA genes is involved in mechanisms governing e.g., maintenance of genome integrity and control of cellular aging. Their copy number can vary in response to environmental cues, in cellular stress sensing, in development of cancer and other diseases. While reaching hundreds of copies in humans, there are records of up to 20,000 copies in fish and frogs and even 400,000 copies in ciliates forming thus a literal subgenome or an rDNAome within the genome. From the compositional and evolutionary dynamics viewpoint, the precursor 45S rDNA represents universally GC-enriched, highly recombining and homogenized regions. Hence, it is not accidental that both rDNA sequence and the corresponding rRNA secondary structure belong to established phylogenetic markers broadly used to infer phylogeny on multiple taxonomical levels including species delimitation. However, these multiple roles of rDNAs have been treated and discussed as being separate and independent from each other. Here, I aim to address nuclear rDNAs in an integrative approach to better assess the complexity of rDNA importance in the evolutionary context.

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Section: The Nucleolus Forming 45s Rdnamentioning

confidence: 99%

Integrative rDNAomics—Importance of the Oldest Repetitive Fraction of the Eukaryote Genome

Symonová

2019

Genes

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“…The emergence of two types of IGS can be attributed to the fact that the establishment of nucleolar dominance requires several generations of selection and screening during the homologous polyploidization process. It is possible that the inhibitory mechanism that controls nuclear dominance in hybrids also control the number of active 45S rRNA gene in pure breeds and may reflect the dose compensation mechanism (Wallace and Langridge, 1971;Pikaard, 1999;Cao et al, 2018). However, regulation of the active 5S rRNA gene may be different.…”

Section: Discussionmentioning

confidence: 99%

“…5′-AGTCGTAACAAGGTTTCCGTAGGTG-3′ and 3′-TTATGGCCGTGCTCTGGCTAT-5′ (Cao et al, 2018). PCR was carried out using the conditions described above but with exception of the annealing temperature (57°C).…”

Section: Expression Sequence (Its1-58s-its2) and Expression (18s) Analysis Of 45s Rdnamentioning

confidence: 99%

“…In eukaryotes, rDNA genes are mainly divided into two categories, 5S rDNA and 45S rDNA repeats. rDNA encodes rRNA that represents a highly conserved gene product in all cells Long and Dawid, 1980;Cao et al, 2018). In animals, 45S rDNA contains 18S, 5.8S, 28S, and spacers (IGS, ITS1 and ITS2), while the 5S rDNA gene is a unit consisting of a gene transcription region (120bp) and a non-transcribed spacer (NTS).…”

Section: Introductionmentioning

confidence: 99%

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

Zhang

Qin

et al. 2021

Preprint

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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.

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“…rDNA encodes rRNA that represents a highly conserved gene product in all cells [ 9 , 10 ]. Because of the predominance of its structure, rDNA often serves as a good resource for studying evolutionary events [ 4 , 11 ]. In animals, 45S rDNA contains 18S, 5.8S, 28S, and spacers (IGS, ITS1 and ITS2), while the 5S rDNA gene is a unit consisting of a gene transcription region (120 bp) and a non-transcribed spacer (NTS).…”

Section: Introductionmentioning

confidence: 99%

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

Zhang

Qin

et al. 2021

BMC Ecol Evo

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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.

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Nucleolar Dominance in a Tetraploidy Hybrid Lineage Derived From Carassius auratus red var. () × Megalobrama amblycephala ()

Cited by 12 publications

References 50 publications

Integrative rDNAomics—Importance of the Oldest Repetitive Fraction of the Eukaryote Genome

Integrative rDNAomics—Importance of the Oldest Repetitive Fraction of the Eukaryote Genome

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

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

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