Genetic and Epigenetic Changes Are Rapid Responses of the Genome to the Newly Synthesized Autotetraploid Carassius auratus

Wang, Chongqing; Zhou, Yuwei; Qin, Huan; Zhang, Chun; Li, Yang; Yu, Tingting; Zhang, Yuxin; Xu, Tao; Qin, Qinbo; Liu, Shaojun

doi:10.3389/fgene.2020.576260

Cited by 5 publications

(4 citation statements)

References 55 publications

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“…Recent studies have uncovered rapid genomic and genetic changes and epigenetic alterations in autotetraploid Carassius auratus ( Huang et al, 2020 ; Wang et al, 2020 ). Nevertheless, the molecular mechanism of reproductive property that diploid gametogenesis and maintenance of fertility have been noticed is rarely indicated but necessary.…”

Section: Introductionmentioning

confidence: 99%

The alternative transcription and expression characterization of Dmc1 in autotetraploid Carassius auratus

Wang

Xiao

et al. 2023

Front. Genet.

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Established autotetraploids often have a highly stable meiosis with high fertility compared with neo-autotetraploids. The autotetraploid Carassius auratus (4n = 200, RRRR) (4nRR), which stemmed from whole-genome duplication of Carassius auratus red var. (2n = 100, RR) (RCC), produces diploid gametes with an adopted diploid-like chromosome pairing in meiosis and maintains the formation of autotetraploid lineages. In this study, we focused on Dmc1, a meiosis-specific recombinase during the prophase of meiosis I, and elaborated on the genetic variation, alternative transcription, expression characterization, and epigenetic modification of Dmc1 in RCC and 4nRR. Two original Dmc1 from RCC were identified in 4nRR, and two duplicated Dmc1 differences in genetic composition were observed in 4nRR. Furthermore, we only noticed that one original and one duplicated Dmc1 were expressed in RCC and 4nRR, respectively. However, both possessed identical gene expression profiles, differential expression of sexual dimorphism, and hypomethylation levels. These results indicated that the specific expression of duplicated Dmc1 may be involve in the progression of meiosis of the diploid-like chromosome pairing in autotetraploid Carassius auratus. Herein, the findings significantly increase knowledge of meiosis of autopolyploid fish and provide meaningful insights into genetic breeding in polyploidy fish.

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Section: Introductionmentioning

confidence: 99%

The alternative transcription and expression characterization of Dmc1 in autotetraploid Carassius auratus

Wang

Xiao

et al. 2023

Front. Genet.

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“…A study of rice showed that ploidy (diploid to haploid and diploid to triploid) affects CHH methylation frequency [ 20 ]. The autotetraploid fish genome of Carassius auratus exhibited a lower genome-wide DNA methylation level than diploid fish [ 21 ]. A small-scale study on brown trout detected only 408 methylation loci and no difference in methylation between tripods and diploid fish [ 22 ].…”

Section: Introductionmentioning

confidence: 99%

Integrated Analyses of DNA Methylation and Gene Expression of Rainbow Trout Muscle under Variable Ploidy and Muscle Atrophy Conditions

Salem

Al-Tobasei

Ali

et al. 2022

Genes

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Rainbow trout, Oncorhynchus mykiss, is an important cool, freshwater aquaculture species used as a model for biological research. However, its genome reference has not been annotated for epigenetic markers affecting various biological processes, including muscle growth/atrophy. Increased energetic demands during gonadogenesis/reproduction provoke muscle atrophy in rainbow trout. We described DNA methylation and its associated gene expression in atrophying muscle by comparing gravid, diploid females to sterile, triploid females. Methyl Mini-seq and RNA-Seq were simultaneously used to characterize genome-wide DNA methylation and its association with gene expression in rainbow trout muscle. Genome-wide enrichment in the number of CpGs, accompanied by depleted methylation levels, was noticed around the gene transcription start site (TSS). Hypermethylation of CpG sites within ±1 kb on both sides of TSS (promoter and gene body) was weakly/moderately associated with reduced gene expression. Conversely, hypermethylation of the CpG sites in downstream regions of the gene body +2 to +10 kb was weakly associated with increased gene expression. Unlike mammalian genomes, rainbow trout gene promotors are poor in CpG islands, at <1% compared to 60%. No signs of genome-wide, differentially methylated (DM) CpGs were observed due to the polyploidy effect; only 1206 CpGs (0.03%) were differentially methylated, and these were primarily associated with muscle atrophy. Twenty-eight genes exhibited differential gene expression consistent with methylation levels of 31 DM CpGs. These 31 DM CpGs represent potential epigenetic markers of muscle atrophy in rainbow trout. The DM CpG-harboring genes are involved in apoptosis, epigenetic regulation, autophagy, collagen metabolism, cell membrane functions, and Homeobox proteins. Our study also identified genes explaining higher water content and modulated glycolysis previously shown as characteristic biochemical signs of rainbow trout muscle atrophy associated with sexual maturation. This study characterized DNA methylation in the rainbow trout genome and its correlation with gene expression. This work also identified novel epigenetic markers associated with muscle atrophy in fish/lower vertebrates.

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“…A study on rice showed that ploidy (diploid to haploid and diploid to triploid) affects CHH methylation frequency [20]. The autotetraploid sh genome of Carassius auratus exhibited a lower genome-wide DNA methylation level than diploid sh [21]. A smallscale study on brown trout detected only 408 methylation loci and detected no difference in methylation between tripods and diploid sh [22].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide integrated analyses of DNA methylation and gene expression of rainbow trout muscle under variable ploidy and muscle atrophy conditions

Salem

Al-Tobasei

Ali

et al. 2022

Preprint

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BackgroundRainbow trout is an important cool, freshwater aquaculture species used as a model for biological research. However, the genome reference has not been annotated for epigenetic markers affecting various biological processes, including muscle growth/atrophy. Increased energetic demands during gonadogenesis/reproduction provoke muscle atrophy in rainbow trout. We described DNA methylation and its associated gene expression in atrophying muscle by comparing gravid, diploid females to sterile, triploid females. ResultsMethyl Mini-seq and RNA-Seq were simultaneously used to characterize genome-wide DNA methylation and its association with gene expression in rainbow trout muscle. Genome-wide enrichment in the number of CpGs, accompanied by depleted methylation levels, was noticed around the gene transcription start site (TSS). Hypermethylation of CpG sites within ±1kb on both sides of TSS (promoter and gene body) was weakly/moderately associated with reduced gene expression. Conversely, hypermethylation of the CpG sites in downstream regions of the gene body +2 to +10 kb was weakly associated with increased gene expression. Unlike mammalian genomes, rainbow trout gene promotors are poor in CpG islands, at <1% compared to 60%. No signs of genome-wide, differentially methylated (DM) CpGs were observed due to the polyploidy effect; only 1,206 CpGs (0.03%) were differentially methylated, and these were primarily associated with muscle atrophy. Twenty-eight genes exhibited differential gene expression consistent with methylation levels of 31 DM CpGs. These 31 DM CpGs represent potential epigenetic markers of muscle atrophy in rainbow trout. The DM CpG-harboring genes are involved in apoptosis, epigenetic regulation, autophagy, collagen metabolism, cell membrane functions, and Homeobox proteins. Our study also identified genes explaining higher water content and modulated glycolysis previously shown as characteristic biochemical signs of rainbow trout muscle atrophy associated with sexual maturation. ConclusionsThis study characterized DNA methylation in the rainbow trout genome and its correlation with gene expression. This work also identified novel epigenetic markers associated with muscle atrophy in fish/lower vertebrates.

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Genetic and Epigenetic Changes Are Rapid Responses of the Genome to the Newly Synthesized Autotetraploid Carassius auratus

Cited by 5 publications

References 55 publications

The alternative transcription and expression characterization of Dmc1 in autotetraploid Carassius auratus

The alternative transcription and expression characterization of Dmc1 in autotetraploid Carassius auratus

Integrated Analyses of DNA Methylation and Gene Expression of Rainbow Trout Muscle under Variable Ploidy and Muscle Atrophy Conditions

Genome-wide integrated analyses of DNA methylation and gene expression of rainbow trout muscle under variable ploidy and muscle atrophy conditions

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