Rapid Genomic and Epigenetic Alterations in Gynogenetic Carassius auratus Red Var. Derived from Distant Hybridization

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

doi:10.1007/s10126-020-09963-6

Cited by 6 publications

(3 citation statements)

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“…Genomic DNA was isolated from peripheral blood of 5 RCC and 5 4nRR using Rapid Blood Genomic DNA Isolation Kit (Sangon Biotech). We subsequently performed the AFLP experiment and analysis based on the method elucidated by Qin et al (2020) . According to the presence or absence of bands, AFLP data for PCR products electrophoresis were converted into a binary matrix of 1 and 0.…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2021

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Whole genome duplication events have occurred frequently during the course of vertebrate evolution. To better understand the influence of polyploidization on the fish genome, we herein used the autotetraploid Carassius auratus (4n = 200, RRRR) (4nRR) resulting from the whole genome duplication of Carassius auratus (2n = 100, RR) (RCC) to explore the genomic and epigenetic alterations after polyploidization. We subsequently performed analyses of full-length transcriptome dataset, amplified fragment length polymorphism (AFLP) and methylation sensitive amplification polymorphism (MSAP) on 4nRR and RCC. By matching the results of 4nRR and RCC isoforms with reference genome in full-length transcriptome dataset, 649 and 1,971 novel genes were found in the RCC and 4nRR full-length geneset, respectively. Compared to Carassius auratus and Megalobrama amblycephala, 4nRR presented 3,661 unexpressed genes and 2,743 expressed genes. Furthermore, GO enrichment analysis of expressed genes in 4nRR revealed that they were enriched in meiosis I, whereas KEGG enrichment analysis displayed that they were mainly enriched in proteasome. Using AFLP analysis, we noted that 32.61% of RCC fragments had disappeared, while 32.79% of new bands were uncovered in 4nRR. Concerning DNA methylation, 4nRR exhibited a lower level of global DNA methylation than RCC. Additionally, 60.31% of methylation patterns in 4nRR were altered compared to RCC. These observations indicated that transcriptome alterations, genomic changes and regulation of DNA methylation levels and patterns had occurred in the newly established autotetraploid genomes, suggesting that genetic and epigenetic alterations were influenced by autotetraploidization. In summary, this study provides valuable novel insights into vertebrate genome evolution and generates relevant information for fish breeding.

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Section: Methodsmentioning

confidence: 99%

“…Here, we sampled 10 RCC and 10 4nRR for isolation of genomic DNA. We performed the MSAP experiment and analysis as per the method described by Qin et al (2020) . Based on the presence or absence of bands, MSAP data for PCR product electrophoresis can be considered as a matrix of 1 and 0.…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2021

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“…121 Following the paternal model, some studies have shown that reprogramming of the methylome occurred at embryogenesis and presented a similar pattern to sperm after reaching the MBT. 43,122 Intriguingly, Qin et al 123 pointed out that DNA methylation in gynogenetic offspring may produce regulated hybrids by reprogramming and developmental patterns.…”

Section: Imprintingmentioning

confidence: 99%

Potential implications of sperm DNA methylation functional properties in aquaculture management

Zhang

Cheng

Vechtova

et al. 2022

Reviews in Aquaculture

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The biology of fish sperm, an important topic in the research of reproduction and fisheries from basic science to evolutionary and applied aspects, has implications for aquaculture management, fish breeding and biological conservation. The quality of spermatozoa plays a vital role in fish fertility, and directly affects the health and performance of offspring. Environmental factors that affect determinants of spermatozoa quality usually reflected in the DNA methylation pattern of the spermatozoa epigenome, which may change offspring's performance. The aim of the present study was to conduct a review on existing data about DNA methylation in fish spermatozoa as a biological tool for identifying the quality of offspring based on their phenotypes and performances. Furthermore, this study provides valuable knowledge from fundamental to applied sciences dealing with enhancement of breeding selection, fish reproduction and environmental adaptation. The review also describes the individual

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Epigenetics in Hybridization and Polyploidization of Aquatic Animals

Zhou

Gui

2023

Epigenetics in Aquaculture

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Rapid Genomic and Epigenetic Alterations in Gynogenetic Carassius auratus Red Var. Derived from Distant Hybridization

Cited by 6 publications

References 50 publications

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

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

Potential implications of sperm DNA methylation functional properties in aquaculture management

Epigenetics in Hybridization and Polyploidization of Aquatic Animals

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