Changes in DNA methylation during epigenetic-associated sex reversal under low temperature in Takifugu rubripes

Abstract

DNA methylation has frequently been implicated in sex determination and differentiation in teleost species. In order to detect the DNA methylation patterns established during sexual differentiation in tiger pufferfish T . rubripes , we performed comprehensive whole genome methylation sequencing and analyses of the gonads of male, female, and pseudo male. We obtained a total of 33.12, 32.44, and 31.60 Gb clean data for male, female, and pseudo male, with a sequencing depth of 66.44×, 60.47× and 54.86×, respectively. The methylation level of cytosine (C) residues in the genomic DNA from gonads was 11.016%, 10.428%, and 11.083% in male, female, and pseudo male, respectively. More than 65% of C methylation was at CpG sites, and less than 1% was at CHG and CHH sites. In each regulatory element, there were low methylation levels on both sides of the transcription start site, and higher methylation levels in exons, introns, and downstream of genes. The highest mCpG was on chromosome 8 and the lowest mCpG was on chromosome 5. Comparisons of whole-genome DNA methylation between pairs of samples revealed that there were 3,173 differentially methylated regions (DMRs) between female and male, and 3,037 DMRs between male and pseudo male, corresponding to 0.232% and 0.223% of the length of the genome, respectively. There were only 1,635 DMRs between female and pseudo male, representing 0.127% of the length of the genome. A number of differentially methylated genes (DMGs) related to sex determination and differentiation were selected, such as amhr2 and pfcyp19a . After Bisulfite Sequencing PCR (BSP) verification, amhr2 was exhibited low methylation level in normal males and pseudo male, and high methylation level in normal females but pfcyp19a showed low methylation level in normal females and high methylation level in normal males and pseudo males. These results provide information about the molecular epigenetic mechanisms of DNA methylation during low-temperature induced masculinization of tiger pufferfish, and increase our understanding of the mechanisms of sex determination and differentiation in this important aquaculture fish species.

Genome-wide DNA Methylation and Gene Expression Patterns of Androgenetic Haploid Tiger Pufferfish (Takifugu Rubripes) Provide Insights into Haploid Syndrome

“…Our analysis on the haploid and diploid methylome profiles of tiger pufferfish found that about 10.80% of C was methylated in both genetic female and male genomes, which is consistent with our previous reports in adult tiger pufferfish [26] and Chinese tongue sole (Cynoglossus semilaevis) [27]. The global DNA methylation level in haploid fish was higher than that in diploid females and males.…”

Comprehensive analysis of genome‐wide DNA methylation and transcriptomics between ovary and testis in Monopterus albus

“…High mC in the CG context is also observed in other vertebrate genomes such as Chinese tongue sole (Cynoglossus semilaevis) (Shao et al, 2014), tiger pufferfish (Takifugu rubripes) (Zhou et al, 2019), human (Lister et al, 2009) and chicken (Li et al, 2011), suggesting that DNA methylation in the nucleus mainly exists in CG sites in vertebrates. Approximate 9% of C in Chinese tongue sole and 11% of C in tiger pufferfish are methylated in their gonadal genomes.…”

Updated Genome Assembly of Bighead Carp (Hypophthalmichthys nobilis) and Its Differences Between Male and Female on Genomic, Transcriptomic, and Methylation Level

“…For example, methylation may abrogate the stimulation of cyp19a1a by gonadotropins in a male-specific fashion in ricefield eel (Zhang et al, 2013). Zhou et al (2019) also found whole genome methylation difference for sex changes under low temperature in Takifugu rubripes. Above all, sex-determination system in fish is complicated and needs different level of data to uncover the key modules which played key roles in it (Ortega-Recalde et al, 2020).…”