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

Abstract

Functional hermaphroditism has been confirmed in 94 teleost genera within 27 families and seven orders (Mitcheson & Liu, 2008), of which the hermaphroditic patterns are diverse, including simultaneous, protogynous, protandrous, bidirectional sex change and androdioecy (Erisman et al., 2013;Kobayashi et al., 2013;Mitcheson & Liu, 2008). Of these hermaphroditic fish, ricefield eel (Monopterus albus) is a protogynous hermaphroditic Synbranchiform species that commonly changes sex from functional female to functional male after ovulation (Liu, 1944). The ricefield eel offers an opportunity to unveil the molecular mechanism of sexual reversal.Ever since the ricefield eel was found to be sequential hermaphroditic, researchers have examined its mechanisms of sex determination and sex change. At the cellular level, histological and ultrastructural changes in the gonad during sex reversal from female to male in ricefield eel were observed under an optical microscope and electron microscope (

Fertilization by short-term stored sperm alters DNA methylation patterns in common carp (Cyprinus carpio) embryos at single-base resolution

“…2). This suggests that short-term storage causes damage to sperm DNA in common carp, which is consistent with previous studies in mammals and fishes (Pérez- (Chen et al 2021). In this study, the average global methylation level in a CpG context across the nine different common carp embryo samples was 79.71% (Table 2), and a lower methylation level was observed in the CHH (0.86-1.01) and CHG (0.78-0.93).…”

“…In general, the contexts of DNA methylation have been identified as CpG, CHH and CHG, but in animal genomes, DNA methylation mostly occurs on the cytosines of a CpG dinucleotide (Lee et al 2010). In fishes, high levels of CpG methylation have been reported, such as 94% in zebrafish (Potok et al 2013), 98% in grass carp ( Ctenopharyngodon idellus ) (He et al 2022), 71-73% in Chinese perch ( Siniperca chuatsi ) (Pan et al 2021), 98% in tiger pufferfish ( Takifugu rubripes ) (Zhou et al 2019), and 76-78% in ricefield eel ( Monopterus albus ) (Chen et al 2021). In this study, the average global methylation level in a CpG context across the nine different common carp embryo samples was 79.71% (Table 2), and a lower methylation level was observed in the CHH (0.86-1.01) and CHG (0.78-0.93).…”

Identification of sex determination locus in sea cucumber Apostichopus japonicus using genome-wide association study

“…The functions of DEGs within the candidate SDR were noteworthy; they were identified associated with gonadal function and reproduction processes. Five male-biased genes, including g2e3 (as mentioned above), nipbl [ 84 ], syce1 [ 85 , 86 ], kmt5a-a and kmt5a-b [ 87 ], and female-biased genes, msh6 [ 88 ] and taf5l [ 89 ]. Among these genes, two copies of kmt5a (kmt5a-a and kmt5a-b) in male gonads of sea cucumber showed significantly higher expression.…”

The role of DNA methylation on gene expression in the vertebrae of ancestrally benzo[a]pyrene exposed F1 and F3 male medaka

“…Since only one biological sample in each treatment was sequenced, the method used to analyse the differentially methylated locis (DMLs) or regions was limited. However, one of the advantages that DSS provides is that the statistical test can be conducted even when there are no biological replicates because the neighbouring CpG sites can be considered pseudo-replicates due to smoothing, while dispersion can still be calculated with reasonable precision [ 23 ]. Data from the bismark output were prepared in the format required by DSS, which contains the following information: chromosome number, genomic coordinate, the total number of reads, and the number of reads with methylation.…”