GSE41129
Gonadal DNA methylomes of half-smooth tongue sole Cynoglossus semilaevis
Environmental sex determination (ESD) occurs in divergent, phylogenetically unrelated taxa, and in some species co-occurs with genetic sex determination (GSD) mechanisms. Although epigenetic regulation in response to environmental effects has long been proposed to be associated with ESD, a systemic analysis on epigenetic regulation of ESD is still lacking. Using half-smooth tongue sole (Cynoglossus semilaevis) as a model – a marine fish which has both ZW chromosomal GSD and temperature-dependent ESD – we investigated the role of DNA methylation in transition from GSD to ESD by comparing gonadal DNA methylomes of parental females, parental pseudo-males, F1 females, F1 pseudo-males and normal males. Overall design: To assess the gonadal DNA methylome patterns across different sexual types of tongue sole, we carried out BS-seq on bisulfite converted DNA extracted from adult gonads of parental females, parental pseudo-males, and F1 pseudo-males and females from a cross between a parental pseudo-male and a normal female. We also sampled normal male individuals as a control for the normal male DNA methylation pattern. For each of the five samples, two biological replicates were utilized, with each replicate being pooled by five fish. The phenotype and genotype of each selected fish was identified by the histological analysis and PCR validation using the W chromosome specific marker. DNA were isolated from five pooled gonads of the same replicate, then 5 µg DNA was used to do the bisulfite conversion and BS-seq. The bisulfite conversion of sample DNA was carried out using a modified NH4HSO3-based protocol (Hayatsu et al. 2006). The paired-end library construction and sequencing were carried out using Illumina HiSeq 2000, according to the manufacturer’s instructions (Illumina). We also mixed 25 ng cl857 Sam7 Lambda DNA in each sample to use as conversion quality control for each library.