Integration of liver methylome and transcriptome provides new insights into the regulation of ovarian development genes in spotted scat (Scatophagus argus)

The liver provides lipids, proteins, and energy to support ovarian development. Liver transcriptomes revealed numerous genes associated with ovarian development in Scatophagus argus . However, the mechanisms governing their expression, particularly the potential role of DNA methylation, remain enigmatic. Here, the global methylation of livers at ovarian development stages II to IV and the integration of methylome and transcriptome were assessed. Whole-genome bisulfite sequencing revealed that CpG methylation in livers at ovary stage II (74.57%) was higher than that at stages III (70.20%) and IV (71.68%). Spearman analysis showed modest associations between expression levels and CpG methylation in the promoter and gene body regions. 28, 256, and 99 overlapping genes were found between the differentially expressed genes and differentially methylated genes in the II vs. III, II vs. IV, and III vs. IV comparisons, respectively. Methylation of genes related to vitellogenesis ( erα , vtgb , and vtgc ) and egg envelope formation ( zp4a and zp4b ) were decreased in the promoter or gene body regions and expression of them were increased in the II vs. IV or III vs. IV comparisons. The BSP validation results for era promoter was consistent with those of WGBS. In the II vs. IV comparison, hsd17b7 and cyp51 , which were related to cholesterol formation showed decreased methylation in the promoter and gene body, respectively, and increased gene expression. Similarly, dgat2 , which are associated with triglyceride formation, showed decreased gene body methylation together with decreased gene expression. Methylation changes of genes associated with vitellogenesis and egg envelope formation in the liver are linked to transcription changes during ovarian development in S. argus . Methylation of genes related to cholesterol formation and triglyceride formation were potential associations with expression. These findings provide new insights into the role of epigenetic mechanisms in fish reproduction.