Correlation between DNA methylation and transcriptomic changes in golden Asian sea bass ( Lates calcarifer ): An integrated approach

Lates calcarifer, commonly known as barramundi perch, Asian sea bass or barramundi, is a significant aquaculture species across the Indo-Pacific. Barramundi typically exhibit a silver to bronze wild-type (WT) skin colour, with occasional golden (xanthic) variants of commercial interest. Although previous studies have identified gene expression differences between golden and WT variants, the genetic mechanism driving golden colouration remains elusive. By combining whole-genome enzymatic methylation sequencing (WGEMS) and RNA sequencing (RNA-seq), this study explores the molecular underpinnings of skin pigmentation within golden barramundi in an integrated approach. A total of 435 differentially methylated regions (DMR) were identified. Among 389 genes examined, an inverse relationship between expression ratio and promoter methylation levels was observed in 145 genes, suggesting a regulatory role of DNA methylation in gene expression. Notably, significant correlations between the changes in methylation and expression levels were identified in key pigment genes such as tyrp1 and pax7a, as well as potassium transmembrane transporter genes kir6.1 and kcnj3a. This suggests that barramundi colouration may result from complex molecular changes rather than the influence of a single or few genes. To further validate these observations, independent reverse transcription quantitative polymerase chain reaction (RT-qPCR) analysis was performed on representative genes, supporting the methylation-expression trends observed. This study is the first to characterize the whole-genome methylation landscape in barramundi, and one of the few to examine integrated methylome and transcriptome changes associated with pigmentation in teleost fish. By shedding light on the potential epigenetic mechanisms influencing rare skin colouration, this research contributes to the broader understanding of methylation-driven phenotypic variation in vertebrates and provides a foundation for future studies exploring environmental and developmental regulation of DNA methylation.