Integration of DNA methylation and gene expression analysis in Gephyrocapsa huxleyi provides insight into genes related to calcification

Coccolithophores, such as Gephyrocapsa huxleyi (formerly Emiliania huxleyi) play a key role in oceanic carbon cycling through calcification. However, the molecular mechanisms regulating coccolith formation remain unclear. In this study, we performed an integrative analysis of whole-genome bisulfite sequencing (WGBS) and RNA-Seq data on two closely related strains of G. huxleyi: the calcifying M217 and the non-calcifying CCMP1516. We identified over 17,000 differentially methylated regions (DMRs) and more than 12,000 differentially expressed genes (DEGs) between the two strains. Our findings reveal statistical associations between DNA methylation patterns-particularly in CpG contexts-and changes in gene expression, implicating epigenetic regulation of calcification. Functional enrichment analyses highlighted genes involved in dynein complex activity, phosphate transport, carbonic anhydrase function, and calcium signaling as key contributors to biomineralization. Statistical modeling confirmed that hypo-methylation in promoter and gene regions is positively associated with gene expression, especially in calcification-related genes. However, the expression differences between the strains are complex and cannot be fully explained by methylation changes alone. This work provides new molecular insights into epigenetic regulation of biomineralization in coccolithophores, with implications for understanding environmental adaptation and biogeochemical cycling.