## 5 Epigenetics  
Epigenetics refers to heritable phenotypic changes resulting from the modification of gene expression, not involving changes in DNA sequence. Epigenetic mechanisms include DNA methylation, histone modification and mi-RNA expression [97; 98]. DNA methylation takes place at the fifth position of the cytosine base (5 mC) in the CG, CHG and CHH context, with H being any base but C. Methylation allows a genome to respond rapidly and dynamically to environmental changes and is essential for many fundamental biological processes [99]. This modification, which can occur on different bases, is best described on cytosines because cytosine methylation in the CG context is the predominant type of cytosine methylation in higher eukaryotes. In addition, photosynthetic organisms can have cytosine methylation in CHG and CHH contexts, where H is any base but C. Furthermore, apart from methylation of cytosines, methylation of adenine bases is also found in microalgae [100; 101], plants, animals and fungi [102]. Methylation is catalyzed by DNA methyltransferases (DNMTs), enzymes which allow the addition of a methyl group to a nucleotide. Up to six families of DNMTs have been described; however, DNMT2s are, in fact, RNA methyltransferases. The main and best known are DNMT1s, which maintain methylation, while DNMT3s induce de novo methylation [103; 104]. DNA methylation in diatom genomes has been shown to occur in varying amounts between species. Previous studies have revealed that in the _P. tricornutum_ genome, the methylation rate ranges between 2.5 and 6%, and that 5 mCs are principally located in repeats (e.g., transposons) but also in some genes [105; 106; 107]. The variations in methylation positions may depend on the detection method, but also on the culture conditions or age. This rate, however, is much lower compared to the rate of CpG methylation, which is above 70% in somatic cells of vertebrates [99]. Methyltransferase domains are highly conserved throughout the kingdoms of life. However, in diatoms, DNMT families have some specific features. A study performed on the diatoms _P. tricornutum_ and _T. pseudonnu_ showed the presence of DNMTs similar to animal DNMTs (DNMT2-3-5). Nonetheless, the authors reported the absence of DNMT1 genes that would potentially be replaced by DNMT5 genes for methylation maintenance [104; 105; 106]. In these microorganisms, a specific \"bacterial-like\" DNMT, whose role is not fully defined yet, has also been found. In addition to these methylation mechanisms, in animals, demethylation is catalyzed by dioxygenases (ten-eleven translocation--TET) [108]. These enzymes catalyze the transition of 5 mC to demethylated cytosine through intermediate steps (5 hmC, 5 fC, 5 caC) (Figure 5). In _P. tricornutum_, homologues of these TETs have been found, implying mechanisms similar to those described in metazoans [109]. By revealing gene expression changes, transcriptome analysis can help evidence epigenetic marks. Regarding epigenetics, research on _H. ostrearia_ is at its infancy and has only focused on DNA methylation. A preliminary investigation of _H. ostrearia_ transcriptome through OthoFinder [110] and comparison with the _P. tricornutum_ methylation gene set has revealed the presence of the whole gene repertoire of DNMTs. The _H. ostrearia_ genome includes DNMT3 and 5, as well as the bacterial-like DNMT (Table 2, Supplementary Information S1). The analysis of a whole genome using bisulfite sequencing in _H. ostrearia_ has highlighted the presence of methylated cytosine bases within the genome. Indeed, Bismark pipeline analysis shows that 2.67% of cytosine bases are methylated with 12.5%, 0.6% and 0.6% in the CH, CHG and CHH context, respectively. The presence of methylated cytosines was confirmed using ELISA tests, which allowed for determination of the global methylation and demethylation state by quantifying the occurrence of 5 mC and 5 hmC, respectively, in a DNA sample.