Comparison of DNA Methylation Pattern in Two Strains of Emiliania Huxleyi

Abstract Emiliania huxleyi (Ehux) is a single-celled marine phytoplankton. It is a species of coccolithophore which plays a large role in the ecology and biogeochemistry of the world's oceans. The purpose of this research is to compare DNA methylation patterns in two strains of the marine alga ‘Ehux’ using Bisulfite sequence. The two strains Ehux-1516 and Ehux-217 share the same genome, but Ehux-1516 is non-calcifying and Ehux-217 is calcifying. Methylation may play a role in the different phenotypes and gene expressions of the two strains. In this study, we used bisulfite sequencing to determine the DNA methylation patterns. When DNA is treated with bisulfite, non-methylated cytosines are converted into thymine, while methylated cytosines remain unchanged. Comparing the reference sequences with each strain of Ehux after bisulfite treatment will give the information about the positions of methylated and non-methylated cytosines. We used Model Based Analysis of Bisulfite Sequencing Data (MOABS) for the analysis of DNA methylation data. The result of this analysis gives us the methylation details of Ehux-1516 and Ehux-217. Around 5.6 % of genome is methylated in Ehux-1516 and 5.5% genome is methylated in Ehux-217. From this result we found differential methylation in the upstream region of 689 genes, the coding region of 2576 genes, and the downstream region of 897 genes. DMR regions that are differentially methylated and DMC is the differentially methylated Cs (single base site). Based on the analysis of DMC, 12464 genes were assigned to upstream region, 21064 genes were assigned to genetic region, and 13322 gene were assigned to downstream region. Then, we compared the protein id of these genes with the first generation JGI Ehux annotation for finding first level gene ontology (GO) of the corresponding protein. We parsed these files into a GO parser for finding the functions characteristics of each protein. Based on the annotation, 519 were assigned to putative biological processes 184 were assigned to specific cellular components and 740 were assigned putative molecular functions. But, 1954 genes in DMR are not annotated by GO Finally, we used Blast2go program for annotation. The annotated the file containing protein id of differentially expressed genes with DMR of two strains of Ehux using Blast2go. The Blast2go gives 50% more coverage of GO terms in biological process than the result from JGI file. We found that Blast2go gives 89% and 82% more coverage of GO terms than the result from JGI file for cellular component and molecular function respectively. KEY WORDS: Methylation Analysis, Bisulfite sequencing, Marine Algae, gene ontology, Blast2go