Fig. 3

DNA methylation is enriched in a subset of gene bodies in O. bimaculoides. A Slot blot of gDNA extracted from the distal arm tip (1.5 cm of right arm 2), brain (optical lobe), and gills of one representative O. bimaculoides adult animal, and whole 30-day-old hatchling (same biological sample used for RNA-seq and RRBS). gDNA extracted from one representative male mouse adult liver and one representative pool of whole 5 dpf zebrafish larvae was blotted on the same membrane for comparison. Water was used as negative control. The 5mC signal was normalized to double-stranded DNA (dsDNA), and then each sample was normalized to levels zebrafish larvae. Each dot represents one biological replicate, bars represent the mean among biological replicates, and error bars represent standard deviations. p-values were calculated by unpaired parametric one-way ANOVA test adjusted with Tukey’s multiple comparisons test. Adjusted p-value are indicated as *** < 0.001, ** < 0.01. Comparisons other than with zebrafish or mouse resulted in not significant adjusted p-values > 0.05 (not indicated in the graph). B Scatter plot of DNA methylation levels of common CpGs across Supra Esophageal (Supra E) and Sub Esophageal (Sub E) brain. Dot color represents DNA methylation levels in hatchling, and size of the dots indicates scaled proportion of CpGs represented by each dot. C Genomic annotation of CpGs contained in O. bimaculoides genome, and of those covered by WGBS in brain and RRBS in hatchling. CpGs were divided into methylated (> 80%) and not methylated (< 20%) CpGs and relative genomic annotation was performed. D Metaplot represents DNA methylation levels of transposable elements in Supra E and Sub E brain and hatchling. CpG density of octopus genome is represented for the same region. Each region is divided in 15 bins. E Metaplot represents the DNA methylation levels in Supra E and Sub E brain and hatchling for full-length transcripts. CpG density of octopus genome has been represented for the same region. Each transcript has been divided in 30 bins from transcription star site (TSS) to transcription termination site (TTS)