Fig. 1

Methylation and physical maps of the Encephalitozoon intestinalis ATCC 50506 genome. Top. Distribution of 5mC and 5hmC methylated sites on the E. intestinalis chromosome I, as inferred from mapping of the individual nanopore sequencing reads against the genome with Megalodon (using the remora base modification model), then plotted with IGV (minimum probability: 0.8). 5mC and 5hmC methylated sites are shown in red and blue, respectively. Small circles. Zoom ins of the E. intestinalis chromosome I ends. Telomere-associated repeat elements (TAREs) and subtelomeric regions are highlighted by beige and grey lines; rRNA loci (LSU, large subunit; SSU, small subunit) are depicted with cyan triangles. Locations of 4mC and unknown base modifications (UBMs) are shown with magenta and green dots, respectively. Circos plot. Physical and methylation metrics of the E. intestinalis genome. From outer to inner concentric rings: a) AT and GC nucleotide biases (grey and red lines, respectively); b) GT and AC nucleotide biases (blue and green lines, respectively); c) GA and CT nucleotide biases (purple and yellow lines, respectively); d and e) relative proportions of 5hmC (blue) and 5mC (red) methylated sites across each chromosome; f) coding density. Shifts in nucleotide biases (rings a to c) are highlighted by dashed grey lines. Repeated loci between chromosomes (in grey) and within chromosomes (color-coded per chromosome) are highlighted by ribbons in the center of the concentric circles