Comparison of 6mA features in trophonts and cysts. (A) Representative inter-pulse duration (IPD) ratios of SMRT sequencing data. Columns indicate the IPD peaks representing the detected 6mA signals on both Watson and Crick strands based on the IPD ratio. (B) 6mA ratios in trophont and cyst genomes. The 6mA ratio was defined as the number of methylated adenine sites divided by the number of total adenine sites. (C) Sequence logos of 6mA sites (at position zero) in trophonts and cysts. (D) Venn diagram of shared 6mA sites in trophonts and cysts (left) and 6mA pattern conversion of asymmetric 6mApT in cysts (right). Three sources of asymmetric 6mApT are shown. (E) Density plot of 6mA distribution, according to methylation levels on Watson (x-axes) or Crick strands (y-axes) in trophonts (left) and cysts (right). Percentages of symmetric and asymmetric 6mA are shown. (F,G) Comparison of 6mA methylation levels in trophonts and cysts for symmetric 6mA (F) and asymmetric 6mA (G). Methylation levels were ranked from low to high and divided into 10 quantiles. Lines represent the percentage of 6mA; columns, the number of 6mA sites. Percentages represents the number of 6mA sites in each quantile divided by the total number of 6mA sites. Linear regression trendlines and 95% confidence intervals are shown as insets. (H) Area-proportional Venn diagram depicting highly methylated 6mA (80%–100%) and symmetric/asymmetric 6mA sites in trophonts (left) and cysts (right).
