Table 1.

Methylation Analysis with Bismark Showed That Ceratonova shasta and Henneguya salminicola Have No DNA Cytosine Methylation.

Bisulfite Sequence Data	Reference Genome Assembly	C Methylated in CpG Context (%)	C Methylated in CHG Context (%)	C Methylated in CHH Context (%)
Ceratonova shasta + rainbow trout + lambda phage	Lambda phage	0.1	0.2	0.1
Ceratonova shasta + rainbow trout	Rainbow trout	73.8	0.2	0.2
Ceratonova shasta	Ceratonova shasta	0.1	0.1	0.1
Henneguya salminicola + Chinook salmon + lambda phage	Lambda phage	0.1	0.1	0.1
Henneguya salminicola + Chinook salmon	Chinook salmon	49.0	11.9	16.2
Henneguya salminicola	H. salminicola	0.1	0.1	0.1

Note.—The table lists the percent cytosine methylation for the CpG, CHG, and CHH methylation contexts for each of the six bisulfite sequence alignments performed using Bismark. The first row summarizes the methylation results for the alignment of the raw WGBS sequence reads for C. shasta to the lambda phage genome. The second row summarizes the results for the alignment of the C. shasta filtered reads from the previous alignment to the rainbow trout genome. The third row summarizes the results for the alignment of the C. shasta final filtered reads from the previous alignment to the C. shasta genome excluding cytosine sites overlapping SNPs from the reference genome. The fourth row summarizes the methylation results for the alignment of the raw WGBS sequence reads for H. salminicola to the lambda phage genome. The fifth row summarizes the results for the alignment of the H. salminicola filtered reads from the previous alignment to the Chinook salmon genome. The sixth row summarizes the results for the alignment of the H. salminicola final filtered reads from the previous alignment to the H. salminicola genome excluding cytosine sites overlapping SNPs from the reference genome. The percent methylation data shown here are from after deduplication and extraction using deduplicate_bismark and bismark_methylation_extractor.