Gene body methylation in Myxozoa

Oxford-Nanopore MinION sequencing, is a PCR-free method that retains epigenetic markers and provides direct quantitative information about DNA methylation. Using this long-read sequencing technology, we present complete and near-complete assemblies of five myxozoan genomes free from host DNA contamination. These genomes did not match any existing sequences in public databases, suggesting a need for updated sequence data for these elusive parasites. The quality of the assemblies surpassed that of existing assemblies, and methylation analysis indicated the presence of DNA methylation in the GC-rich regions within gene bodies. Enzymes related to DNA methylation were also identified in the genomes. Experimental and in silico analyses revealed variable methylation levels across genomes, suggesting a "transcription switch" mechanism regulating gene expression. Overall, this study highlights the importance of long-read sequencing methods to better understand epigenetic processes in parasites like myxozoans. The findings challenge existing paradigms and could inform new strategies to control myxozoan fish pathogens.