Reference Genome Sequences and Annotation

All sequenced organisms have publicly available reference genome sequences, and gene annotation files deposited in NCBI and IMG [51]. Accession numbers and summary statistics of reference genomes used in the analyses are provided in S1 Table. The majority of reference sequences were complete (assembled into a single circular molecule), with more than 90% genomes containing less than 10 scaffolds. The inclusion of data from draft genome sequences increases our overall yield of MTase gene annotations, but limits the ability to comprehensively annotate the methylome in all cases.