Fig. 5: Gene regulation, DNA methylation and trans-splicing.

a, DNA methylation in P. gotoi has reverted to exclusive transposon targeting. The metaplots show average methylation levels at CpG dinucleotides (mCG %) at protein-coding genes and repeats, classified for major transposable element type. Only repeats larger than 500 bp were used. TES, transcriptional end site. b, Diagram showing the expansion and simplification of the ancestral bilaterian DNA methylation toolkit in P. gotoi. Paralogues with simplified domain architectures are coloured in a lighter shade than those that retained the ancestral state. Full domain architectures of each gene are shown in Extended Data Fig. 10d. zf, zinc finger. c, Number of genes receiving trans-splicing and classified as belonging to an operon in P. gotoi. d, Occurrence of different annotated splice leaders and their combination in trans-splicing and operonic genes. e, Gene ontology enrichment (orange) and depletion (blue) for genes belonging to operons (Fisher’s exact test, two-sided). ncRNA, noncoding RNA. f, Trans-spliced and operonic genes exhibit a lower expression specificity as measured by coefficient of variation calculated using cell-type averaged expression. g, Fraction of operonic, trans-spliced and other genes among marker genes in single-cell clusters with enrichment in germline marked by an arrow. h, Number of open chromatin regions associated with the different gene categories (box plot shows median, quartiles and extrema, n = 2,643, 5,586 and 8,851 genes for operons, trans-spliced genes and other genes, respectively), indicating the higher number of putative regulatory elements in genes that are not trans-spliced. i, Example of an enriched motif in open chromatin regions related to operons.