Characteristics of analyzed genomes.

Species are ordered according to the phylogeny (Fig 1). (a) MIC genome size (in Mb) was estimated based on k-mer counts (see S1 Table for additional estimates based on flow cytometry). (b) Sequencing depth in MIC-specific regions estimated from the distribution of k-mer counts (S2 Fig). (c) Size of constitutive MAC genome assembly. (d) The sensitivity of IES detection was limited in P. caudatum and P. sonneborni because of the relatively low sequencing depth of their MIC genome. Estimates of total number of IESs, based the IES density observed in regions with sufficient read depth (see e), are indicated in parenthesis for these 2 species. (e) IES density measured in MAC-destined sequences, after exclusion of regions with insufficient MIC read depth (<15X).