Fig. 2

Comparison of different Paramecium genomes. a Seventy-five percent of P. bursaria genes have orthologs in other Paramecium species. The phylogenetic tree was constructed using the core gene set of ciliates listed in Table 1 (see the “Methods” section). Numbers beside each node are posterior probability values obtained from Bayesian posterior probability. The scale bar represents the number of amino acid substitutions per site. The Venn diagram shows the number of orthologous genes shared among three Paramecium species. Orthologous genes were defined by comparing all protein sequences using OrthoFinder [61]. Different colors indicate the gene number of each species. The gene number of P. tetraurelia is more than that of other species due to the species having undergone two whole-genome duplication events [47]. b Heat map of the protein families and duplicated genes enriched in the P. bursaria genome. The gene numbers in each protein family/group of paralogs of each species are shown. The proportion of genes belonging to each protein family/group of paralogs to the whole genome gene number in each species was converted into a z-score by z-transformation (z = (x − μ)/σ, where μ is the population mean and σ is the population standard deviation). A two-proportional test was conducted and proteins or gene families are shown having a p value ≤ 0.05 after Benjamini-Hochberg adjustment