Fig. 3

Pan-genome analysis of Methanomassiliicoccales. A PCoA showing the genomic divergence based on the gene orthologs of these 243 genomes plus five outgroup taxa from the order Thermoplasmatales and colored by their assigned genus. ANOSIM tests were used to assess the significance of dissimilarities between the genera calculated by the Bray-Curtis method. B A two-color heatmap showing the ancestral gene and gained events for each genus. The top lines represent the functional category of orthologous genes in each column and are colored according to the COG annotations. The number of gene gain events among different genera is shown on the line plot. CPS, cellular processes and signaling; MET, metabolism; ISP, information storage and processing; PC, poorly characterized; NA, no annotation. C The number of ancestral gene families in genera from the environmental and gastrointestinal clades were compared using Wilcoxon rank-sum test. Histograms showing KO annotations of core (≥ 80% of genera have) and flexible (< 50% of genera have) genes in the 1656 ancestral gene families of Methanomassiliicoccales. Genes encoding Cas proteins and choloylglycine hydrolase (cbh) are present in different genera. D The number of unique genes specific to each genus among the 968 gained genes is shown at the top, and their KO annotations are shown at the bottom. The heatmap of the 40 annotated genes distributed across 8 genera is expanded to the right