Fig. 1

Evolutionary genomic analyses of Methanomassiliicoccales. A A phylogeny of 146 complete Euryarchaeota genomes and 46 outgroup taxa from the phylum Crenarchaeota (represented by different colored circles) was reconstructed based on 26 ribosomal proteins. The gray background represents the topological divergence of the three monophyletic clades, and the yellow stars represent the known methanogenic Euryarchaeota (except for Methanonatronarchaeales). The numbers in the brackets represent the number of genomes corresponding to each order. B PCoA depicting the genomic divergence based on a predicted function presence/absence matrix determined from 192 genomes colored by their taxonomy. The random forest classifier defined the importance score for each putative gene in Methanomassiliicoccales to the overall variance. C Heatmap constructed from a gene count matrix of 31 important genes identified by random forest analysis. The upper colored strips represent the genome classification in each column, and the right side shows the ranked genes. D Schematic showing a functional B₁₂ acquisition system, including the periplasmic binding protein BtuF and ABC transporter BtuCD. The phylogenetic tree of BtuC was constructed based on the alignments of 762 protein sequences with 281 aligned positions. The branches are colored according to the taxonomic source of these sequences, and the assumed five clades, along with the outgroup, are labeled on the phylogenetic tree. Mmc, Methanomassiliicoccales; M. stadtmanae, Methanosphaera stadtmanae