Phylogenetic analyses
Representative genomes identified by Pasoli et al. (2019) from each SGB were used to construct a phylogeny of SGBs. Alignments for phylogenetic analyses were generated using the Genome Taxonomy Database Toolkit (GTDB-Tk) (Chaumeil et al., 2020). Marker genes in each SGB representative genome were identified with ‘gtdbtk identify’ using default settings and aligned against the BAC120 reference gene set with ‘gtdbtk align’ using default settings. Alignments were then used for phylogenetic inference with IQTree2 (Minh et al., 2020). For these analyses, model search was constrained to only LG and WAG models of protein substitution, and 1000 ultrafast bootstrap replicates were performed. Phylogenetic tree off SGBs was visualized in the Interactive Tree of Life (iTOL) web interface (Letunic and Bork, 2021).