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).