Marker gene alignment for phylogenetic symbiont tree

All available MAGs (irrespective of completion) were used to generate a concatenated gene tree. The CheckM version 1.1.3 lineage workflow was used to locate, align, and concatenate the default set of 43 universal marker genes. Checkm’s automatically generated concatenated protein alignment of these 43 marker genes was then submitted to the W-IQ-TREE server using the default settings (auto substitution model detection, 1000 ultrafast bootstraps, and 1000 replicates of SH-aLRT branch tests).