Figure 3. Alignment and newick tree of new MAGs in the global lucinid symbiont tree

Concatenated alignment of 120 conserved bacterial marker genes from the MAGs was obtained with the GTDB-Tk v2.1.1 (Genome Taxonomy Database Toolkit) classify workflow, including MAGs published in this work and in Osvatic et al. 2023 ISMEJ. Maximum likelihood phylogenomic tree inferred from GTDB’s multiple sequence alignment with IQ-Tree v2.2.2.1 (Minh et al. 2020; Hoang et al. 2018; Kalyaanamoorthy et al. 2017) including MAGs published in this work and in Osvatic et al. 2023 ISMEJ. The tree was inferred with auto substitution model detection, 1,000 ultrafast bootstrap (UFB) replicates and 1,000 samples for SH-aLRT branch testing. Nodes with values of UFB greater or equal to 95% and of SH-aLRT greater or equal to 80% were considered to be strongly supported. The best-fit model was Q.plant+F+I+G4.