Individual marker gene and MLSA phylogenies

CDS alignments and gene trees were extracted from the ‘41NeoPseudo’ Pantagruel database (Dataset https://doi.org/10.6084/m9.figshare.8320142) for the following genes atpD (gene family id: RHIZOC034665, OG id: 1), glnII (RHIZOC002590, 0), gyrB (RHIZOC002739, 0), recA (RHIZOC040013, 0) and rpoB (RHIZOC004093, 0). Note that R. marinum MGL06^T sequence for glnII gene was missing in gene family RHIZOC002590, probably due to incomplete genome assembly. CDS alignments were concatenated and a tree was computed with MrBayes as described in Dataset https://doi.org/10.6084/m9.figshare.8320199.