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 MGL06T 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.