Generation of Multi-Locus Sequence Analysis (MLSA) phylogenetic tree

MAFFT v. 7.245 [47] was used to generate alignments for gyrB, rpoD, rpoB, and 16S rRNA from the type strains of the P. fluorescens group (S5 Table) and from the ten strains of Pseudomonas sp. listed in Table 1. Accession numbers for all sequences are provided in S5 Table. Alignments of gappy columns were trimmed using Gblocks [48]. The concatenated nucleotide sequences from each organism were used as input for a partitioned maximum-likelihood phylogenetic analysis using RAxML v. 8.1.21 [49], using GTR+GAMMA as the substitution model for each partition. Trees were generated according to the guidelines provided in the RAxML v. 8 user’s manual, with 100 individual maximum-likelihood searches performed and 450 bootstrap replicates were completed using the extended majority rule-based bootstrapping criterion [49].

Abbreviation: Rif^R, resistant to rifampicin (100 μg/ml).