Fig 1.
Phylogeny of the Pseudomonas genus inferred by MLSA.
Phylogenetic tree of 451 Pseudomonas strains along with 107 type strains based on the concatenated partial sequences of the 16S rDNA, gyrB, rpoD and rpoB, ML method, Tamura-Nei. Only bootstrap values above 75% (from 1,000 replicates) are shown. Cellvibrio japonicum Ueda 107 was used as outgroup. Details are found in S1 Fig.
Fig 2.
Phylogeny of the P. fluorescens complex inferred by MLSA.
Phylogenetic tree of 127 sequenced and type strains belonging to the P. fluorescens complex based on the concatenated partial sequences of the 16S rDNA, gyrB, rpoD and rpoB genes, the ML method and the Tamura-Nei model. Only bootstrap values above 50% (from 1,000 replicates) are shown. The P. aeruginosa type strain was used as outgroup. Bold text as well as superscript T indicates type strains. Strains are colored according to the groups established in this work.
Fig 3.
Phylogeny of the P. fluorescens complex based on ANIb and GBDP.
Whole-genome phylogenies based on nucleotide data from 93 sequenced strains belonging to the P. fluorescens complex. Strains are colored according to the groups established in this work. The left-hand phylogeny (A) was inferred by using ANIb values converted to distances (100 –ANIb % similarity) calculated with BLAST algorithm and the NJ method. The right-hand phylogeny (B) is based on all pairwise intergenomic distances as calculated by the latest GBDP version and inferred using FastME v2.07 with TBR postprocessing. Only greedy-with-trimming pseudo-bootstrap values above 50% (from 100 replicates) are shown. For both phylogenies P. aeruginosa PAO1 was used as outgroup.
Fig 4.
Heatmap of reciprocal dDDH values under species and groups thresholds.
(A) Species-level clusters at a dDDH threshold of 70% and (B) group-level clusters at 31.8% dDDH threshold. The phylogenomic tree from Fig 3B was used for ordering strains in the symmetric matrix. Black boxes on the heatmap matrix represent species or group clusters according to the OPTSIL results.
Fig 5.
Simulation of the variation in several clusters dependent on the number of genomes.
(A) Number of GBDP dDDH clusters observed for subspecies, species and groups over the number of randomly sampled P. fluorescens complex genomes. (B) Number of ANIb clusters observed for species and groups over the number of randomly sampled P. fluorescens complex genomes. Clusters were established under the best OPTSIL parameters. Black dots indicate the mean of the calculated values, while gray shades indicate the first and third quartile.
Fig 6.
Number and percentages of orthologous CDSs belonging to the core, strain-specific and group-specific genome.
From outside to inside, the outer most circle shows the strain names of the P. fluorescens complex used in this work. The second circle represents the number of group-specific orthologous CDSs (bold) and the percentage it represents from the average of CDSs in all the genomes. The third circle indicates the strain-specific number of CDSs (bold) and its percentage relative to the total number of CDSs from each strain. The fourth circle represents the number of CDSs (bold) in the core-genome of each group and its percentage of the average number of CDSs in all the genomes. The fifth circle represents the core-genome CDSs of the P. fluorescens complex and their percentages of the average number of CDSs in all the genomes. Coloring is according to the groups established in this work.
Fig 7.
Simulations for the variation in core, strain-specific and pan-genome fractions over the number of genomes.
(A) Number of core CDSs depending on the number of genomes sampled. (B) Number of strain-specific CDSs depending on the number of genomes sampled. (C) Pan-genome size (CDSs) depending on the number of genomes sampled. In all cases, genomes were sampled with 200 replicates. Black dots indicate the mean of the calculated values, while grey shades indicate the first and third quartile.
Fig 8.
Distribution of the selected group-defining clusters in the groups from the P. fluorescens complex.
Numbers within the boxes represent the percentage of strains from each group having the complete gene cluster or at least the core functional CDSs. PHL: DAPG (2,4-diacetylphloroglucinol) biosynthesis (PhlABCDEFGH); PHZ: phenazine biosynthesis (PhzABCDEFGOIR); PRN: Pyrrolnitrin biosynthesis (PrnABCD); HRP: 2-hexyl, 5-propyl resorcinol biosynthesis (DarABCRS); PLT: Pyoluteorin biosynthesis (PltABCDEFGIJKLMNOPRZ); HCN: hydrogen cyanide (HcnABC); HAS: Hemophore biosynthesis (HasADEFIRS); E-PCH: Enantio-pyochelin biosynthesis (PchABCDEFHIKR); PFE: Ferric- enterobactin receptor (PfeARS); ACS: Achromobactin biosynthesis (AcsABCDEF+YhcA); CBR: Achromobactin transport (CbrABCD); Nar: Nitrate reductase (NarGHIJKLUX); Nir: Nitrite reductase (NirCDEFGHJLM1NOPS+NorQ); Nor: Nitric oxide reductase (NorBCD); Nos: Nitrous oxide reductase (NosDFLRYZ); FIT: FitD toxin (FitABCDEFGH); ITC: Insecticidal toxin complex; 2-ND: 2-nitropropane dioxigenase; IAA: Indole-3-acetic acid metabolism (IaaMH); PAA: Phenylacetic acid catabolism (PaaABCDEFGHIJKLNWXY); SPR: spermidin biosynthesis (S-adenosylmethionine decarboxylase and spermidine synthase).