Olored lines connect syntenous blocks of sequence {between|in between|among
  • Olored lines connect syntenous Title Loaded From File blocks of sequence in between the strains. The tree around the left hand side of (A) shows the relatedness of the strains as determined by MSLA (Figure 1). (TIF) Figure S5 Chromosomal alignments of strains inside Sub-clade three generated utilizing Progressive MAUVE [151]. Regions of substantial synteny amongst the strains (P. fluorescens SBW25, Pseudomonas sp. BG33R, P. fluorescens A506 and P. fluorescens SS101) are shown as colored blocks in the mauve alignment. Regions of sequence not shared in between the strains are noticed as white gaps inside the blocks or spaces between the blocks. Breaks among scaffolds are designated by vertical red lines extending through and under the blocks of genome BG33R. Colored lines connect syntenous blocks of sequence among the strains. The tree around the left hand side of your figure shows the relatedness in the strains as determined by MSLA (Figure 1). (TIF) Figure S6 REP frequency. Local spacing of REPa sequence elements. The frequency of the distance (bp) between adjacent REPa sequences separated by fewer than 200 bp is shown for each and every from the seven newly-sequenced strains. Distances had been measured from the center of REPa sequences. (TIF) Figure S7 Similarities amongst cargo genes in diverse mobile genetic elements present in genomes in the P. fluorescens group. The amount of similarity is depicted by the strength of grey shading in boxes representing overlap amongst two components. Abbreviations: pro (prophage); isl (island); plas (plasmid); tn (transposon). +ni = integrase present and not intact; + = integrase present and intact; two = integrase not present. Data for Pf-5 was published previously [54]; SBW25 and Pf0-1 had been not examined within this evaluation. (PDF) Figure S8 Phylogenetic tree depicting the relationships of pyocin-like bacteriocins located in genomes in the P. fluorescens group. Translocation domains (Pfam: PF06958) were applied for this evaluation; they're by far the most conserved domain inside the pyocin-like proteins. Proteins found inside the ten genomes examined within this study are bolded; characterized proteins are italicized. Interior node values with the tree are representative with the quantity of bootstraps out of 1000. Colour coding is as follows: bacteriocin group N1 (Red), group N2 (Dark blue), carocin (Light blue), Pyocin S1/2/AP41-like (Green). (TIF)Supporting InformationFigure S1 Phylogenetic tree depicting the relationships amongsequenced strains of Pseudomonas spp. The tree is based on 16S rDNA alignments and was generated making use of the MrBayes package [152]. The interior node values in the tree are clade credibility values, which represent the likelihood of the clade existing, according to the posterior probability values made by MrBayes. (TIF)Figure S2 Phylogenetic tree depicting the relationships amongsequenced strains of Pseudomonas spp. This maximum likelihood tree is depending on the concatenated alignments of 726 shared proteins identified inside all of the genomes and was generated making use of the Hal pipeline [153].The ten strains of this study (Table 1) were evaluated for all phenotypes shown and classified as shown in Table S16 as outlined by this crucial. Abbreviations and definitions are as follows: Fluorescence (fluorescence of colonies viewed below UV light); Arginine (arginine dihydrolase activity); Oxidase (oxidase activity); HR on Tobacco (hypersensitivity response on tobacco); Levan (levan sucrase activity); Gelatin (gelatinase activity); L-ara (L-arabinose); L-trp (L-tryptophan); P. fluor. (P.