Table 1.
Genome characteristics.
Fig 1.
Genome map of Pseudomonas fluorescens PCL1751.
Rings from the outside in: (1) scale marks (unit: Mb), (2 and 3), protein-coding genes on the forward and reverse strand, respectively (color-coded by the functional categories), (4) rRNA gene clusters (green) and prophages (red), (5) GC skew (positive: purple; negative: yellow), and (6) GC content (above average: orange; below average: blue).
Fig 2.
Selected metabolic pathways of Pseudomonas fluorescens PCL1751.
This figure provides a visual summary of the gene content analysis described in the main text. Boxes drawn with dotted lines indicate the genes missing in the annotation.
Fig 3.
Distribution pattern of homologous gene clusters.
The maximum likelihood phylogeny was inferred from the concatenated protein alignment of 2,374 single-copy genes shared by all strains (with 783,597 aligned amino acids). All internal nodes received 100% bootstrap support based on 1,000 re-sampling and maximum likelihood inference. The numbers above each branch and proceeded by a ‘+’ sign indicate the numbers of homologous gene clusters that are uniquely present in all daughter lineages; the numbers below each branch and proceeded by a ‘-‘ sign indicate the numbers of homologous gene clusters that are uniquely absent.
Fig 4.
Secretion system gene clusters.
The figure provides a visual summary of the presence (filled circles) and absence (empty circles) of genes involved in secretion systems in these genomes. Multi-copy genes are labeled by their copy number inside the filled circles.
Fig 5.
Pairwise genome alignments between Pseudomonas fluorescens PCL1751 and other related strains. The nucleotide (nt) and amino acid (aa) sequence similarities are calculated based on the concatenated alignment of 2,374 single-copy genes shared by all strains.
Fig 6.
Synteny of prophage insertion sites.
Gene organization near the three prophage insertion sites in the Pseudomonas fluorescens PCL1751 genome and the syntenic regions in the two closely related strains. Putative homologs are linked by thin gray lines.