Figure 1.
Circular genome map of P. sp. UW4.
From the outside in, the outer black circle shows the scale line in Mbps; circles 2 and 3 represent the coding region with the colors of the COG categories; circle 4 and 5 show tRNA (green) and rRNA (red), respectively; circle 6 displays the IS elements (blue); circle 7 shows the genomic islands (orange); circle 8 represents mean centered G+C content (bars facing outside-above mean, bars facing inside-below mean); circle 9 shows GC skew (G−C)/(G+C). GC content and GC skew were calculated using a 10-kb window in steps of 200 bp.
Table 1.
General Features of P. sp. UW4 Genome.
Table 2.
COG Functional Categories of P. sp. UW4.
Figure 2.
Genomic islands of P. sp. UW4 predicted by IslandViewer.
The outer black circle shows the scale line in Mbps. Predicted genomic islands are colored based on the following methods: SIGI-HMM, orange; IslandPath-DIMOB, blue; Integrated detection, red. Black plot represents the GC content (%).
Table 3.
General Features of the Pseudomonas Genomes.
Figure 3.
Schematic overview of metabolic pathways and transport systems in P. sp. UW4.
Individual pathways are denoted by single-headed arrows, while reversible pathways are denoted by double-headed arrows.
Figure 4.
Phylogenetic tree of 21 different Pseudomonas species, base on 1,679 conserved genes.
Numbers on nodes represent percentages of individual trees containing that relationship. The scale bar corresponds to the number of substitutions per site.
Figure 5.
Comparative synteny line plots of the complete six-frame translations of the whole genome sequences of P. sp. UW4 with other P. fluorescens.
P. protegens, and P. putida genomes. The analysis was carried out using Artemis Comparison Tool and computed using TBLASTX with a cutoff E value of 1 E-5. The red bars between the DNA lines indicate individual TBLASTX matches, and the blue lines exhibit inverted matches. The cutoff identities and alignments length are 75% and 30 amino acids, respectively.
Figure 6.
ML phylogenetic tree of 16S rRNA sequences from completely sequenced Pseudomonas genomes.
Nodal support was evaluated by aLRT. Different species are shown in different colors. Only unique sequences from each genome were included for this analysis.
Figure 7.
Phylogenetic tree of 128 Pseudomonas strains based on four concatenated genes including 16S rRNA, gyrB, rpoB and rpoD.
Dendrogram was generated by neighbor-joining and distance matrix was calculated by the Jukes-Cantor algorithm. The bar at the bottom indicates sequence divergence. Nodal support was evaluated with 1000 bootstrap pseudoreplications and values of greater than 50% are shown at the nodes.