Table 1.
Genome survey of 11 strains in family Planctomycetaceae.
Figure 1.
Gene length distribution in the 11 Planctomycetaceae genomes.
The values above each bar (in percent) were calculated as the number of genes that are of specified length divided by the number of total genes in each Planctomycetaceae genome.
Figure 2.
Gene family clusters and core genome/pan genome analyses based on whole-genome sequences.
(A) The histogram reveals the number of unique gene families in each of the 11 Planctomycetaceae strains. The color bar on the right shows the number of common gene families between crossed strains. (B) The box plot at the left indicates the number of core genes that correspond with the strain genomes. The box plot at the right indicates the pan gene numbers that correspond with the strain genomes. The box in the figures indicates half the distribution of values in the random sampling; the bold line in box indicates the median.
Figure 3.
Phylogenetic tree constructed using proteomes predicted from 11 genomes of Planctomycetaceae.
The rooted tree generated in MEGA 4.0 with the concatenated alignments of the conserved regions of the orthologous core protein sequences, topology of which illustrates the relationships among Planctomycetaceae species and related taxa. Bootstrap values (in percent) of 1000 simulations are indicated at all branches. Bar represents 0.05 amino acid substitutions per site. Coraliomargarita akajimensis, Parachlamydia acanthamoebae, and Phycisphaera mikurensis were selected as outgroups [31].
Figure 4.
(A) The inner ring: number of genes in the genomes; The outer ring: characterized/uncharacterized genes. (B) Gene function classification based on COG annotation. Heatmap at the left shows the functional prediction of 11 Planctomycetaceae genome. The core genome consists of the nonredundant core protein families. Heatmap at the right shows the functional prediction of the core genome. The color bar shows gene numbers. (C) ICM structure of four Planctomycetaceae species. These pictures shows the the ICM structure of four Planctomycetaceae species, namely S. acidiphila, R. baltica, Z. formosa, and S. paludicola (left to right), which were observed under transmission electron microscopy.
Figure 5.
Collinearity of the five completed Planctomycetaceae genomes.
P. limnophilus was set as the reference genome. Different colored lines in each genome indicate its similarity profile. The height of the similarity profile corresponds to the average level of conservation in that region of the genome sequence and was calculated to be inversely proportional to the average alignment column entropy over a region of the alignment. Parts of the similarity plot which are colored mauve are conserved among all the five genomes. The other colors shows the similarity of segments not in all the five genomes, but they are too small to notice in a whole-genome view. The similarity profile above the centerline of the aligned region is in the forward orientation relative to the first genome sequence, and profiles below the centerline indicate regions that align in the inverse orientation. Areas that are completely white were not aligned and probably contain sequence elements specific to a particular genome. The Mauve software was used for this analysis [55]. The seed (minimum match size) we used was 15 mer.
Figure 6.
Overview of genomic islands in the five completed genomes.
GI prediction was performed by integrating the following software: SIGI-HMM, IslandPath-DIMOB and IslandPick. The prediction was implemented in Web server IslandViewer (http://pathogenomics.sfu.ca/islandviewer/query.php) [44].
Figure 7.
Plasmid integration in the 11 genomes.
PL and IS represents the plasmid reported in P. limnophilus and I. pallid respectively. The outermost ring shows the two plasmids’ genes which divided by bold lines. The colors in each genome ring accord with the identity illustrated in the legend. The 11 Planctomycetaceae genomes were arranged according to their genome sizes, the outer the larger. Phycisphaera mikurensis and Saccharomyces cerevisiae were used as a control.