Table 1.
Phages infecting Bacillus pumilis.
Figure 1.
Transmission electron micrographs of phiAGATE virions.
Panels A and B show typical morphologies observed under the electron microscope. Panel C depicts a phage particle with contracted tail.
Figure 2.
Replication and adsorption dynamics of phiAGATE.
Panel A shows an adsorption curve and panel B one-step growth curve. Error bars represent standard deviation.
Figure 3.
Genome organization of phiAGATE.
Panel A shows a circular map of the genome unique sequence (right LTR not shown). The predicted CDSs, tRNA genes, and repeated regions are marked with arrows. Panel B shows distribution of Biological Process GO terms among the predicted protein products. Panel C explains color code in terms of GO identifiers of ontological terms. Colors are consistent in all sections of the figure: blue – GO:0019068– virion assembly, pink – GO:0055086– nucleobase-containing small molecule metabolic processes, green – GO:0006355– regulation of transcription, DNA-dependent, red – GO:0006260– DNA replication, mauve – GO:0000270– peptidoglycan metabolic processes, yellow – GO:0006310– DNA recombination, teal – GO:0007049– (host) cell cycle, light brown – GO:0090116– DNA methylation, dark grey – no GO term assigned, light grey – no function predicted, black – tRNA genes, azure – tandem repeats.
Figure 4.
Results of clustering of Spounavirinae phages based on genomic similarity.
Panel A shows result of cluster analysis of the whole group of studied phages. Panel B is a close-up showing layout of the Bastille group and panel C is a similar close-up depicting the Twort group. Edge weights were calculated from the P values of BLASTn high-scoring segment pairs (e-value cut-off equals 1e-5), and the resulting network was visualized in the CLANS software package (10000 layout rounds). Nodes are colored by the proposed in-subfamily clustering: blue – Bastille group, green – Twort group, red – Bacillus phage SPO1. Abbreviations include the name of host taxon (Ba – Bacillus, Bx – Brochothrix, En – Enterococcus, Lb – Lactobacillus, Li – Listeria, St – Staphylococcus) and the bacteriophage name. All analyzed sequences are listed in Table S2.
Figure 5.
Heatmap showing the results of genome comparison of the studied spounaviruses, and the resulting phylogenomic tree.
The similarity values were calculated using Gegenees software based on pairwise translated comparison of the analyzed sequences (tBLASTx method, fragment size –50, step size –25). The heat plot colors reflect this similarity, ranging from low (red) to high (green). The heatmap is asymmetric because the variable contents of genomes differ in sizes and a similarity is calculated as a fraction of similar sequences in each genome. The tree was constructed with SplitsTree using the neighbor joining method. The scale bar represents a 10% difference in average tBLASTx score. Leaves of the tree are colored by proposed in-subfamily clustering: blue – Bastille group, green – Twort group, red – Bacillus phage SPO1. Abbreviations include name of host taxon (Ba – Bacillus, Bx – Brochothrix, En – Enterococcus, Lb – Lactobacillus, Li – Listeria, St – Staphylococcus) and the bacteriophage name. All analyzed sequences are listed in Table S2.
Figure 6.
Majority consensus maximum likelihood tree (250 bootstrap replicates) based on comparison of all analyzed protein markers, showing the relationships between the analyzed spounaviruses.
Branch labels indicate their percent bootstrap support. Leaves are colored by proposed in-subfamily clustering: blue – Bastille group, green – Twort group, red – Bacillus phage SPO1. Abbreviations include name of host taxon (Ba – Bacillus, Bx – Brochothrix, En – Enterococcus, Lb – Lactobacillus, Li – Listeria, St – Staphylococcus) and the bacteriophage name. All analyzed sequences are listed in Table S1.
Figure 7.
Genome comparison of phage phiAGATE, other members of the Bastille group, phage SPO1, and phage Twort, visualized with BRIG.
The central ring is a circular map of the reference genome, in this case genome of phiAGATE. Each further ring represents a genome of another bacteriophage. Their order (starting from center) and colors are explained at the right side. The map color scheme is the same as in Figure 3 and should not be confused with the BRIG color code included in this figure (CDSs are colored according to assigned Biological Process GO terms: blue – virion assembly, pink - nucleobase-containing small molecule metabolic processes, green – regulation of transcription, DNA-dependent, red – DNA replication, mauve - peptidoglycan metabolic processes, yellow – DNA recombination, teal – (host) cell cycle, light brown – DNA methylation, dark grey – no GO term assigned, light grey – no function predicted, and tRNA genes are marked with black arrows while tandem repeats with azure ones).
Figure 8.
Whole genome comparisons between Bastille-group phages and type species of ICTV-recognized genera in the Spounavirinae subfamily.
The genomes were compared using the progressive Mauve algorithm and visualized with the MAUVE plugin in the Geneious software suite. Each colored box represents a region that aligned to part of another genome (locally collinear block – LCB). Similarity inside the block is indicated by the height of the colored bars. The placement of a block below the axis indicates inversion, while the line connecting blocks represents a match between the regions. The putative functional modules (inferred from the annotation of the analyzed records) are shown as black and white boxes beneath LCBs (lowered position of the box indicates inverted orientation of genes in the module, symbols inside the boxes indicate: P – packaging module, H – head morphogenesis module, T – tail morphogenesis module, R – DNA replication module). All sequences (except the one of phage SPO1, which displays only negligible similarity to all others) were colinearized at the position indicated in brackets (based on the arrangement of the modules and pre-computed locally collinear blocks) to simplify the visualization. ‘R’ indicates that the genome was reversed prior to linearization. All analyzed sequences are listed in Table S2.