Table 1.
Characteristics of whole genome assemblies derived from individual Tannerella BU063 cells and combined data from highly identical cells.
Figure 1.
Histograms of blast alignments of all BU063 single cell assemblies.
In each graph, the fraction of the total length aligned is graphed by percent nucleotide identity. Comparisons that showed a high degree of alignments with over 99% identity are highlighted in yellow.
Table 2.
Prediction of Tannerella BU063 full genome size based on overlap of partial genomes.
Table 3.
Core gene presence in Tannerella BU063 genome assemblies.
Figure 2.
Venn diagrams showing numbers of shared protein-coding genes between various assembled genomes.
The first number is the total number of genes in each section, while the number in parentheses is the number of genes that were assigned to COGs. The distribution of COG categories is shown as a pie chart with colors as in the legend A) Venn diagram for the three most complete assemblies of Tannerella BU063. B) Venn diagram showing average numbers comparing BU063 to Tannerella forsythia.
Figure 3.
Promer dot plots showing extent of synteny between genomes.
The program compares amino acid translations of the genomic sequences. Blue dots indicate identity from + to + or − to − strands, red dots indicate identity from + to − or − to +. The gray grid lines indicate the borders of contigs in the draft assemblies. The bars indicate lengths of 500 kb. A) Plot of the 20 largest contigs of BU063 cell no. 5 assembly against the 20 largest contigs of the cell no. 2 assembly. In either case about half the genome is represented. Note that the program attempts to flip and order contigs to generate a diagonal but this is not fully possible because of missing regions. One non-syntenous region is shown with the arrow. B) Plot of the 20 largest contigs of cell no. 2 vs. T. forsythia C) Plot of the 20 largest contigs of cell no. 5 vs. T. forsythia.
Figure 4.
Genome maps of a gene cluster in T. forsythia and other organisms.
The cluster was identified by a bioinformatics screen for possible virulence genes, identifying genes with homologs in T. forsythia and at least one of six Bacteroidetes organisms associated with chronic periodontitis, but absent from the five longest BU063 assemblies (protein BLAST results with cut-offs 30% identity and e-value 10−5). A cluster of genes including many with apparent cell-surface function was identified within the results. The predicted gene functions are shown above the T. forsythia map, with colors indicating conserved genes in the other organisms. The boxed genes are more similar to the other periodontitis-associated organisms than to BU063. Gray bars in the background show the pattern of sequence conservation by connecting genes to homologous genes in the other organisms.
Table 4.
Clusters of genes present in T. forsythia and other pathogens but missing from BU063.