Figure 1.
Size of pan-genome, core genome and unique genes for Streptococcus.
(A) Total number of genes. The curve was fitted to the function and parameters
,
,
,
were determined under correlation
. (B) Number of genes in common. The curve was fitted to the function
. The best fit was obtained with correlation
for
,
,
(C) Number of unique genes. The curve was fitted to the function
, the best fit was obtained with correlation
for
,
,
. The upper and lower edges of the boxes respectively indicate 25 and 75 percentiles, and the horizontal carmine lines indicate 50 percentile under 1,000 different random input orders of genomes. The central vertical lines extend from each box as far as the data extends to a distance of at most 1.5 interquartile ranges. Colors represent Pyogenic (red), Mitis (orange), Anginosus (yellow), Bovis (green), Mutans (cyan), and Salivarius (blue) species groups, respectively.
Figure 2.
Population structure of streptococcal species groups.
(A) The population memberships of the inspected species groups for a priori defined number of clusters K = 1–7 inferred by the Structure software. Each individual is represented by a thin vertical line divided into K colored segments that represent the individual’s estimated membership fractions in K clusters. Black lines separate individuals of different populations. Populations are labeled below the figure. (B) The detection of the true number of clusters inferred by the Structure software and set as a function of K. ΔK attains its highest value when K = 2, generated by Structure, according to Evanno et al.
Figure 3.
Phylogenomic tree of Streptococcus.
The supermatrix tree was constructed based on maximum likelihood (ML, bootstrap value indicated as numerator) and neighbor-joining (NJ, bootstrap value indicated as denominator) algorithms, using a concatenated alignment of 278 orthologous proteins. All the 138 Streptococcus strains analyzed were assigned to the corresponding species groups and were marked with related colored circles. Different color-coded branches denoted different species.
Figure 4.
Gene content dendrogram of Streptococcus.
The dendrogram was constructed by hierarchical clustering (UPGMA) based on the dissimilarities in gene content among 138 Streptococcus strains, using paired Jaccard distances which range from 0 to 1. Different color-coded branches denoted different species.
Figure 5.
Phylogenomic relationships of streptococcal species groups.
The clustering results of seven species groups were based on phylogenomic tree and gene content dendrogram. Each species group was painted with the assigned color as the above analysis.
Figure 6.
Phylogenetic dendrograms of seven conserved genes related to virulence factors.
A, B, C and D represent trees of pavA, srtA, slrA, plr/gapA from adhesion factor, respectively; E represents tree of eno from exoenzyme factor; F and G represent trees of htrA/degP and tig/ropA from protease factor, respectively.