Fig. 2

Metapangenomic analysis of Haemophilus parainfluenza reveals hidden diversity and habitat-specific subgroups. The inner radial dendrogram shows the 4318 gene clusters in the pangenome, clustered by presence/absence across genomes. The 33 genomes of H. parainfluenzae strains are plotted on the innermost 33 layers (black 270° arcs), spaced to reflect discernable groups based on genomic composition. Gene clusters within a given genome are filled in with black; gene clusters not present remain unfilled. Genomes are ordered by gene cluster frequency (top right dendrogram), with radial spacing added between major groups to improve visibility. The outermost three layers show the proportion of genes within each gene cluster determined to be environmental accessory (red) or core in HMP metagenomes from TD (blue), BM (violet), and SUPP (green), from inside to outside, respectively. If a genome was not well detected (< 0.5 of nucleotides covered by all metagenomes), all its genes were NA (gray) instead of environmentally core or accessory. Extending off the pangenome above 3 o’clock are bar charts of relevant information for each genome, with the y-axis limits in parentheses. Above the genome content summaries, each genome’s median coverage across all TD, BM, and SUPP metagenomes is shown in the colored bar graph. Per-sample coverage of each genome is shown in the heatmap above, where each row represents a different sample, and cell color intensity reflects the coverage. Coverage is normalized to the maximum value of that sample (black = 0, bright = maximum; colors as before for each site)