Fig. 3

Pangenome structural features and presence/absence polymorphisms across the 21 chromosomes of reference isolate IPO323. A Total number of cumulative SNP mutations conferring modifier, moderate (M) and high (H—loss of function—LoF) impact changes expressed as a feature of the average protein length (aa) per chromosome. B Total number of cumulative SNP mutations conferring moderate and high impact changes expressed as a feature of the average protein length per chromosome. C Total number of cumulative SNP mutations conferring High impact changes expressed as a feature of the average protein length per chromosome. D Mean average expression of all genes present on each of the 21 chromosomes across all isolates. E Presence and absence (PaV) polymorphism of the genes predicted on core chromosome 1 of isolate IPO323 in the 17 newly sequenced isolates. F PaV for genes on core chromosome 7. G PaV for genes on accessory chromosome 15. G–F PaV for genes on accessory chromosome 15. The data highlight extensive regional variation and mark a clear distinction between the levels of overall sequence polymorphisms and presence/absence evident on the core and accessory chromosomes