Fig. 3

Pan-genome statistics. A Scatter plot showing the number of proteins and average protein length in short- and long-read assemblies. B, C Progression of sizes of the pan-genome (blue), core genome (orange), and accessory (green) genomes with an increasing number of strains. To build the graph, we randomly grouped strains in groups of increasing sizes, from one to the maximum number of strains (21) and for that subset of strains we calculated the size of the pan-genome, core genome, and accessory genome. This was repeated 100 times for each group size, and for each size the average number of proteins in the pan-genome, core genome, and accessory genome were calculated. Standard deviation is shown as a shadow surrounding each line. B Build with all orthogroups predicted with orthofinder. C Build with all core groups and curated accessory groups. Accessory groups related to miss-annotations or miss-predictions were excluded from the analysis