Fig. 3
Pan- and core-genome analyses of the 84 Pectobacterium genomes. The number of genes in the pan-genomes and core-genomes, and the unique genes among the genomes were classified using CD-HIT, with a threshold of 70% pairwise identity and a 0.6 length difference cut-off in amino acid sequences. a Venn diagram of Pectobacterium genus for 56 P. carotovorum, 4 P. polaris, 8 Candidatus P. maceratum, 10 P. atrosepticum, and 6 P. parmentieri genomes. b Venn diagram of P. carotovorum species for 29 Pcb, 9 Pcc, 15 Pco, and 3 Pca genomes. The core orthologous genes are not the genes that are shared by all of the tested genomes of a given group; rather these are the genes that were present in a minimum of one genome from each of the targeted subgroup. c-f Flower plots of each of four subspecies for 29 Pcb, 9 Pcc, 15 Pco, and 3 Pca genomes, respectively. The figures of 84 Pectobacterium genomes in (g) and (h) were produced using PanGP. g Plot in which the blue line shows the impact on the number clusters for the pan-genome resulting from the addition (simulated, randomized) of further genomes to the analysis, with the asymptotic value of y = AxB + C; the green line shows how such addition influenced the number of core genes, with the asymptotic value of y = AeBx + C. h Histogram showing the increases in the number of new (unique) genes as the number of genomes was increased in our pan-genome analysis. The horizontal dashed line (orange) indicates the asymptotic value with the function of y = AxB