The CDS of the pan-genome (forward and reverse) are depicted in the two outermost circles (aqua). Moving inwards, the core genome is depicted in yellow and the accessory genome in black. The accessory genome of the individual strains of E. amylovora continue inwards as follows: Rubus-infecting strains MR1 (red), Ea644 (pink) and ATCC BAA-2158 (purple), and Spiraeoideae-infecting strains CFBP 1430 (light blue), ATCC 49946 (royal blue), Ea266 (dark green), CFBP 2585 (tan), 01SFR-BO (sky blue), Ea356 (teal), UPN527 (navy blue), ACW 56400 (orange) and CFBP 1232T (light green). Variable regions of interest are numbered with a pan-genome locus (PL) of 1 to 32 and are described in Supplementary and . Of note are PL 4 (ICE flanking PAI-1), PL 20 (secondary metabolite cluster only found in Rubus-infecting strains), PL 27 (sequence from the Rubus-infecting strains that could not be assembled into contiguous sequence), PL 28 (pEA72), PL 29 (pEA29), PL 30 (pEI70), PL 31 (pEAR5.2 and pEAR4.3) and PL 32 (pEA30).