RIF primers developed in this study.

aNo genome sequence was available for Pantoea agglomerans when these primers were developed.
bPrimer pairs for three genera of Enterobacteriaceae were initially developed by comparison of the dnaA gene of Dickeya, Pectobacterium and Erwinia available in 2007 (Table 1, Supplemental Figure S1). Primers were developed using the criteria applied for selection of the Clavibacter and Ralstonia primers and alignment of the respective dnaA gene (see methods). The initial Pectobacterium and Dickeya primers failed to produce amplicons for two strains of Dickeya (one D. chrysanthemi and one D. paradisiaca), three strains of Pantoea (one that also failed to amplify with the ITS marker) and nine strains of Pectobacterium (eight of which failed to amplify with the ITS marker). Pectobacterium strains K0509, K0522 and K0574 and Pantoea strains required an annealing temperature of 51°C.
cPrimer sets were derived using newly sequenced strains of Dickeya (Dz_1591, Dd_703) and Pectobacterium (Pc_PCC1 and Pw_Wpp163). The Dickeya primers amplified all nine reference Dickeya strains. The new Pectobacterium primers no longer amplified any Pantoea strains at 51°C and they amplified strain K0522, K0574 and one additional Pectobacterium strain, K0510, but still did not amplify strain K0509 at 61°C.
dPrimers developed from Pseudomonas accessions NZ_CH482384, NZ_CM001020, NC_011770, NC_009656, NC_002516, NC_008463, NC_008027, NC_004129, NC_012660, NZ_CM001025, NC_009439, NC_009512, NC_010322, NC_002947, NC_010501, NZ_GG774590, NZ_DS997060, NC_005773, NC_007005, NZ_GG700508, NC_004578, NZ_GG699506 and NC_009434.
ePrimers developed from Xylella fastidiosa accessions CP002165, CP001011, AE009442, CP000941 and AE003849.