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. 2019 Jul 11;14(7):e0218530. doi: 10.1371/journal.pone.0218530

Table 1. Fifty-nine strains of plant-associated bacteria were used in inclusivity and exclusivity panels to validate the specificity of multiplex TaqMan real-time PCR developed to detect all Clavibacter michiganensis subspecies and specifically, C. michiganensis subsp. nebraskensis.

Sample code Other IDa Accession number Strain Host Origin Average CT valueb
CM Cmn
A6203c DP104A MH560461 C. michiganensis subsp. nebraskensis (Cmn) corn OK, USA 19.2 23.7
A6204c DP114A MH560462 Cmn corn TX, USA 14.65 19.26
A6205c DP115 MH560463 Cmn corn IA, USA 12.03 17.68
A6206c DP117 MH560464 Cmn corn NE, USA 11.88 17.32
A6207c DP121 MH560465 Cmn corn TX, USA 11.05 16.49
A6208c DP122A MH560466 Cmn corn NE, USA 12.92 17.47
A6209cc DP134 MH560467 Cmn corn TX, USA 15.81 20.09
A6210c DP137 MH560468 Cmn corn TX, USA 13.09 17.87
A6211c DP139B MH560469 Cmn corn TX, USA 13.64 18.82
A6212c DP164 MH560470 Cmn corn NE, USA 11.08 15.22
A6213c DP165c MH560471 Cmn corn IA, USA 12.48 17.59
A6094c NCPPB 2579; LMG 3698 MH560472 Cmn corn NE, USA 15.94 19.09
A6095c 20037 MH560473 Cmn corn NE, USA 10.06 14.91
A6096c 200800460 MH560474 Cmn corn NE, USA 12.05 16.84
K-1*   MH560475 Cmn corn KA, USA 11.71 15.65
K-2*   MH560476 Cmn corn KA, USA 10.01 14.71
A2058 H-160 MH560477 C. michiganensis subsp. michiganensis (Cmm) tomato ID, USA 17.5 X
A4004 47 MH560481 Cmm tomato OH, USA 12.23 X
A4763 N 7388A; K075 MH560485 Cmm tomato Morocco 9.01 X
A4758 N 212; K074 MH560484 Cmm tomato China 8.86 X
A4598 Cmm038 MH560482 Cmm tomato WA, USA 10.71 X
A4690 CMM 461 MH560483 Cmm tomato Portugal 10.01 X
A2645 S47 MH560480 Cmm tomato CA, USA 10.25 X
A1746 A 518–1 MH560479 Cmm tomato HI, USA 9.32 X
A6268 70049 MH560492 Cmm tomato Unknown 16.88 X
A2041 R8 MH560493 C. michiganensis subsp. sepedonicus potato Unknown 19.08 X
A6172 ATCC33113 MH560494 C. michiganensis subsp. sepedonicus potato Canada 16.52 X
A6101 ATCCBAA-2690; ZUM3936; CFBP 8217 MH560495 C. michiganensis subsp. chiloensis tomato Chile 16.36 X
A6112 1646; P5005 MH560497 C. michiganensis subsp. capsici pepper China 11.49 X
A6113 1647; P5006 MH560498 C. michiganensis subsp. capsici pepper China 13.81 X
A6134 C55 MH560499 C. michiganensis subsp. californiensis tomato CA, USA 10.13 X
A6135 LPPA982; LMG 27667 MH560500 C. michiganensis subsp. phaseoli bean Spain 15.66 X
A1149 QR-80 MH560501 C. michiganensis subsp. insidiosus alfalfa KS, USA 16.5 X
A6109 ZUM 4260; LMG7294; ATCC33566 MH560502 C. michiganensis subsp. tessellarius wheat USA 14.8 X
A1148 QR-79; ATCC6887 – Curtobacterium flaccumfaciens pv. flaccumfaciens  bean Unknown X X
A1150 QR-81a; ATCC12975 – Rhodococcus fascians unknown USA X X
A1151 QR-81b – R. fascians unknown USA X X
A1147 QR-78; ATCC9682 – Curtobacterium flaccumfaciens pv. poinsettiae poinsettia USA X X
A6266 70002 – C. flaccumfaciens pv. poinsettiae poinsettia Unknown X X
A6267 70008 – Corynebacterium flaccumfaciens subsp. oortii tulip Unknown X X
A6272 70423 – C. flaccumfaciens subsp. oortii tulip Unknown X X
A1152 QR-82; ATCC13659 – Rathayibacter rathayi grass United Kingdom X X
A6214 DP101 MH547375 Microbacterium sp. corn IA, USA X X
A6218 DP122B MH547376 C. flaccumfaciens pv. flaccumfaciens  corn NE, USA X X
A6216 DP114B MH547381 Erwinia sp. corn TX, USA X X
A6222 DP138 MH547382 Pantoea agglomerans corn WI, USA X X
A6223 DP140 MH547379 Klebsiella sp. corn IA, USA X X
A6225 DP143 MH547388 Pantoea ananatis corn NM, USA X X
A6276 DP150B MH547383 P. agglomerans corn MO, USA X X
A6220 DP133 MH547386 P. ananatis corn IA, USA X X
A6227 DP149 MH547390 P. ananatis corn TX, USA X X
A6224 DP142 MH547377 Pseudomonas sp. corn IA, USA X X
A6230 DP162A MH547378 Pseudomonas sp. corn SD, USA X X
A6234 D36-1 – Xanthomonas axonopodis pv. dieffenbachiae anthurium HI, USA X X
A5422  CFBP2052 – Dickeya zeae corn USA X X
A5371 CC26 – Pectovacterium carotovorum aglaonema HI, USA X X
A3830 CC46 – Pseudomonas syringae pv. syringae rice South Africa X X
A6178 CC36 – P. syringae pv. tomato tomato USA X X
A3617 CC93R – Xanthomonas vesicatoria tomato South America X X

aStrains designated names from literature; ATCC: American Type Culture Collection; CFBP: Collection Française de Bactéries associées aux plantes (French Collection of Plant associated bacteria); LMG: Collection of Laboratorium voor Microbiologie en Microbiele Genetica, Belgicum; DP: strains isolated from corn leaf samples; CM: Clavibacter michiganensis specific; Cmn: C. michiganensis subsp. nebraskensis specific

baverage CT values calculated using Rotor-Gene Q Series Software (Qiagen Inc, Valencia, CA)

c strains used for corn leaf infection; identity of all C. michiganensis and non-C. michiganensis strains were confirmed using dnaA and 16S rRNA gene regions, respectively

*DNA naturally infected corn samples received from James P. Stack (Kansas State University-2017); “-”no sequencing was performed.