Table 1.
Details of the bacterial strains used in inclusivity and exclusivity panels to validate the multiplex RPA assay for specific detection of genus Clavibacter in general and C. nebraskensis.
| Strain ID | Other ID | Micro-organism | Host | Geographic origin | GenBank accesion numberc | Multiplex RPA Results | |
|---|---|---|---|---|---|---|---|
| CM | Cmn11 | ||||||
| A6203 | DP104A | Clavibacter nebraskensis | Corn | OK, USA | MH560461 | + | + |
| A6204 | DP114A | C. nebraskensis | Corn | TX, USA | MH560462 | + | + |
| A6205 | DP115 | C. nebraskensis | Corn | IA, USA | MH560463 | + | + |
| A6206b | DP117 | C. nebraskensis | Corn | NE,USA | MH560464 | + | + |
| A6207 | DP121 | C. nebraskensis | Corn | TX, USA | MH560465 | + | + |
| A6208 | DP122A | C. nebraskensis | Corn | NE, USA | MH560466 | + | + |
| A6209 | DP134 | C. nebraskensis | Corn | TX, USA | MH560467 | + | + |
| A6210b | DP137 | C. nebraskensis | Corn | TX, USA | MH560468 | + | + |
| A6211 | DP139B | C. nebraskensis | Corn | TX, USA | MH560469 | + | + |
| A6212 | DP164 | C. nebraskensis | Corn | NE, USA | MH560470 | + | + |
| A6213 | DP165c | C. nebraskensis | Corn | IA, USA | MH560471 | + | + |
| A6094b | NCPPB 2579; LMG 3698 | C. nebraskensis | Corn | NE, USA | MH560472 | + | + |
| A6095 | 20037 | C. nebraskensis | Corn | NE, USA | MH560473 | + | + |
| A6096 | 200800460 | C. nebraskensis | Corn | NE, USA | MH560474 | + | + |
| K-1a | C. nebraskensis | Corn | KA, USA | MH560475 | + | + | |
| K-2a | C. nebraskensis | Corn | KA, USA | MH560476 | + | + | |
| A2058b | H-160 | C. michiganensis | Tomato | ID, USA | MH560477 | + | − |
| A4004 | 47 | C. michiganensis | Tomato | OH, USA | MH560481 | + | − |
| A4763 | N 7388A | C. michiganensis | Tomato | Morocco | MH560485 | + | − |
| A4758b | N 212 | C. michiganensis | Tomato | China | MH560484 | + | − |
| A4598 | Cmm038 | C. michiganensis | Tomato | WA, USA | MH560482 | + | − |
| A4690 | CMM 461 | C. michiganensis | Tomato | Portugal | MH560483 | + | − |
| A2645 | S47 | C. michiganensis | Tomato | CA, USA | MH560480 | + | − |
| A1746 | A 518–1 | C. michiganensis | Tomato | HI, USA | MH560479 | + | − |
| A6262b | C222; A5747 | C. michiganensis | Tomato | OR, USA | MH560488 | + | − |
| A2041 | R8 | C. sepedonicus | Potato | Unkown | MH560493 | + | − |
| A6172 | ATCC 33113 | C. sepedonicus | Potato | Canada | MH560494 | + | − |
| A6101 | ATCCBAA-2690; ZUM3936; CFBP 8217 | C. m. spp. chiloensis | Tomato | Chile | MH560495 | + | − |
| A6112 | 1646, P5005 | C. capsici | Peper | China | MH560497 | + | − |
| A6113 | 1647, P5006 | C. capsici | Peper | China | MH560498 | + | − |
| A6134 | C55 | C. m. spp. californiensis | Tomato | CA, USA | MH560499 | + | − |
| A6135 | LPPA982/LMG 27667 | C. m. spp. phaseoli | Bean | Spain | MH560500 | + | − |
| A1149 | QR-80 | C. insidiosus | Alfalfa | KS, USA | MH560501 | + | − |
| A6109 | ZUM 4260; LMG7294; ATCC33566 | C. tessellarius | Wheat | USA | MH56502 | + | − |
| A6214 | DP101 | Microbacterium sp. | Corn | IA, USA | MH547375 | − | − |
| A1150 | ATCC 12975 | Rhodococcus fascians | Unknown | USA | MH605375 | − | − |
| A1147 | ATCC 9682 | Curtobacterium flaccumfaciens pv. poinsettiae | Poinsettia | USA | MH605380 | − | − |
| A2118 | A602.18 | Xanthomonas axonopodis pv. phaseoli | Bean | Unknown | * | − | − |
| A6187 | CC87 | Paenibacillus validus | Unknown | Unknown | * | − | − |
| A1152 | ATCC 13,659 | Rathayibacter rathayi | Orchard grass | United Kingdom | MH605382 | − | − |
| A5735 | T0012 | Microbacterium oleivorans | Tomato | Guatemala | * | ||
| A6218 | DP122B | Curtobacterium flaccumfaciens pv. flaccumfaciens | Corn | NE, USA | MH547376 | − | − |
| PL22 | GBp1A | D. dianthicola | Potato | HI, USA | MK189269 | − | − |
| A6222 | DP138 | Pantoea agglomerans | Corn | WI, USA | MH517382 | − | − |
| A6223 | DP140 | Klebsiella sp. | Corn | IA, USA | MH547379 | − | − |
| A2961 | C58 | Agrobacterium tumefaciens | Cherry | NY, USA | * | − | − |
| A3465 | 26 | Ralstonia solanacearum | Tomato | GE, USA | * | − | − |
| A5058 | A-4 | Xanthomonas campestris pv. campestris | Cabbage | GE, USA | * | − | − |
| A3453 | 256 | Ralstonia solanacearum | Potato | Costa Rica | * | − | − |
| A6230 | DP162A | Pseudomonas sp. | Corn | SD, USA | MH547378 | − | − |
| A5371 | CC26 | Pectobacterium carotovorum | Aglaonema | HI, USA | MH453528 | − | − |
| A1790 | PSS | Pseudomonas syringae pv. syringae | Rice | South Africa | * | − | − |
| A6178 | CC36 | Pseudomonas syringae pv. tomato | Tomato | GA, USA | MH605378 | − | − |
| A1702 | K618; B-111 | Xanthomonas euvesicatoria | Tomato | CA, USA | MG847407 | − | − |
+ Indicated positive amplification.
− Indicated negative amplification.
aDNA extracted from infected corn tissues; no purified strain. bStrains used to infect corn/tomato plants.
cReference number (GenBank accession numbers) are adopted from Larrea-Sarmiento et al. 2019. Most of the strains included to validate this assays were also previously used by Larrea-Sarmiento et al. 2019.
ATCC American Type Culture Collection, USA.
CFBP Collection Française de Bactéries associées aux plantes (French Collection of Plant associated bacteria),
LMG Collection of Laboratorium voor Microbiologie en Microbiele Genetica, Belgicum.
*Sequences were not reported by Larrea-Sarmiento et al.. 2019.