Table 6. Results from species-specific TaqMan real-time PCR assays using environmental samples.
| Isolate | Expected result a | Genus gene copy number b | Specific TaqMan assay Ct value (± SD) | Target gene region copy number c |
|---|---|---|---|---|
| Ceratocystis laricicola | + | |||
| CEM5 | + | 712 | 29.3 (0.1) | 121 |
| CEM8 | + | 1,701 | 29.7 (0.1) | 97 |
| CEM10 | + | 542 | 29.4 (0.2) | 117 |
| CEM11 | + | 1,621 | 27.9 (0.1) | 284 |
| CEM13 | + | 1,638 | 28.0 (0.2) | 271 |
| CEM19 | + | 2,227 | 29.4 (0.1) | 111 |
| CEM25 | + | 964 | 28.3 (0.1) | 220 |
| TYP1 | - | 910 | None | - |
| TYP2 | - | 818 | None | - |
| TYP3 | - | 751 | None | - |
| TYP11 | - | 555 | None | - |
| TYP16 | - | 373 | None | - |
| TYP17 | - | 613 | None | - |
| TYP19 | - | 176 | None | - |
| Ceratocystis polonica | ||||
| TYP1 | + | 910 | 34.7 (0.4) | 4 |
| TYP2 | + | 818 | 35.0 (0.5) | 4 |
| TYP3 | + | 751 | 35.3 (0.3) | 3 |
| TYP11 | + | 555 | 34.6 (0.1) | 5 |
| TYP16 | + | 373 | 31.8 (ND) d | 28 |
| TYP17 | + | 613 | 34.6 (0.1) | 5 |
| TYP19 | + | 176 | 36.1 (ND) d | 2 |
| CEM5 | - | 712 | None | - |
| CEM8 | - | 1,701 | None | - |
| CEM10 | - | 542 | None | - |
| CEM11 | - | 1,621 | None | - |
| CEM13 | - | 1,638 | None | - |
| CEM19 | - | 2,227 | None | - |
| CEM25 | - | 964 | None | - |
| Ceratocystis fagacearum | ||||
| SAP-1 | + | 148 | 36.8 (1.9) | 7 |
| SAP-2 | + | 5 | 37.4 (0.9) | 5 |
| SAP-3 | + | 91 | 36.5 (0.3) | 9 |
| SAP-4 | + | 54 | 39.1 (ND) d | 2 |
| SAP-5 | + | 2 | 37.1 (0.6) | 6 |
| SAP-6 | + | 1 | 38.1 (0.3) | 3 |
| CS1 | + | 4,626 | 26.5 (0.2) | 4,326 |
| CS2 | + | 3,467 | 25.8 (0.2) | 6,805 |
| CS3 | + | 2,593 | 27.5 (0.0) | 2,409 |
| CS4 | + | 3,342 | 27.4 (0.1) | 2,518 |
| CS5 | + | 4,872 | 27.3 (0.0) | 2,682 |
| CS6 | + | 2,261 | 28.1 (0.1) | 1,694 |
| CS7 | + | 3,293 | 25.6 (0.1) | 8,041 |
| CS8 | + | 2,677 | 24.7 (0.3) | 12,421 |
| CS9 | + | 1,334 | 24.5 (0.1) | 15,351 |
| EC1 | + | 7,081 | 27.0 (0.1) | 3,195 |
| EC2 | + | 8,918 | 26.9 (0.0) | 3,478 |
| EC3 | + | 13,140 | 28.3 (0.1) | 1,476 |
| GS1 | + | 6,724 | 25.8 (0.1) | 6,794 |
| GS2 | + | 2,838 | 27.5 (0.1) | 2,361 |
| GS3 | + | 3,313 | 27.2 (0.1) | 2,940 |
| GS4 | + | 6,087 | 27.2 (0.0) | 2,902 |
| GS5 | + | 41,882 | 22.7 (0.1) | 48,405 |
| Fusarium circinatum | ||||
| SB1a | + | 1 | None | - |
| SB3a | + | 6 | 34.0 (0.8) | 11 |
| SB4a | + | 300,332 | 18.1 (0.0) | 170,090 |
| 71-1A | + | 1 | None | - |
| 77-1A | + | 45 | 34.5 (0.1) | 8 |
| 124a | + | 1,936 | 28.0 (0.1) | 434 |
| 819A | + | 8 | 35.9 (ND) d | 4 |
| 860B | + | 262 | 28.4 (0.1) | 332 |
| MP1Ab | + | 6,096 | 24.0 (0.1) | 4,944 |
| MP1Ba | + | 737 | 27.0 (0.3) | 771 |
| MP2A | + | 200 | 30.1 (0.2) | 118 |
| MP3a | + | 700 | 27.0 (0.1) | 795 |
| MP4Ba | + | 346 | 27.9 (0.4) | 455 |
| MP5Aa | + | 49 | 31.2 (0.0) | 63 |
| MP5Ba | + | 35 | 31.6 (0.9) | 48 |
| MP6a | + | 1,399 | 26.5 (0.1) | 1,087 |
| MP7a | + | 551 | 27.5 (0.0) | 588 |
| S10-14 | + | 1 | 34.8 (ND) d | 7 |
| S50-13 | + | 1 | 36.0 (ND) d | 3 |
| S100-15 | + | 5 | 32.7 (0.4) | 24 |
| Geosmithia morbida | ||||
| JN2 Poz | + | 4 | 31.7 (0.3) | 29 |
| JN3 Neg | - | 23 | None | - |
| WTB-G3-1 | + | 1 | 34.5 (0.3) | 5 |
| WTB-G3-2 | + | 4 | 34.5 (0.2) | 5 |
| WTB-G3-3 | + | 1 | 35.7 (1.0) | 2 |
| WTB-G3-4 | + | 3 | 34.2 (0.2) | 6 |
| WTB-G3-5 | + | 1 | 34.9 (0.4) | 4 |
| WTB-G3-6 | + | 13 | 31.7 (0.1) | 30 |
| WTB-G3-7 | + | 3 | 34.7 (0.2) | 4 |
| WTB-G3-8 | + | 11 | 32.5 (0.1) | 17 |
| WTB-G3-9 | + | 2 | 35.2 (0.7) | 3 |
| WTB-G3-10 | + | 6 | 33.2 (0.5) | 11 |
| WTB-G8-1 | + | 3 | 34.3 (0.2) | 5 |
| WTB-G8-2 | + | 3 | 34.3 (0.0) | 5 |
| WTB-G8-3 | + | 2 | 34.8 (0.4) | 4 |
| WTB-G8-4 | + | 1 | 36.7 (0.7) | 1 |
| WTB-G8-5 | + | 1 | 36.1 (0.4) | 2 |
| WTB-G8-6 | + | 0 | 37.4 (0.8) | 1 |
| WTB-G8-7 | + | 1 | 35.7 (0.0) | 2 |
| WTB-G8-8 | + | 0 | 36.8 (0.8) | 1 |
| WTB-G8-9 | + | 0 | 37.8 (ND) d | 1 |
| WTB-G8-10 | + | 2 | 34.0 (0.1) | 7 |
| Gremmeniella abietina (EU race) | ||||
| 64667 | - | 7,370 | None | - |
| 64668 | - | 5,509 | None | - |
| 64672 | - | 1,820 | None | - |
| 64673 | - | 9,569 | None | - |
| 65097 | + | 5912 | 25.4 (0.3) | 1,608 |
| 65171 | + | 65,081 | 21.9 (0.2) | 19,176 |
| 65181 | - | 916 | None | - |
| 65539 | - | 26,396 | None | - |
| 67161 | + | 16,236 | 24.1 (0.0) | 4,139 |
| Rosellinia necatrix | ||||
| A | + | 15,891 | 24.6 (0.1) | 340 |
| B | + | 2,064 | 25.1 (0.1) | 250 |
| D | + | 5,842 | 28.8 (0.0) | 25 |
| E | + | 3,974 | 26.9 (0.1) | 84 |
| H | + | 24,804 | 25.9 (0.0) | 153 |
| I | + | 3,091 | 25.4 (0.2) | 211 |
| Sclerotinia pseudotuberosa | ||||
| 1C | + | 6,492,200 | 21.3 (0.1) | 23,180 |
| 2C | + | 5,530,494 | 21.6 (0.1) | 18,600 |
| Phytophthora ramorum | ||||
| 16883 | + | 12,377 | 33.6 (0.2) | < 1 |
| 16885 | + | 17,646 | 33.2 (0.2) | 3 |
| 17085 | + | 3,883 | 39.1 (0.2) | <1 |
| 17385 | + | 10,515 | 35.8 (0.1) | 1 |
| 17358 | + | 10,131 | 37.4 (0.0) | < 1 |
| 07-Qr3-2i | + | 10 | None | - |
| 07-Ab3-1i | + | 4 | 34.2 (0.3) | 2 |
| 07-As2-4i | + | 44 | 38.3 (0.7) | < 1 |
| 07-Ll1-3i | + | 15 | 34.6 (0.2) | 1 |
| 07-Fa3-1i | + | 686 | 28.2 (0.1) | 63 |
| 07-Ba1-2i | + | 2,254 | 26.5 (0.1) | 170 |
| 07-Rho1-4i | + | 2,743 | 26.0 (0.4) | 241 |
| 07-Rho1-2c | - | 0 | None | - |
| 02045 | - | 0 | None | - |
| 19347 | - | 9 | None | - |
| 20181 | - | 263 | None | - |
| 20644 | - | 10 | None | - |
| 20816 | - | 758 | None | - |
| Phytophthora kernoviae | ||||
| 16833 | + | 7,911 | 30.5 (0.4) | 570 |
| 16876 | + | 983 | 31.7 (0.2) | 292 |
| 17072 | + | 76 | 35.0 (0.4) | 47 |
| 02045 | - | 0 | None | - |
| 19347 | - | 9 | None | - |
| 20644 | - | 10 | None | - |
a According to the environmental samples’ provider.
b Calculated with the results obtained from a SYBRGreen real-time PCR reaction.
c Values obtained by plotting Ct values from the species-specific TaqMan assay into the standard curve-derived equation (Fig 2).
d ND: one of the two replicates did not amplify.