Table 2.
Primers used in this study.
| Name | Isolate | Description | Sequence | Publication |
|---|---|---|---|---|
| GSP_F | All | Forward gene specific primer UMI PCR1 | CAAGCAGAAGACGGCATACGAGAT NNNYRNNNYRNNNYRNNN GCTCGCGTTGGTTGTAGC |
Gene specific primer—this study UMI and UVP – Karst et al. 2021 |
| GSP_R | All | Reverse gene specific primer UMI PCR1 | AATGATACGGCGACCACCGAGATC NNNYRNNNTRNNNYRNNN TTACCGCCTCTCCCAGCA |
Gene specific primer—this study UMI and UVP – Karst et al. 2021 |
| UVP_F | All | Forward universal primer UMI PCR2 | CAAGCAGAAGACGGCATACGAGAT | Karst et al. 2021 |
| UVP_R | All | Reverse universal primer UMI PCR2 | AATGATACGGCGACCACCGAGATC | Karst et al. 2021 |
| Ptt_R1ID1_F3 | KO103 | Forward primer Ptt species identification | GACGCGGCTAATGTCGTAA | Knight et al. 2023 |
| Ptt_R1ID1_B3_R | Reverse primer Ptt species identification | GGCGGTAACAGCACCAAG | Knight et al. 2023 | |
| Ptt_R1ID1_P | Probe Ptt species identification | AATCGGCGGACCGTCAGGAT | Knight et al. 2023 | |
| Ptm_r5ID12_F3.2 | 18FRG003 17FRG178 16FRG073 19FRG001 18FRG195 | Forward primer Ptm species identification | GTTGGCTGACTTGTGTAGACAC | Knight et al. 2023 |
| Ptm_r5ID12_B3_R | Reverse primer Ptm species identification | AAACGCCCTTTAGCAGTCTT | Knight et al. 2023 | |
| Ptm_r5ID12_P | Probe Ptm species identification | CGCTTGCGCGCATGTTCATT | Knight et al. 2023 | |
| PtTi-1_F | 16FRG073 | Forward primer insertion at –74 bp in Cyp51A promoter | AGAACTGTGTCCAAAAGTAGAGTGTC | Knight et al. 2023 |
|
Pt_CYP51A_ promoter_R |
Reverse primer insertion at –74, -46, -75, -66 and -90 bp in Cyp51A promoter | GGAGAGATGGGCGTAGAACA | Knight et al. 2023 | |
| PtTi-1_P | Probe insertion at –74 bp in Cyp51A promoter | TGTCCTACATCCGACATAGAGAACCATTTC | Knight et al. 2023 | |
| PtTi-2_F | 17FRG089 | Forward primer insertion at –46 bp in Cyp51A promoter | TCATCCTATCGACTTGCTTTATGTC | Knight et al. 2023 |
| PtTi-2_P | Probe insertion at –46 bp in Cyp51A promoter | TACCTCTGTCCTACATCCGACACTTTACTG | Knight et al. 2023 | |
| PtTi-3_F | 17FRG178 | Forward primer insertion at –75 bp in Cyp51A promoter | CTAAGAACTGTGTCCAAAAGTAGATGTC | Knight et al. 2023 |
| PtTi-3_P | Probe insertion at –75 bp in Cyp51A promoter | TGTCCTACATCTGACAGTAGAGAACCATTTC | Knight et al. 2023 | |
| PtTi-4_F | 18FRG003 | Forward primer insertion at –46 bp in Cyp51A promoter | TCCAAAAGTAGAGAACCATTTTGTC | Knight et al. 2023 |
| PtTi-4_P | Probe insertion at –66 bp in Cyp51A promoter | TCCTACATCCGACACATTTCACCCTAT | Knight et al. 2023 | |
| PtTi-5_F | 19FRG001 | Forward primer insertion at –90 bp in Cyp51A promoter | ACCCTGACGCTAAGAACTTGTC | Knight et al. 2023 |
| PtTi-5_P | Probe insertion at –90 bp in Cyp51A promoter | TCCTACATCTGACAGAACTGTGTCCAAA | Knight et al. 2023 | |
|
CYP51_mm2L_ L489-1_F |
KO103-A1 17FRG089 Field samples |
Forward primer a1467 (L489) in Cyp51A | GTACCGACTATAGCACCAAGTT + A | Knight et al. 2023 |
|
CYP51A1_ F-L489_R |
Reverse primer a1467/c1465 (L489) in Cyp51A | GCCTCTCCCAGCAAATCT | Knight et al. 2023 | |
|
CYP51A1_mm1_ L489-1_P |
Probe a1467 (L489) in Cyp51A | CTCTAGGGGGCGCGA + TAAC | Knight et al. 2023 | |
|
CYP51_mm2L_ L489-3_F |
18FRG195 | Forward primer c1465 (L489) in Cyp51A | GTACCGACTATAGCACAATG + C | Knight et al. 2023 |
|
CYP51A1_mm1_ L489-3_P |
Probe c1465 (L489) in Cyp51A | CTAGGGGGCGCGAGA + GCAT | Knight et al. 2023 | |
| CYP51_F489_mm2L_F | Field samples | Forward primer c1467 (F489) in Cyp51A | GTACCGACTATAGCACCAAGTT + C | Knight et al. 2023 |
| CYP51_F489_mm1_P | Field samples | Probe c1467 (F489) in Cyp51A | GCCTCTCCCAGCAAATCT | Knight et al. 2023 |