Table 1.
Oligonucleotide sequences of real-time PCR primers and probes used in this study
| Name | Sequence (5’–3’) | Target gene or flanking region | Reference |
|---|---|---|---|
| Prophage FP1-specific primer | |||
| FP1-gp110F | GAAGTGAGACGCCAGGAAAG | Possible holin | 30 |
| FP1-gp110R | TCGTACATGCACCCCTGATA | ||
| FP1-gp235F | AAGGGGTCTAATCTACCGCC | Putative phage-related protein | 30 |
| FP1-gp235R | TTTGTATGGCTTGCCTCAAC | ||
| Prophage FP2-specific primer | |||
| FP2-gp240F | GCACGCATGGAGAGAGATTT | Putative trimeric autotransporter adhesin | 30 |
| FP2-gp240R | CCAGTCAAACCCTTTAGCCA | ||
| FP2-gp065F | AATGTTTCCAAATCCGCAAG | Possible integrase | 30 |
| FP2-gp065R | GTATCGCAAGCTCAAGCACA | ||
| Primers for both FP1 and FP2 | |||
| gp-025F | TATGAGGAGCTCTGGGGCTA | Putative phage tail fiber protein; lectin-binding | This study |
| gp-025R | TGATGTCGATGGGTTAAACG | ||
| gp-030F | CAAACTCCCGTTTCACACCT | Putative phage structural protein | This study |
| gp-030R | CGCTTTCCCGTTCTGAAATA | ||
| gp-035F | TCAAAGATGCGGTAATGCTG | Possible endolysin | This study |
| gp-035R | GGGCAGTGTTGAATGTTCCT | ||
| gp-200F | CCTCTTCCGATAACGACGAA | Putative Bro-N family phage antirepressor | This study |
| gp-200R | AGCCACCTGAGACCTTGCTA | ||
| Pro-R.O. F | CGCACGAGGTGTAGCTTATG | rep_origin in UF506 | This study |
| Pro-R.O. R | GAGGACAGCCGACGATTACT | ||
| Primers for Las | |||
| Las-R.O. F | TTACCAATGCGGATGGTTCT | Las oriC region in psy62 | This study |
| Las-R.O. R | ATCCGAATCCCTGTTGTGAT | ||
| HLBasfa | TCGAGCGCGTATGCGAATACG | 16S rDNA | 31 |
| HLBr | GCGTTATCCCGTAGAAAAAGGTAG | ||
| HLBp | bAGACGGGTGAGTAACGCGc | ||
aAdditional guanine nucleotide (bold, underlined “G”) was added to HLBas primer sequence63 based on 16S rDNA sequence in ‘Ca. Liberibacter asiaticus’ Psy62 genome and named as HLBasf
b6-FAM™ at 5’-end
cIowa Black FQ at 3’-end