TABLE 1.
Primers and probes used in this study
| Name | Sequence (5′ to 3′) | Purpose |
|---|---|---|
| HindIII-virus construction fragment 1F′ | AAGCTTAGATTTGCATTTAAATTATGA | CLCuMuV infectious clone |
| XbaI-virus construction fragment 1R′ | TCTAGACAGGATCTTTCAGGAGC | |
| XbaI-virus construction fragment 2F′ | TCTAGATTTGCATTTAAATTATGAAATTG | |
| KpnI-virus construction fragment 2R′ | GGTACCAATCAAAGTACAGCACA | |
| V1 ATG-ACG mutant F′ | CGTAATTACGTCGAAGCGAGCT | CLCuMuV ΔV1 |
| V1 ATG-ACG mutant R′ | AGCTCGCTTCGACGTAATTAC | |
| V2L76S mutation F′ | GGCGTCTGAATCTCGGC | CLCuMuV V2L76S |
| V2L76S mutation R′ | GCTGCCGAGATTCAGACG | |
| Lic1 + AGO4-2 F′ | CGACGACAAGACCGTCACCATGGCTGAAGAAGATAAGAATGG | pcLUC-NbAGO4-2, pMYC-NbAGO4-2, pAD-NbAGO4-2, pBD-NbAGO4-2, pMYC-NbAGO4-1, cLUC-NbAGO4-1 |
| Lic2 + AGO4-2 R′ | GAGGAGAAGAGCCGTCGTTAACAAAAGAACATGGAACTGG | |
| Lic1 + AGO4-1 F′ | CGACGACAAGACCGTCACCATGGCTGAAGAAGACAATGGT | |
| Lic2 + AGO4-1 R′ | GAGGAGAAGAGCCGTCGCTAACAGAAGAACATGGAACTAGAAA | |
| Lic1 + AGO4 PAZ F′ | CGACGACAAGACCGTCACCATGGGGCCTGTTGTGG | pMYC-NbAGO4 PAZ domain, pAD-NbAGO4 PAZ domain, pAD-NbAGO4 PIWI domain |
| Lic2 + AGO4 PAZ R′ | GAGGAGAAGAGCCGTCGCTATGACACCAAATTGCATAGCTC | |
| Lic1 + AGO4 PIWI F′ | CGACGACAAGACCGTCACCATGCTGCTTCGTGCCTG | |
| Lic2 + AGO4 PIWI R′ | GAGGAGAAGAGCCGTCGCTTCATCCACTGTCCCATCT | |
| Lic1 + V2 F′ | CGACGACAAGACCGTCACCATGTGGGATCCATTGTTAAACGAAT | pGFP-V2, pnLUC-V2, pGST-V2, PVX-V2, pGFP-V2L76S, pnLUC-V2L76S, pGST-V2L76S, PVX-V2L76S |
| Lic2 + V2 with stop codon R′ | GAGGAGAAGAGCCGTCGTCACAACCCTTTGGAACATCCGGACT | |
| Lic1 + V1 F′ | CGACGACAAGACCGTCACCATGTCGAAGCGAGCTGC | PVX-V1, PVX-V1F23L |
| Lic2 + V1 with stop codon R′ | GAGGAGAAGAGCCGTCGTCAATTCGTTACAGAGTCATAAAAATATAT | |
| V1F23L mutation F′ | GGCGTCTGAATCTCGGC | PVX-V1F23L |
| V1F23L mutation R′ | GCTGCCGAGATTCAGACG | |
| Lic1 + AGO4 VIGS F′ | CGACGACAAGACCGTCACCTCGTTGGAGCTATGCATTG | pTRV-NbAGO4 |
| Lic2 + AGO4 VIGS R′ | GAGGAGAAGAGCCGTCGTGTTTGAAGAAGTCCAGTCAAA | |
| 35S BIS F′ | AAGGCAAGTAATAGAGATTGGAGT | 35S promoter bisulfate sequence |
| 35S BIS R′ | CACCTTCCTTTTCCACTATCTTCACAAT | |
| CLCuMuV IR BIS F′ | TGATTTTGGTTAATTGGAGATAA | CLCuMuV IR bisulfate sequence |
| CLCuMuV IR BIS R′ | TAAATTTAAAACTTAATACACAA | |
| Tnt1 BIS F′ | GTGATGGGGTTTAGTTTTTTTAAAT | Tnt1 bisulfate sequence |
| Tnt1 BIS R′ | TTACTCTTTATTTTCTCTCTTTTATTAATA | |
| TE1 BIS F′ | GAGGTTGTTTATTTTGGAGATTTGA | TE1 bisulfate sequence |
| TE1 BIS R′ | TATTTAACAACCTACCCACCCTAAA | |
| qeIF4a F′ | CCCAGAGAGGAAATACAGTG | RT-qPCR and qPCR |
| qeIF4a R′ | CAATAGACGGACCAGATTCG | |
| qCLCuMuV C3 F′ | GGCGCATATATCTGGGAGGT | qPCR |
| qCLCuMuV C3 R′ | GTCTGAGGGTGTAAGGTCGT | |
| qGFP F′ | ATGGGCACAAATTTTCTGTCA | RT-qPCR |
| qGFP R′ | TCCTCTCCTGCACGTATCC | |
| qNbAGO1 F′ | TGCGGAAGAAGAGAACTGATGT | |
| qNbAGO1 R′ | CACGGCCACCATGTCCTC | |
| qNbAGO2 F′ | AATCGTGGTGGTGGTGGTG | |
| qNbAGO2 R′ | GGCCTTGCTCCTGTTCGTAT | |
| qNbAGO4-2 F′ | GCTGTCTACTTGTTCGTCAGTC | |
| qNbAGO4-2 R′ | GCTATCAGAAAGTCCACAACAGG | |
| qNbAGO4-1 F′ | GCTTTGCGAGGTCAAGAGTC | |
| qNbAGO4-1 R′ | CACCTCCAACTTCCGCAAAA | |
| 32P-probe F′ | ATGTGGGATCCATTGTTAAAC | Viral Southern blot label |
| 32P-probe R′ | ACATGGGCCTTCACAACC | |