TABLE 1.
Chrysanthemum yellows phytoplasma genes selected for gene expression analysis and their function and product localization within the phytoplasma cell compartment, qPCR primer sequences and concentration in the reaction mix, amplicon melting temperature, and qPCR parametersa
| Product category and target gene | Gene product | Product localization | Primer: sequence (reference) | Primer concn (nM) (primer category) | Melting temp (°C) | R2 | E (%) |
|---|---|---|---|---|---|---|---|
| Immunodominant membrane proteins | |||||||
| amp | Antigenic membrane protein | Membrane | Amp64: GCTTTAATGTTTGTTGGCGTTC (37) | 100 | 82.5 | 0.993 | 78.7 |
| CY02-101Rev: AGCTTTTCCAGCATCACCAT | 300 | ||||||
| imp | Immunodominant membrane protein | Membrane | CY06-376Fw: ATTCCAAACTTGCCAGCATT | 300 | 78.5 | 1.000 | 96.0 |
| CY06-376Rev: TCTTGGAGGTTTTTGGCATT | 100 | ||||||
| Generic transporters | |||||||
| mscL | Mechanosensitive channel of large conductance | Membrane | CY05-67Fw: ACTGGGGCTTTAAAAGATTTG | 200 | 77.5 | 0.993 | 75.3 |
| CY05-67Rev: CCTTTTGCAAAGGATTTTTCC | 200 | ||||||
| mdlB | Multidrug transporter | Membrane | CY04-67Fw: CGCAAATGCCTTTTCAAACT | 200 | 81.5 | 0.998 | 83.5 |
| CY04-67Rev: AAGGCGAGGAATAAGCCCTA | 200 | ||||||
| oppC | Oligopeptide transporter | Membrane | CY02-378Fw: CCAAGATGCCATTTCTAGCC | 200 | 80.0 | 0.996 | 84.3 |
| CY02-378Rev: ATTCCGCCTGAAAGTTGATG | 200 | ||||||
| ftsY | SecY translocase component | Membrane | CY03-2292Fw: TGAAGGCATCGAACTTGCTA | 100 | 81.5 | 0.999 | 83.3 |
| CY03-2292Rev: GCTCCTGAAAGTGGAGTTGC | 300 | ||||||
| Specific transporters | |||||||
| artI | Arginine transporter | Membrane | CYartIFw: AATTCCTGTAGCTGCCCAAG | 200 | 80.0 | 1.000 | 88.1 |
| CYartIRev: ATGAGCGGCTTCAATTTGTC | 200 | ||||||
| zntA | Cation transporter | Membrane | CY036-368Fw: GACAAACAACCAGGCGATTT | 100 | 83.5 | 0.997 | 81.5 |
| CY036-368Rev: CTGCAAGACCAAGGACAACA | 300 | ||||||
| Secreted proteins | |||||||
| sap54 | Symptom effector | Secreted | CY01-1720Fw: TCAACAAGTAATGGGGATGAA | 200 | 76.5 | 0.999 | 90.5 |
| CY01-1720Rev: AATTGTTGTATTTCGCTTTCTGT | 200 | ||||||
| sap67 | Unknown | Secreted | CY01-420Fw: TCAAGTGATGGCAATGGGTA | 100 | 78.0 | 0.992 | 78.8 |
| CY01-420Rev1: TTGTATAGAACTTTCTGGTTGTTCAGA | 300 | ||||||
| sap68 | Unknown | Secreted | CY03-1700Fw: ATGGCAATGAATAACGGTCA | 200 | 79.0 | 0.999 | 88.5 |
| CY03-1700Rev: TTGTTGAGCAGCGATACGAC | 200 | ||||||
| tengu | Symptom effector | Secreted | CY04-87Fw1: ATTTGCTGGCTTTTGGGCTA | 200 | |||
| CY04-87Rev1: TTTCAATTAGAGTTATCACGTTTTCAA | 200 | 77.5 | 0.999 | 74.8 | |||
| General metabolism | |||||||
| pgsA | Phosphatidylglycerol synthase | Cytoplasm | CY06-96Fw: TCGTTTGTCTGCTACGCAAG | 200 | 81.0 | 0.996 | 84.6 |
| CY06-96Rev: AAAAGGCAAATGATGGCAAC | 200 | ||||||
| rpsU | rpsU RNA ribosomal subunit | Cytoplasm | CY08-364Fw: GGAGAAACTATCGAAGAAACGCTAC | 200 | 81.5 | 0.995 | 86.0 |
| CY08-364Rev: TTAACGCTTTTTACTACGCATATTTT | 200 |
a
R2, correlation coefficient; E %, reaction efficiency.