Table 1.
List of primers and probes used for detection of Ca. P. prunorum, endogenous control for host plant (Plants) and PPV.
Fig 1.
Ct value comparison of CTAB and spot extraction of 37 positive samples after RT-qPCR.
The first chart represent ESFY 16S Ct values while the second chart shows DiSTA 18S (plant control) Ct values. On average, the spot method showed a 5.16 (p value = 2.8E-12) and 5.58 (p value = 1.3E-27) higher Ct values for ESFY 16S and DiSTA 18S assay, respectively.
Fig 2.
RT-qPCR relative quantification of ESFY on 9 infected samples (1 to 9) and 1 healthy sample (10) extracted with the spot method.
Serial dilutions of crude sap were used to calculate the relative quantification using the relative standard curve method. Results from each sample were normalized to the highest value (from sample no. 6) and expressed as percentages.
Fig 3.
DNA and RNA contribution to detection.
Ct value comparison of DNA+RNA (RT-qPCR), DNA alone (qPCR) and RNA alone (RT-qPCR after DNase treatment) on 8 ESFY-positive samples extracted by either CTAB (a, b) or the spot method (c, d). ESFY 16S assay (a, c) detects ‘Ca. P. prunorum’ while DiSTA 18S detects the host plant. Samples were: 1 (plum), 2 (apricot), 3 (apricot), 4 (apricot), 5 (plum), 6 (apricot), 7 (plum) and 8 (peach).
Table 2.
Averages of the ΔCt values calculated from the DNase treatment experiment (Fig 3).
ΔCt values represent the differences between average Ct values of each group, as indicated in the table header: DNA+RNA (RT-qPCR), DNA alone (qPCR) or RNA alone (RT-qPCR after DNase treatment). Analyses have been performed on 8 ESFY-positive samples extracted by either CTAB or the spot method. ESFY 16S assay detects ‘Ca. P. prunorum’ while DiSTA 18S detects the host plant. Negative values indicate a gain of Ct value while positive values indicate a delay on Ct values. Student’s t-test was used to determine the statistical significance among the three groups.
Table 3.
Ct values of two samples at time 0 or after 2 months and 4 months of storage at RT or 4°C.