Supplementary File S1 : Experimental evaluation an optimisation of AY-SA LAMP assays
Supplementary File S2 : Report on the results of the test performance study for
molecular detection South African aster yellows
Figure S1 : Synthetic target dsDNA standard curve data. Standard curves were performed as two and three technical repeats for LAMP and real-time PCR. A, standard curve for LAMP AY-SA_ftsH assay recorded on QuantStudio 3 Flex real-time PCR systems. B, standard curve for LAMP AY-SA_ftsH assay recorded on QuantStudio 7 Flex real-time PCR systems. C, standard curve for real-time PCR AY- SA_ftsH assay recorded on QuantStudio 3 Flex real-time PCR systems. D, standard curve for real-time PCR AY-SA_ftsH assay recorded on QuantStudio 7 Flex real-time PCR systems. One representative standard curve is shown for each instrument.
Figure S2. Non-linear modeling of the probability of detection for the AY-SA-specific LAMP (A) and real-time AY-SA-specific PCR assays (B). For both assays two parameter Weibull function fitted the best to experimental data. Log concentration, expressed as log(target dsDNA molecules/ml); dotted line, 95% probability of detection.
Table S1. List of genomes used as a negative data set input for pipeline analysis for the identification of the specific sequences using RUCS software.
The list contains 73 complete or draft genomes of phytoplasma (18 genomes) and mycoplasma (55 genomes) derived from NCBI/Genbank database.
Table S2. Nucleotide sequences of the target dsDNA (gBlock sequnces) used for experimental evaluation of LAMP assays.
Table S3. Nucleotide sequences specific to AY-SA genomes and selected for LAMP primer design based on predefined criteria.
Table S4. The list of designed LAMP assays selected for experimental evaluation. All the assays were designed on three different genomic sequences,
named Seq1, Seq3 and Seq11, specific to AY-SA phytoplasma. Best performing assay, LAMP AY-SA_ftsH, was selected for validation.
