Additional file 1 of A portable, nanopore-based genotyping platform for near real-time detection of Puccinia graminis f. sp. tritici lineages and fungicide sensitivity

Additional file 1: Tables S1-S10. Microsoft Excel Workbook containing 10 worksheets. Table S1: Description of Pgt isolates analysed in this study. Table S2: Percentage of reads aligned to the Pgt reference genome assembly CRL 75-36-700-3. Table S3: Amplification of polymorphic genes in Puccinia striiformis f. sp. tritici (Pst) from Pst-infected wheat field samples. Table S4: The 1,611 Pgt genes selected between 1 and 2 kb in length that had a minimum of 0.025 SNPs/bp variation between the 86 Pgt isolates analysed. Table S5: Pgt-infected wheat field samples collected in Kenya and Ethiopia and analysed using the Pgt MARPLE diagnostics platform. Table S6: Non-synonymous mutations previously reported in the fungicide target genes (Cyp51, SdhA, SdhB, SdhC and SdhD) from various fungal plant pathogens. Table S7: Location of fungicide target genes in the Pgt21-0 reference assembly. Table S8: Primer pairs and pooling strategy for the 276 Pgt genes included in the MARPLE diagnostics platform. Table S9: Annotation of the 276 polymorphic Pgt genes included in the MARPLE diagnostics platform. Table S10: A total of 39 of the 276 polymorphic Pgt genes encoded predicted secreted proteins. Table S11: Details of the known pathotypes of 16 additional Pgt isolates that had previously been typed to 9 major Pgt race groups, termed Clades I, II, III, IV, VI-A, VI-B, VI-C, VII, IX.