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Fig. 2 | BMC Biology

Fig. 2

From: MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens

Fig. 2

The sequences of 242 highly polymorphic Pst genes are sufficient to reconstruct the topology of the global phylogeny generated from full transcriptome and genome sequencing. a Ordered distribution of average SNP content per gene across the 301 Pst global isolates. To determine the minimum number of gene sequences required to accurately reconstruct the global phylogeny, the 1690 genes identified as polymorphic (SNPs/kb ≥ 0.001) between Pst isolates were ordered according to number of polymorphic sites across the 301 global Pst isolates. b The 242 polymorphic genes selected were not biased in their selection by a high degree of divergence from the reference race PST-130 for any particular group of individuals. Box plots represent the total number of SNPs across these 242 genes for Pst isolates belonging to each of the five major genetic groups identified through DAPC analysis. Bar represents median value, box signifies the upper (Q3) and lower (Q1) quartiles, data falling outside the Q1–Q3 range are plotted as outliers. c The 242 genes selected could be used successfully to reconstruct the global phylogeny and assign Pst isolates to the 14 previously defined groups (numbers in circles). Phylogenetic analysis was performed using sequence data for the 242 genes from the 301 global Pst isolates using a maximum-likelihood model and 100 bootstraps. Bootstrap values are provided in Additional file 7

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