FIGURE 2.

OrthoMCL clustering of the predicted proteomes in R. solani AGs. (A) Heatmap showing protein conservation across all sequenced R. solani AGs and T. calospora. Each row represents one orthoMCL cluster, and color is proportional to the number of protein members shared within a given cluster from the given species (black: no member protein present; red: large number of protein members present). The hierarchical clustering (hclust; method: complete) analysis enumerates the similarities between different fungal isolates based on proteins shared by them across all orthoMCL clusters. (B) Cluster frequency. The line plot represents the number of orthoMCL clusters shared by different fungal isolates used in this study. Example, > 1,400 orthoMCL clusters are shared by 14 different fungal isolates (including positive and negative controls) used in this study. The bimodal nature of the plot represents high similarities across independent proteomes as large numbers of clusters share protein members from 13 fungal isolates. The red line represents the smoothed curves after averaging out the number of clusters. (C) Protein classification based on the orthoMCL clusters. The “core” proteins represent the sub-set of proteomes (from each R. solani AG and T. calospsora) with a conserved profile across all the isolates. Similarly, the “unique” sets represent the isolate-specific protein subset. The rest of the protein subsets make up the “Auxiliary” proteome which are conserved in a limited number of isolates. (D) Shared orthoMCL clusters. The number of orthoMCL clusters shared between any two isolates. A shared cluster means, a given orthoMCL cluster contains proteins from both the isolates.