Fig 6. Hierarchical clustering of Pseudocercospora musae, Pseudocercospora eumusae, and Pseudocercospora fijiensis based on copy number changes in different groups of KOG gene families.

Hierarchical clustering of the species based on (A) the KOG distribution profile (i.e. the number of genes assigned to each category of KOG) of their entire proteomes, (B) the KOG distribution profiles of the 575 core gene families with copy number variation (CNV), and (C) a subset of 190 core gene families with CNV that are predicted to be involved in metabolism based on KOG assignments. The reliability of the clustering patterns was assessed by bootstrap tests (1000 replicates) and obtained bootstrap values are indicated next to their corresponding branching nodes. While clustering of the species based on the KOG distribution profiles of the entire proteomes follows a pattern that is respective of the their phylogenetic relations (Fig 2), clustering of the species based on the KOG profiles of core gene families with CNV or their subset of gene families involved in metabolism, indicates a swapped topology in which P. eumusae is clustered together with P. fijiensis suggesting that these two species share a more similar pattern of gene family expansions and contractions.