Fig. 4

Characterization of genes showing gain/loss and excess of nonsynonymous substitutions. a-c The pie charts indicate the number of proteins whose domains were detected more than once or only once in the genome in four categories. The high percentage of genes experiencing loss (a) and with outlier values of dN/dS when dN/dS = 99 was included (b) or excluded (c) encodes proteins whose domains are present in multiple copies in each genome. d The percentage of shared domains of proteins whose genes showing presence/absence polymorphisms between two host-specific subgroups. e-f The percentage of shared domains of proteins whose genes showing outlier values of dN/dS between two host-specific subgroups when dN/dS = 99 was included (e) or excluded (f). The numbers in (d-f) are corresponding to the number of pfam domain. The values in (a-f) are shown when Z-1 gene model was used