The bacterium Xanthomonas campestris pathovar musacearum (Xcm) is the
causal agent of banana Xanthomonas wilt (BXW). This disease has devastated economies
based on banana and plantain crops (Musa species) in East Africa. Here we use genome-wide
sequencing to discover a set of single-nucleotide polymorphisms (SNPs) among East
African isolates of Xcm. These SNPs have potential as molecular markers for phylogeographic
studies of the epidemiology and spread of the pathogen. Our analysis reveals two major
sub-lineages of the pathogen, suggesting that the current outbreaks of BXW on Musa
species in the region may have more than one introductory event, perhaps from Ethiopia.
Also, based on comparisons of genome-wide sequence data from multiple isolates of Xcm
and multiple strains of X. vasicola pathovar vasculorum, we identify genes specific to Xcm
that could be used to specifically detect Xcm by PCR-based methods.