Xanthomonas campestris pv. musacearum NCPPB4433 Genome Sequencing

Although classified as a member of the species Xanthomonas campestris, we recently showed that Xcm is more properly considered to be derived from the species Xanthomonas vasicola. We previously generated complete genome sequences for a single isolate of Xcm from banana in Uganda and for a single isolate of X. vasicola pathovar vasculorum (Xvv) that is non-pathogenic on banana and was isolated from sugarcane in South Africa. These two isolates share identical gyrase B DNA sequences. Differences between these two genome sequences revealed several candidate genes that might play a role in adaptation to the banana host. These may also be useful tools in identifying genes for deployment of disease resistance. Specifically, these included homologues of effectors secreted and translocated by the type III secretion system (T3SS). T3SS effectors have previously been shown to contribute to host-specificity acting as virulence and/or avirulence factors [refs]. Previous work showed that Xcm is a highly monomorphic pathogen and no specific genetic differences have yet been detected among different isolates using traditional typing and diagnostic methods . Affordable complete genome sequencing now makes it feasible to discover previously hidden genetic diversity among isolates of a monomorphic pathogen, though this approach has rarely been applied to phytopathogens as yet. Here we use genome-wide sequence data 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 suggests the presence of at least two major sub-lineages of the pathogen; Xcm isolates from Uganda, Kenya, Tanzania and Burundi are genetically distinct from isolates collected in Ethiopia, DR Congo and Rwanda, suggesting that the current outbreaks of BXW on Musa species in the region have more than one origin.