Abstract
BackgroundThe genetic diversity in Australian populations of Xanthomonas species associated with bacterial leaf spot in tomato, capsicum and chilli were compared to worldwide bacterial populations. The aim of this study was to confirm the identities of these Australian Xanthomonas species and classify them in comparison to overseas isolates. Analysis of whole genome sequence allows for the investigation of bacterial population structure, pathogenicity and gene exchange, resulting in better management strategies and biosecurity.ResultsPhylogenetic analysis of the core genome alignments and SNP data grouped strains in distinct clades. Patterns observed in average nucleotide identity, pan genome structure, effector and carbohydrate active enzyme profiles reflected the whole genome phylogeny and highlight taxonomic issues in X. perforans and X. euvesicatoria. Circular sequences with similarity to previously characterised plasmids were identified, and plasmids of similar sizes were isolated. Potential false positive and false negative plasmid assemblies were discussed. Effector patterns that may influence virulence on host plant species were analysed in pathogenic and non-pathogenic xanthomonads.ConclusionsThe phylogeny presented here confirmed X. vesicatoria, X. arboricola, X. euvesicatoria and X. perforans and a clade of an uncharacterised Xanthomonas species shown to be genetically distinct from all other strains of this study. The taxonomic status of X. perforans and X. euvesicatoria as one species is discussed in relation to whole genome phylogeny and phenotypic traits. The patterns evident in enzyme and plasmid profiles indicate worldwide exchange of genetic material with the potential to introduce new virulence elements into local bacterial populations.
Highlights
The genetic diversity in Australian populations of Xanthomonas species associated with bacterial leaf spot in tomato, capsicum and chilli were compared to worldwide bacterial populations
Taxonomic status of bacterial leaf spot (BLS)-causing Xanthomonas species The phylogenies and homologue matrix generated in this study support the current taxonomic status of X. euvesicatoria, X. perforans and X. vesicatoria [28], confirming previous findings [4] that X. gardneri was not detected in Australian strains of this study
Our study found an Average nucleotide identity (ANI) of 98.6% between strains of X. euvesicatoria and X. perforans, supporting these findings
Summary
The genetic diversity in Australian populations of Xanthomonas species associated with bacterial leaf spot in tomato, capsicum and chilli were compared to worldwide bacterial populations. A draft genome comparison of BLS-causing X. vesicatoria, X. euvesicatoria, X. gardneri and X. perforans provided the basis for many subsequent studies using genomic data. Insights into the virulence and pathogenicity of Xanthomonas has been provided by genomic studies that have revealed much about plasmids and secretion systems that deliver effectors and host cell wall degrading enzymes [1, 5]. Other features of Xanthomonas genomes include products of bacterial secretion systems involved with host interactions such as effectors and carbohydrate active enzymes. Understanding these elements of the bacterial genome are key to understanding how genetics reflects species phylogeny and pathogenicity
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