Comparative genomics of strains of varying virulence of the Gram-positive bacterial pathogen of maize, Clavibacter nebraskensis

Background Clavibacter nebraskensis ( Cn ) is a Gram-positive bacterial plant pathogen that infects the vascular tissue of maize, causing Goss’s Wilt and Leaf Blight. Detection of highly virulent strains since the mid-2000s suggests that genetic divergence has contributed to the re-emergence of the disease following its effective management and subsequent disappearance in the 1980s. However, few genomic resources exist for this pathogen, and little is known about genomic variation in the species. Our study aimed to characterize genomic diversity across a set of differentially virulent strains isolated from both historic epidemics and recent outbreaks. Results We sequenced 17 Cn strains of varying virulence isolated from epidemics spanning their earliest detection to subsequent outbreaks in the mid-2010s across various US states and Manitoba, Canada. Contrary to previous studies, we found no strong population structure associated with geographic origin or year of isolation based on haplotype analysis. We detected five heterogeneous plasmids in strains CDK032, CDK039, CDK044, CDK045, and CDK046, whereas to date, only one plasmid has been sequenced in a single Cn strain. Genomic islands were detected in all strains, and the putative virulence gene celA was found to be encoded in one such island. Secreted CAZymes, hypothesized to be involved in pathogenicity, are well conserved across all Cn genomes, indicating that allelic or expression diversity, and not gene copy number, might be implicated in virulence diversity. Importantly, we identified deletions in a secreted cellulase within the linker peptide region between the carbohydrate-binding domain and the cellulase domain that have not been reported in the literature previously. Conclusion Our analyses provide insight into genomic diversity within the species, revealing five novel plasmids and genomic islands harboring CAzymes, including the celA gene. Genes encoding cell wall degrading enzymes are well-conserved across strains of all virulence phenotypes. Deletions within a secreted cellulase not previously reported have been described for future functional analysis.