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Comparative genomic analyses reveal functional insights into key determinants of the pathogenesis of Pectobacterium actinidiae to kiwifruit.

The Gram-negative (G-) bacterial species Pectobacterium actinidiae causes summer canker in kiwifruit plants. However, little is known about its virulence factors and the mechanisms of genetic adaptation. We aimed to identify the key determinants that control the virulence of P. actinidiae to kiwifruit by genomic and functional analyses. Within four P. actinidiae isolates, low genetic variability displayed and shared an average 98.7% and 82% in genome-level sequence similarity and coding genes. Phylogenetic analysis, based on both the bulk of single nucleotide polymorphisms (SNPs) and genomes single-copy genes, revealed that P. actinidiae strains cluster into a sole clade, whichclosly related to the clades of P. odoriferum, the pathogen of vegetable soft rot from a completely different host range. By comparison with these two clades of genomes, 746 unique core orthologs/genes were enriched in the clades of P. actinidiae, especially for the key virulence determinants involved in the biosynthesis of secretion systems (type III, III and IV), iron, flagellar and the quorum-sensing system. Our results provide insights into the pathogenomics basis underlying the genetic diversification and evolution of pathogenicity in the species of P. actinidiae.