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The gram‐positive bacterial species  Clavibacter capsici  causes necrosis and canker in pepper plants. Genomic and functional analyses of  C. capsici  type strain PF008 have shown that multiple virulence genes exist in its two plasmids. We aimed to identify the key determinants that control the virulence of  C. capsici . Pepper leaves inoculated with 54 natural isolates exhibited significant variation in the necrosis. Six isolates showed very low virulence, but their population titres in plants were not significantly different from those of the highly virulent isolates. All six isolates lacked the pCM1 Cc  plasmid that carries  chpG , which has been shown to be required for virulence and encodes a putative serine protease, but two of them, isolates 1,106 and 1,207, had the intact  chpG  elsewhere in the genome. Genomic analysis of these two isolates revealed that  chpG  was located in the pCM2 Cc  plasmid, and two highly homologous regions were present next to the  chpG  locus. The  chpG  expression in isolate 1,106 was not induced in plants. Introduction of  chpG  of the PF008 strain into the six low‐virulence isolates restored their virulence to that of PF008. Our findings indicate that there are at least three different variant groups of  C. capsici  and that the plasmid composition and the  chpG  gene are critical for determining the virulence level. Moreover, our findings also indicate that the virulence level of  C. capsici  does not directly correlate with bacterial titres in plants.

Plasmid composition and the chpG gene determine the virulence level of Clavibacter capsici natural isolates in pepper