Comparative Genomics of Pathogenic Clavibacter michiganensis subsp. michiganensis Strains from Chile Reveals Potential Virulence Features for Tomato Plants

Abstract

The genus Clavibacter has been associated largely with plant diseases. The aims of this study were to characterize the genomes and the virulence factors of Chilean C. michiganensis subsp. michiganensis strains VL527, MSF322 and OP3, and to define their phylogenomic positions within the species, Clavibacter michiganensis. VL527 and MSF322 genomes possess 3,396,632 and 3,399,199 bp, respectively, with a pCM2-like plasmid in strain VL527, with pCM1- and pCM2-like plasmids in strain MSF322. OP3 genome is composed of a chromosome and three plasmids (including pCM1- and pCM2-like plasmids) of 3,466,104 bp. Genomic analyses confirmed the phylogenetic relationships of the Chilean strains among C.michiganensis subsp. michiganensis and showed their low genomic diversity. Different virulence levels in tomato plants were observable. Phylogenetic analyses of the virulence factors revealed that the pelA1 gene (chp/tomA region)—that grouped Chilean strains in three distinct clusters—and proteases and hydrolases encoding genes, exclusive for each of the Chilean strains, may be involved in these observed virulence levels. Based on genomic similarity (ANIm) analyses, a proposal to combine and reclassify C. michiganensis subsp. phaseoli and subsp. chilensis at the species level, as C. phaseoli sp. nov., as well as to reclassify C. michiganensis subsp. californiensis as the species C. californiensis sp. nov. may be justified.

Analyses of Virulence Genes of Clavibacter michiganensis subsp. michiganensis Strains Reveal Heterogeneity and Deletions That Correlate with Pathogenicity

“…Cluster analysis using virulence gene sequences showed the same strain grouping of strains obtained in previous analysis [15,16,28], except for the pelA1 gene, wherein the strain VQ519 separated from the group of strains belonging to ST32. Some studies of variability of virulence genes have reported low polymorphism values.…”

Microbial Diversity of Psychrotolerant Bacteria Isolated from Wild Flora of Andes Mountains and Patagonia of Chile towards the Selection of Plant Growth-Promoting Bacterial Consortia to Alleviate Cold Stress in Plants

“…The strain BmP21 that was isolated from the phyllosphere of Berberis sp. is closely related to Clavibacter michiganensis [ 44 , 62 , 63 ]. Both strains HsR18 and BmP21 were discarded for further analysis.…”

“…Members of the Frondihabitans genus has only been associated with plants and lichens [ 96 , 97 , 98 , 99 , 100 ]. On the other hand, some members of the Xanthomonas and Clavibacter genera are phytopathogens, which are in the rhizosphere, the phyllosphere, and the endosphere of different plants [ 44 , 63 , 101 , 102 ]. In the present study, the bacterial strains that are closely related to phytopathogens, Xanthomonas sp.…”

“…In addition, antimicrobial activities against well-known phytopathogenic and ice nucleation active bacteria ( Table 4 ), such as Pseudomonas syringae and Pectobacterium carotovorum that magnify the stress caused by cold in plants [ 2 , 116 ], Agrobacterium tumefaciens that infects a wide range of plants and causes plant tumors called crown galls [ 117 ], and Clavibacter michiganensis subsp. michiganensis, which is an important tomato phytopathogen [ 44 , 63 , 101 ], were analyzed. These PGP activities have also been used to select bacterial consortia for plant growth–promotion under stress (cold, drought, salinity) and non-stressful conditions [ 28 , 42 , 118 , 119 , 120 , 121 , 122 ].…”

Screening of eggplant genotypes for resistance to bacterial wilt disease caused by Clavibacter michiganensis subsp. michiganensis

“…However, in a re-classification study, some of the subgroups of C. michiganensis mentioned above have been given the consideration of new species. These new species were called as Clavibacter capsici, Clavibacter insidiosus, Clavibacter nebraskensis, Clavibacter sepedonicus (Li et al 2018;Méndez et al 2020). Although the tomato is the primary natural host of Cmm, peppers (Capsicum annuum) and eggplants (Solanum melongena) can also be infected in the field (Yim et al 2012).…”