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.
Highlights
The common tomato, Solanum lycopersicum L. var. lycopersicum, one of the most essential vegetable crops world-wide, was domesticated in Mesoamerica from S. lycopersicum L. var.cerasiforme, that evolved naturally, initially, in Ecuador and, later, in Peru, from the wild, red-fruited S. pimpinellifolium L. [1]
We postulated that the Chilean Clavibacter michiganensis subsp. michiganensis strains VL527, MSF322 and OP3, that are representatives of three different phylogenetic clades, based on the previous multi-locus sequence analysis (MLSA)-multi-locus sequence typing (MLST) and variable number tandem repeat (VNTR)-MLVA studies [21], present differences in virulence for tomato plants
The symptoms were observed earliest and were more severe, according to the calculated disease index (DI), in plants inoculated with strain VL527 (DI value of 65.33), wherein canker extended along the stem and wilting of the entire plants was observed in most of the tomato seedlings (Figure 1B)
Summary
The common tomato, Solanum lycopersicum L. var. lycopersicum, one of the most essential vegetable crops world-wide, was domesticated in Mesoamerica from S. lycopersicum L. var.cerasiforme, that evolved naturally, initially, in Ecuador and, later, in Peru, from the wild, red-fruited S. pimpinellifolium L. [1]. Michiganensis belongs to the bacterial family, Microbacteriaceae, within the phylum Actinobacteria and is the causal agent of bacterial canker, which is one of the most important diseases of tomatoes in Chile and world-wide with reports of yield losses up to 80% in commercial fields, being declared by the European Union and other countries as a quarantine organism [2]. Well-known pathogens include species (previously classified as C. michiganensis subspecies) related to diseases of important agricultural crops, including bacterial ring rot of potatoes (C. sepedonicus species), wilting and stunting in alfalfa (C. insidiosus species), which are quarantined plant pathogens in several countries in America (including Chile), Europe, Asia and Africa. Other species of the Clavibacter genus include C. nebraskensis and C. tessellarius species, which cause wilt and blight of maize, and leaf freckles and spots in wheat, respectively, C. capsici species, which is a pathogen of pepper plants, and C. michiganensis subsp. Tomato seed-associated non-pathogenic strains of C. michiganensis subsp. californiensis and subsp. chilensis, have been described as two subpopulations that are phylogenetically related to C. michiganensis-like bacteria [8]
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