Comparative Genomics of Pathogenic <i>Clavibacter michiganensis</i> subsp. <i>michiganensis</i> Strains from Chile Reveals Potential Virulence Features for Tomato Plants
The genus <i>Clavibacter</i> has been associated largely with plant diseases. The aims of this study were to characterize the genomes and the virulence factors of Chilean <i>C. michiganensis</i> subsp. <i>michiganensis</i> strains VL527, MSF322 and OP3, and to def...
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MDPI AG
2020-10-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/8/11/1679 |
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| author | Valentina Méndez Miryam Valenzuela Francisco Salvà-Serra Daniel Jaén-Luchoro Ximena Besoain Edward R. B. Moore Michael Seeger |
| author_facet | Valentina Méndez Miryam Valenzuela Francisco Salvà-Serra Daniel Jaén-Luchoro Ximena Besoain Edward R. B. Moore Michael Seeger |
| author_sort | Valentina Méndez |
| collection | DOAJ |
| description | The genus <i>Clavibacter</i> has been associated largely with plant diseases. The aims of this study were to characterize the genomes and the virulence factors of Chilean <i>C. michiganensis</i> subsp. <i>michiganensis</i> strains VL527, MSF322 and OP3, and to define their phylogenomic positions within the species, <i>Clavibacter michiganensis</i>. 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 <i>C.</i><i>michiganensis</i> subsp. <i>michiganensis</i> and showed their low genomic diversity. Different virulence levels in tomato plants were observable. Phylogenetic analyses of the virulence factors revealed that the <i>pelA1</i> gene (<i>chp/tomA</i> 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 <i>C. michiganensis</i> subsp. <i>phaseoli</i> and subsp. <i>chilensis</i> at the species level, as <i>C. phaseoli</i> sp. nov., as well as to reclassify <i>C. michiganensis</i> subsp. <i>californiensis</i> as the species <i>C</i>. <i>californiensis</i> sp. nov. may be justified. |
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| publishDate | 2020-10-01 |
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| spelling | doaj.art-fae6591f3d4640ee90ed5c56295caa412023-11-20T18:58:20ZengMDPI AGMicroorganisms2076-26072020-10-01811167910.3390/microorganisms8111679Comparative Genomics of Pathogenic <i>Clavibacter michiganensis</i> subsp. <i>michiganensis</i> Strains from Chile Reveals Potential Virulence Features for Tomato PlantsValentina Méndez0Miryam Valenzuela1Francisco Salvà-Serra2Daniel Jaén-Luchoro3Ximena Besoain4Edward R. B. Moore5Michael Seeger6Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso 2390123, ChileMolecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso 2390123, ChileDepartment of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 46 Gothenburg, SwedenDepartment of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 46 Gothenburg, SwedenEscuela de Agronomía, Pontificia Universidad Católica de Valparaíso, Quillota 2260000, ChileDepartment of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 46 Gothenburg, SwedenMolecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso 2390123, ChileThe genus <i>Clavibacter</i> has been associated largely with plant diseases. The aims of this study were to characterize the genomes and the virulence factors of Chilean <i>C. michiganensis</i> subsp. <i>michiganensis</i> strains VL527, MSF322 and OP3, and to define their phylogenomic positions within the species, <i>Clavibacter michiganensis</i>. 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 <i>C.</i><i>michiganensis</i> subsp. <i>michiganensis</i> and showed their low genomic diversity. Different virulence levels in tomato plants were observable. Phylogenetic analyses of the virulence factors revealed that the <i>pelA1</i> gene (<i>chp/tomA</i> 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 <i>C. michiganensis</i> subsp. <i>phaseoli</i> and subsp. <i>chilensis</i> at the species level, as <i>C. phaseoli</i> sp. nov., as well as to reclassify <i>C. michiganensis</i> subsp. <i>californiensis</i> as the species <i>C</i>. <i>californiensis</i> sp. nov. may be justified.https://www.mdpi.com/2076-2607/8/11/1679<i>Clavibacter michiganensis</i><i>Clavibacter</i>bacterial cankertomatopathogenicityvirulence |
| spellingShingle | Valentina Méndez Miryam Valenzuela Francisco Salvà-Serra Daniel Jaén-Luchoro Ximena Besoain Edward R. B. Moore Michael Seeger Comparative Genomics of Pathogenic <i>Clavibacter michiganensis</i> subsp. <i>michiganensis</i> Strains from Chile Reveals Potential Virulence Features for Tomato Plants Microorganisms <i>Clavibacter michiganensis</i> <i>Clavibacter</i> bacterial canker tomato pathogenicity virulence |
| title | Comparative Genomics of Pathogenic <i>Clavibacter michiganensis</i> subsp. <i>michiganensis</i> Strains from Chile Reveals Potential Virulence Features for Tomato Plants |
| title_full | Comparative Genomics of Pathogenic <i>Clavibacter michiganensis</i> subsp. <i>michiganensis</i> Strains from Chile Reveals Potential Virulence Features for Tomato Plants |
| title_fullStr | Comparative Genomics of Pathogenic <i>Clavibacter michiganensis</i> subsp. <i>michiganensis</i> Strains from Chile Reveals Potential Virulence Features for Tomato Plants |
| title_full_unstemmed | Comparative Genomics of Pathogenic <i>Clavibacter michiganensis</i> subsp. <i>michiganensis</i> Strains from Chile Reveals Potential Virulence Features for Tomato Plants |
| title_short | Comparative Genomics of Pathogenic <i>Clavibacter michiganensis</i> subsp. <i>michiganensis</i> Strains from Chile Reveals Potential Virulence Features for Tomato Plants |
| title_sort | comparative genomics of pathogenic i clavibacter michiganensis i subsp i michiganensis i strains from chile reveals potential virulence features for tomato plants |
| topic | <i>Clavibacter michiganensis</i> <i>Clavibacter</i> bacterial canker tomato pathogenicity virulence |
| url | https://www.mdpi.com/2076-2607/8/11/1679 |
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