Beyond the Basics: Taxonomic Classification and Pathogenomics in Recently Discovered <i>Dickeya dadantii</i> Isolates
The genus <i>Dickeya</i> consists of Gram-negative bacteria capable of causing soft rot symptoms in plants, which involves tissue breakdown, particularly in storage organs such as tubers, rhizomes, and bulbs. These bacteria are ranked among the top ten most relevant phytopathogens and se...
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2024-09-01
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| author | Mateus Sudario Pereira Diego Lucas Neres Rodrigues Juan Carlos Ariute Douglas Vinícius Dias Carneiro Pedro Alexandre Sodrzeieski Marco Aurélio Siqueira Gama Elineide Barbosa de Souza Vasco Azevedo Bertram Brenig Ana Maria Benko-Iseppon Flavia Figueira Aburjaile |
| author_facet | Mateus Sudario Pereira Diego Lucas Neres Rodrigues Juan Carlos Ariute Douglas Vinícius Dias Carneiro Pedro Alexandre Sodrzeieski Marco Aurélio Siqueira Gama Elineide Barbosa de Souza Vasco Azevedo Bertram Brenig Ana Maria Benko-Iseppon Flavia Figueira Aburjaile |
| author_sort | Mateus Sudario Pereira |
| collection | DOAJ |
| description | The genus <i>Dickeya</i> consists of Gram-negative bacteria capable of causing soft rot symptoms in plants, which involves tissue breakdown, particularly in storage organs such as tubers, rhizomes, and bulbs. These bacteria are ranked among the top ten most relevant phytopathogens and seriously threaten economically valuable crops and ornamental plants. This study employs a genomic analysis approach to taxonomically classify and characterize the resistome and virulome of two new strains, CCRMP144 and CCRMP250, identified as <i>Dickeya dadantii</i>. These strains were found to be the causative agents of soft rot symptoms in chili pepper (<i>Capsicum</i> spp.) and lettuce (<i>Lactuca sativa</i>), respectively, in the northeastern region of Brazil. The methodology employed in silico techniques, including tetra correlation search (TCS) and Average Nucleotide Identity (ANI) analysis, in association with a phylogenomic tree inference. TCS and ANI analysis showed that the studied strains belong to the <i>Dickeya dadantii</i> species. The phylogenomic analysis grouped the studied strains in the <i>D. dadantii</i> clade. The genomic characterization demonstrates 68 virulence genes, 54 resistances of biocide and heavy metal genes, and 23 antibiotic resistance genes. As far as we know, this is the first genomic study with Brazilian <i>D. dadantii</i> strains. This study demonstrates the efficacy to taxonomic classification and provides insights into the pathogenesis, host range, and adaptability of these strains which are crucial for the development of more effective management and control strategies for soft rot diseases. |
| format | Article |
| id | doaj-art-519cd32ebf9b40429be7bf499c80ab4f |
| institution | OA Journals |
| issn | 2673-6500 |
| language | English |
| publishDate | 2024-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Taxonomy |
| spelling | doaj-art-519cd32ebf9b40429be7bf499c80ab4f2025-08-20T02:01:24ZengMDPI AGTaxonomy2673-65002024-09-014469671210.3390/taxonomy4040036Beyond the Basics: Taxonomic Classification and Pathogenomics in Recently Discovered <i>Dickeya dadantii</i> IsolatesMateus Sudario Pereira0Diego Lucas Neres Rodrigues1Juan Carlos Ariute2Douglas Vinícius Dias Carneiro3Pedro Alexandre Sodrzeieski4Marco Aurélio Siqueira Gama5Elineide Barbosa de Souza6Vasco Azevedo7Bertram Brenig8Ana Maria Benko-Iseppon9Flavia Figueira Aburjaile10Preventive Veterinary Medicine Department, Veterinary School, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, BrazilPreventive Veterinary Medicine Department, Veterinary School, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, BrazilPreventive Veterinary Medicine Department, Veterinary School, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, BrazilPreventive Veterinary Medicine Department, Veterinary School, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, BrazilPreventive Veterinary Medicine Department, Veterinary School, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, BrazilDepartment of Agronomy, Universidade Federal Rural de Pernambuco, Recife 52171-900, Pernambuco, BrazilDepartment of Agronomy, Universidade Federal Rural de Pernambuco, Recife 52171-900, Pernambuco, BrazilGenetics, Ecology and Evolution Department, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, BrazilInstitute of Veterinary Medicine, University Göttingen, 37077 Göttingen, GermanyGenetics Department, Universidade Federal de Pernambuco, Recife 50740-600, Pernambuco, BrazilPreventive Veterinary Medicine Department, Veterinary School, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, BrazilThe genus <i>Dickeya</i> consists of Gram-negative bacteria capable of causing soft rot symptoms in plants, which involves tissue breakdown, particularly in storage organs such as tubers, rhizomes, and bulbs. These bacteria are ranked among the top ten most relevant phytopathogens and seriously threaten economically valuable crops and ornamental plants. This study employs a genomic analysis approach to taxonomically classify and characterize the resistome and virulome of two new strains, CCRMP144 and CCRMP250, identified as <i>Dickeya dadantii</i>. These strains were found to be the causative agents of soft rot symptoms in chili pepper (<i>Capsicum</i> spp.) and lettuce (<i>Lactuca sativa</i>), respectively, in the northeastern region of Brazil. The methodology employed in silico techniques, including tetra correlation search (TCS) and Average Nucleotide Identity (ANI) analysis, in association with a phylogenomic tree inference. TCS and ANI analysis showed that the studied strains belong to the <i>Dickeya dadantii</i> species. The phylogenomic analysis grouped the studied strains in the <i>D. dadantii</i> clade. The genomic characterization demonstrates 68 virulence genes, 54 resistances of biocide and heavy metal genes, and 23 antibiotic resistance genes. As far as we know, this is the first genomic study with Brazilian <i>D. dadantii</i> strains. This study demonstrates the efficacy to taxonomic classification and provides insights into the pathogenesis, host range, and adaptability of these strains which are crucial for the development of more effective management and control strategies for soft rot diseases.https://www.mdpi.com/2673-6500/4/4/36genomicplant pathogenresistomesoft rottaxogenomicvirulome |
| spellingShingle | Mateus Sudario Pereira Diego Lucas Neres Rodrigues Juan Carlos Ariute Douglas Vinícius Dias Carneiro Pedro Alexandre Sodrzeieski Marco Aurélio Siqueira Gama Elineide Barbosa de Souza Vasco Azevedo Bertram Brenig Ana Maria Benko-Iseppon Flavia Figueira Aburjaile Beyond the Basics: Taxonomic Classification and Pathogenomics in Recently Discovered <i>Dickeya dadantii</i> Isolates Taxonomy genomic plant pathogen resistome soft rot taxogenomic virulome |
| title | Beyond the Basics: Taxonomic Classification and Pathogenomics in Recently Discovered <i>Dickeya dadantii</i> Isolates |
| title_full | Beyond the Basics: Taxonomic Classification and Pathogenomics in Recently Discovered <i>Dickeya dadantii</i> Isolates |
| title_fullStr | Beyond the Basics: Taxonomic Classification and Pathogenomics in Recently Discovered <i>Dickeya dadantii</i> Isolates |
| title_full_unstemmed | Beyond the Basics: Taxonomic Classification and Pathogenomics in Recently Discovered <i>Dickeya dadantii</i> Isolates |
| title_short | Beyond the Basics: Taxonomic Classification and Pathogenomics in Recently Discovered <i>Dickeya dadantii</i> Isolates |
| title_sort | beyond the basics taxonomic classification and pathogenomics in recently discovered i dickeya dadantii i isolates |
| topic | genomic plant pathogen resistome soft rot taxogenomic virulome |
| url | https://www.mdpi.com/2673-6500/4/4/36 |
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