Comparison of Highly and Weakly Virulent Dickeya solani Strains, With a View on the Pangenome and Panregulon of This Species
Bacteria belonging to the genera Dickeya and Pectobacterium are responsible for significant economic losses in a wide variety of crops and ornamentals. During last years, increasing losses in potato production have been attributed to the appearance of Dickeya solani. The D. solani strains investigat...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-08-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2018.01940/full |
| _version_ | 1818963336774025216 |
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| author | Malgorzata Golanowska Marta Potrykus Agata Motyka-Pomagruk Michal Kabza Giovanni Bacci Marco Galardini Marco Bazzicalupo Izabela Makalowska Kornelia Smalla Alessio Mengoni Nicole Hugouvieux-Cotte-Pattat Ewa Lojkowska |
| author_facet | Malgorzata Golanowska Marta Potrykus Agata Motyka-Pomagruk Michal Kabza Giovanni Bacci Marco Galardini Marco Bazzicalupo Izabela Makalowska Kornelia Smalla Alessio Mengoni Nicole Hugouvieux-Cotte-Pattat Ewa Lojkowska |
| author_sort | Malgorzata Golanowska |
| collection | DOAJ |
| description | Bacteria belonging to the genera Dickeya and Pectobacterium are responsible for significant economic losses in a wide variety of crops and ornamentals. During last years, increasing losses in potato production have been attributed to the appearance of Dickeya solani. The D. solani strains investigated so far share genetic homogeneity, although different virulence levels were observed among strains of various origins. The purpose of this study was to investigate the genetic traits possibly related to the diverse virulence levels by means of comparative genomics. First, we developed a new genome assembly pipeline which allowed us to complete the D. solani genomes. Four de novo sequenced and ten publicly available genomes were used to identify the structure of the D. solani pangenome, in which 74.8 and 25.2% of genes were grouped into the core and dispensable genome, respectively. For D. solani panregulon analysis, we performed a binding site prediction for four transcription factors, namely CRP, KdgR, PecS and Fur, to detect the regulons of these virulence regulators. Most of the D. solani potential virulence factors were predicted to belong to the accessory regulons of CRP, KdgR, and PecS. Thus, some differences in gene expression could exist between D. solani strains. The comparison between a highly and a low virulent strain, IFB0099 and IFB0223, respectively, disclosed only small differences between their genomes but significant differences in the production of virulence factors like pectinases, cellulases and proteases, and in their mobility. The D. solani strains also diverge in the number and size of prophages present in their genomes. Another relevant difference is the disruption of the adhesin gene fhaB2 in the highly virulent strain. Strain IFB0223, which has a complete adhesin gene, is less mobile and less aggressive than IFB0099. This suggests that in this case, mobility rather than adherence is needed in order to trigger disease symptoms. This study highlights the utility of comparative genomics in predicting D. solani traits involved in the aggressiveness of this emerging plant pathogen. |
| first_indexed | 2024-12-20T12:43:36Z |
| format | Article |
| id | doaj.art-7459adae28d94e7a85a997164a144ef9 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-20T12:43:36Z |
| publishDate | 2018-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-7459adae28d94e7a85a997164a144ef92022-12-21T19:40:23ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2018-08-01910.3389/fmicb.2018.01940329217Comparison of Highly and Weakly Virulent Dickeya solani Strains, With a View on the Pangenome and Panregulon of This SpeciesMalgorzata Golanowska0Marta Potrykus1Agata Motyka-Pomagruk2Michal Kabza3Giovanni Bacci4Marco Galardini5Marco Bazzicalupo6Izabela Makalowska7Kornelia Smalla8Alessio Mengoni9Nicole Hugouvieux-Cotte-Pattat10Ewa Lojkowska11Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, PolandDepartment of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, PolandDepartment of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, PolandDepartment of Integrative Genomics, Faculty of Biology, Adam Mickiewicz University, Poznan, PolandDepartment of Biology, University of Florence, Florence, ItalyEMBL, EBI, Wellcome Trust Genome Campus, Cambridge, United KingdomDepartment of Biology, University of Florence, Florence, ItalyDepartment of Integrative Genomics, Faculty of Biology, Adam Mickiewicz University, Poznan, PolandDepartment of Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants, Braunschweig, GermanyDepartment of Biology, University of Florence, Florence, ItalyUMR5240 Microbiologie Adaptation et Pathogénie, Univ Lyon, CNRS, Univ Claude Bernard Lyon 1, INSA Lyon, Villeurbanne, FranceDepartment of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, PolandBacteria belonging to the genera Dickeya and Pectobacterium are responsible for significant economic losses in a wide variety of crops and ornamentals. During last years, increasing losses in potato production have been attributed to the appearance of Dickeya solani. The D. solani strains investigated so far share genetic homogeneity, although different virulence levels were observed among strains of various origins. The purpose of this study was to investigate the genetic traits possibly related to the diverse virulence levels by means of comparative genomics. First, we developed a new genome assembly pipeline which allowed us to complete the D. solani genomes. Four de novo sequenced and ten publicly available genomes were used to identify the structure of the D. solani pangenome, in which 74.8 and 25.2% of genes were grouped into the core and dispensable genome, respectively. For D. solani panregulon analysis, we performed a binding site prediction for four transcription factors, namely CRP, KdgR, PecS and Fur, to detect the regulons of these virulence regulators. Most of the D. solani potential virulence factors were predicted to belong to the accessory regulons of CRP, KdgR, and PecS. Thus, some differences in gene expression could exist between D. solani strains. The comparison between a highly and a low virulent strain, IFB0099 and IFB0223, respectively, disclosed only small differences between their genomes but significant differences in the production of virulence factors like pectinases, cellulases and proteases, and in their mobility. The D. solani strains also diverge in the number and size of prophages present in their genomes. Another relevant difference is the disruption of the adhesin gene fhaB2 in the highly virulent strain. Strain IFB0223, which has a complete adhesin gene, is less mobile and less aggressive than IFB0099. This suggests that in this case, mobility rather than adherence is needed in order to trigger disease symptoms. This study highlights the utility of comparative genomics in predicting D. solani traits involved in the aggressiveness of this emerging plant pathogen.https://www.frontiersin.org/article/10.3389/fmicb.2018.01940/fulladhesingenome comparisonPectobacteriaceaeprophagesregulon comparison |
| spellingShingle | Malgorzata Golanowska Marta Potrykus Agata Motyka-Pomagruk Michal Kabza Giovanni Bacci Marco Galardini Marco Bazzicalupo Izabela Makalowska Kornelia Smalla Alessio Mengoni Nicole Hugouvieux-Cotte-Pattat Ewa Lojkowska Comparison of Highly and Weakly Virulent Dickeya solani Strains, With a View on the Pangenome and Panregulon of This Species Frontiers in Microbiology adhesin genome comparison Pectobacteriaceae prophages regulon comparison |
| title | Comparison of Highly and Weakly Virulent Dickeya solani Strains, With a View on the Pangenome and Panregulon of This Species |
| title_full | Comparison of Highly and Weakly Virulent Dickeya solani Strains, With a View on the Pangenome and Panregulon of This Species |
| title_fullStr | Comparison of Highly and Weakly Virulent Dickeya solani Strains, With a View on the Pangenome and Panregulon of This Species |
| title_full_unstemmed | Comparison of Highly and Weakly Virulent Dickeya solani Strains, With a View on the Pangenome and Panregulon of This Species |
| title_short | Comparison of Highly and Weakly Virulent Dickeya solani Strains, With a View on the Pangenome and Panregulon of This Species |
| title_sort | comparison of highly and weakly virulent dickeya solani strains with a view on the pangenome and panregulon of this species |
| topic | adhesin genome comparison Pectobacteriaceae prophages regulon comparison |
| url | https://www.frontiersin.org/article/10.3389/fmicb.2018.01940/full |
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