Comparison of highly and weakly virulent Dickeya solani strains, with a view on the pangenome and panregulon of this species

Małgorzata Golanowska , Marta Potrykus , Agata Motyka-Pomagruk , Michał Kabza , Giovanni Bacci , Marco Galardini , Marco Bazzicalupo , Izabela Makalowska , Kornelia Smalla , Alessio Mengoni , Nicole Hugouvieux-Cotte-Pattat , Ewa Łojkowska

Abstract

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.
Author Małgorzata Golanowska (IFB / IB / DBiotech)
Małgorzata Golanowska,,
- Department of Biotechnology
, Marta Potrykus (IFB / IB / DBiotech)
Marta Potrykus,,
- Department of Biotechnology
, Agata Motyka-Pomagruk (IFB)
Agata Motyka-Pomagruk,,
- Intercollegiate Faculty of Biotechnology UG
, Michał Kabza
Michał Kabza,,
-
, Giovanni Bacci
Giovanni Bacci,,
-
, Marco Galardini
Marco Galardini,,
-
, Marco Bazzicalupo
Marco Bazzicalupo,,
-
, Izabela Makalowska
Izabela Makalowska,,
-
, Kornelia Smalla
Kornelia Smalla,,
-
, Alessio Mengoni
Alessio Mengoni,,
-
et al.`
Journal seriesFrontiers in Microbiology, ISSN 1664-302X, (A 35 pkt)
Issue year2018
Vol9
Pages1-19
Publication size in sheets0.9
Keywords in Englishadhesin, genome comparison, Pectobacteriaceae, prophages, regulon comparison
DOIDOI:10.3389/fmicb.2018.01940
URL https://www.frontiersin.org/articles/10.3389/fmicb.2018.01940/pdf
Languageen angielski
LicenseJournal (articles only); published final; Uznanie Autorstwa (CC-BY); with publication
Score (nominal)35
ScoreMinisterial score = 35.0, 03-10-2018, ArticleFromJournal
Ministerial score (2013-2016) = 35.0, 03-10-2018, ArticleFromJournal
Publication indicators WoS Impact Factor: 2016 = 4.076 (2) - 2016=4.526 (5)
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