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Open Access Research article

Genomic and metabolic comparison with Dickeya dadantii 3937 reveals the emerging Dickeya solani potato pathogen to display distinctive metabolic activities and T5SS/T6SS-related toxin repertoire

Jacques Pédron12, Samuel Mondy3, Yannick Raoul des Essarts34, Frédérique Van Gijsegem12* and Denis Faure3*

Author Affiliations

1 UPMC Univ Paris 06, UMR 1392, IEES Paris (Institute of Ecology and Environmental Sciences), 46 rue d’Ulm, F-75005 Paris, France

2 INRA, UMR 1392, IEES Paris (Institute of Ecology and Environmental Sciences), 46 rue d’Ulm, F-75005 Paris, France

3 CNRS, UPR2355, ISV (Institut des sciences du végétal), Avenue de la terrasse, F-91198, Gif-sur-Yvette, France

4 FN3PT/RD3PT, Fédération Nationale des Producteurs de Plants de Pomme de Terre, 43-45 Rue de Naples, F-75008 Paris, France

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BMC Genomics 2014, 15:283  doi:10.1186/1471-2164-15-283

Published: 15 April 2014

Abstract

Background

The pectinolytic enterobacteria of the Pectobacterium and Dickeya genera are causative agents of maceration-associated diseases affecting a wide variety of crops and ornamentals. For the past decade, the emergence of a novel species D. solani was observed in potato fields in Europe and the Mediterranean basin. The purpose of this study is to search by comparative genomics the genetic traits that could be distinctive to other Dickeya species and be involved in D. solani adaptation to the potato plant host.

Results

D. solani 3337 exhibits a 4.9 Mb circular genome that is characterized by a low content in mobile elements with the identification of only two full length insertion sequences. A genomic comparison with the deeply-annotated model D. dadantii 3937 strain was performed. While a large majority of Dickeya virulence genes are shared by both strains, a few hundreds genes of D. solani 3337, mostly regrouped in 25 genomic regions, are distinctive to D. dadantii 3937. These genomic regions are present in the other available draft genomes of D. solani strains and interestingly some of them were not found in the sequenced genomes of the other Dickeya species. These genomic regions regroup metabolic genes and are often accompanied by genes involved in transport systems. A metabolic analysis correlated some metabolic genes with distinctive functional traits of both D. solani 3337 and D. dadantii 3937. Three identified D. solani genomic regions also regroup NRPS/PKS encoding genes. In addition, D. solani encodes a distinctive arsenal of T5SS and T6SS-related toxin-antitoxin systems. These genes may contribute to bacteria-bacteria interactions and to the fitness of D. solani to the plant environment.

Conclusions

This study highlights the genomic specific traits of the emerging pathogen D. solani and will provide the basis for studying those that are involved in the successful adaptation of this emerging pathogen to the potato plant host.

Keywords:
PKS; NRPS; CDI; Rhs; Dickeya dadantii; Dickeya solani; Plant pathogen interactions