Genome Sequence of the Emerging Plant Pathogen Dickeya solani Strain RNS 08.23.3.1A

Khayi, Slimane; Mondy, Samuel; Beury-Cirou, Amélie; Moumni, Mohiéddine; Hélias, Valerie; Faure, Denis

doi:10.1128/genomea.01270-13

Cited by 21 publications

(25 citation statements)

References 5 publications

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“…D. dianthicola and D. solani pathogens successively emerged in Europe (Toth et al ., ; van der Wolf et al ., ). In this work, comparison of genome, transcriptome and metabolic capacity highlighted the common and distinctive traits between the strains D. dianthicola RNS04.9 (Ddi04.9) and D. solani 3337 (Dso3337) that have been collected from potato symptoms in French fields in 2004 and 2008 respectively (Raoul des Essarts et al ., ; Khayi et al ., ). The transcriptomic analysis was performed by comparing the expression profiles of the two strains grown either in rich medium or on filters placed on potato tuber slices.…”

Section: Discussionmentioning

confidence: 97%

“…D. dianthicola RNS04.9 and D. solani PRI3337 (=RNS 08.23.3.1A) were isolated in 2004 and 2008 from a potato plant with blackleg symptom sampled in a French field during the epidemiological annual survey monitored by the FN3PT/RD3PT (des Essarts et al ., ; Khayi et al ., ). They were routinely cultured in TY medium (tryptone 5 g/l, yeast extract 3 g/l, agar 1.5%) at 30 °C.…”

Section: Methodsmentioning

confidence: 97%

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Common and distinctive adaptive traits expressed in Dickeya dianthicola and Dickeya solani pathogens when exploiting potato plant host

Essarts

Pédron

Blin

et al. 2019

Environmental Microbiology

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Summary Blackleg and soft rot are devastating diseases on potato stem and tuber caused by Pectobacterium and Dickeya pectinolytic enterobacteria. In European potato cultures, D. dianthicola and D. solani species successively emerged in the past decades. Ecological traits associated to their settlement remain elusive, especially in the case of the recent invader D. solani. In this work, we combined genomic, metabolic and transcriptomic comparisons to unravel common and distinctive genetic and functional characteristics between two D. solani and D. dianthicola isolates. The two strains differ by more than a thousand genes that are often clustered in genomic regions (GRs). Several GRs code for transport and metabolism functions that correlate with some of the differences in metabolic abilities identified between the two Dickeya strains. About 800 D. dianthicola and 1100 D. solani genes where differentially expressed in macerated potato tubers as compared to when growing in rich medium. These include several genes located in GRs, pointing to a potential role in host interaction. In addition, some genes common to both species, including virulence genes, differed in their expression. This work highlighted distinctive traits when D. dianthicola and D. solani exploit the host as a resource.

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Section: Discussionmentioning

confidence: 97%

Section: Methodsmentioning

confidence: 97%

Common and distinctive adaptive traits expressed in Dickeya dianthicola and Dickeya solani pathogens when exploiting potato plant host

Essarts

Pédron

Blin

et al. 2019

Environmental Microbiology

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“… D. solani species is genetically highly homogenous with 99.9% in genomic similarity (ANI value) [19, 20]. Between two given D. solani genomes, the number of variations (SNPs/InDels) is below one hundred.…”

Section: Insights From the Genome Sequencementioning

confidence: 99%

Complete genome anatomy of the emerging potato pathogen Dickeya solani type strain IPO 2222T

Khayi

Blin

Chong

et al. 2016

Stand in Genomic Sci

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Several species of the genus Dickeya provoke soft rot and blackleg diseases on a wide range of plants and crops. Dickeya solani has been identified as the causative agent of diseases outbreaks on potato culture in Europe for the last decade. Here, we report the complete genome of the D. solani IPO 2222T. Using PacBio and Illumina technologies, a unique circular chromosome of 4,919,833 bp was assembled. The G + C content reaches 56% and the genomic sequence contains 4,059 predicted proteins. The ANI values calculated for D. solani IPO 2222T vs. other available D. solani genomes was over 99.9% indicating a high genetic homogeneity within D. solani species.Electronic supplementary materialThe online version of this article (doi:10.1186/s40793-016-0208-0) contains supplementary material, which is available to authorized users.

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“…The bacterial strains used are listed in Table 1 (50,51,(62)(63)(64). All of them were routinely cultivated in TY medium (Bacto tryptone, 5 g/liter; yeast extract, 3 g/liter; agar, 15 g/liter) at 30°C for the Dickeya strains and at 25°C for the other bacteria.…”

Section: Methodsmentioning

confidence: 99%

Biocontrol of the Potato Blackleg and Soft Rot Diseases Caused by Dickeya dianthicola

Essarts

Cigna

Quêtu-Laurent

et al. 2016

Appl Environ Microbiol

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Development of protection tools targetingDickeya species is an important issue in the potato production. Here, we present the identification and the characterization of novel biocontrol agents. Successive screenings of 10,000 bacterial isolates led us to retain 58 strains that exhibited growth inhibition properties against several Dickeya sp. and/or Pectobacterium sp. pathogens. Most of them belonged to the Pseudomonas and Bacillus genera. In vitro assays revealed a fitness decrease of the tested Dickeya sp. and Pectobacterium sp. pathogens in the presence of the biocontrol agents. In addition, four independent greenhouse assays performed to evaluate the biocontrol bacteria effect on potato plants artificially contaminated with Dickeya dianthicola revealed that a mix of three biocontrol agents, namely, Pseudomonas putida PA14H7 and Pseudomonas fluorescens PA3G8 and PA4C2, repeatedly decreased the severity of blackleg symptoms as well as the transmission of D. dianthicola to the tuber progeny. This work highlights the use of a combination of biocontrol strains as a potential strategy to limit the soft rot and blackleg diseases caused by D. dianthicola on potato plants and tubers. The Pectobacterium and Dickeya pectinolytic bacteria are phytopathogens responsible for several macerating diseases on a wide range of crop and ornamental plants (1-3). The damage caused by these pathogens remains an important issue in many countries worldwide. In Europe, the pectinolytic pathogens on potato crops include Pectobacterium atrosepticum, Pectobacterium carotovorum subsp. carotovorum, Dickeya dianthicola, and Dickeya solani (4-8). Recently, new Pectobacterium taxa, i.e., P. wasabiae and P. carotovorum subsp. brasiliense, have been characterized (2, 9, 10). Pectobacterium sp. populations are qualified as endemic, as their presence has been observed for almost a century in Europe, while the presence of Dickeya spp. as a cause of the symptoms in potato fields was sporadic until the 2000s and the Dickeya sp. damages were probably exclusively due to the species D. dianthicola. In contrast, D. solani seems to have emerged in the 2000s (3).Pectobacterium and Dickeya potato pathogens induce blackleg on stems and soft rot on tubers (11,12). A polyphyletic pathogen population may be isolated from a single sample of symptomatic plant tissues (13). The pathogens penetrate in host plants through natural pores or wounds (i.e., the lenticels, the elongation zones of roots, or insect wounds) as well as mechanical wounds. Insects can act as vectors; surface water and aerosols may also contribute to the dissemination of the pathogens (12, 14-21). Once the pathogens have infected the plant, they may propagate throughout the whole plant and son tubers by the vascular vessels. Losses due to Pectobacterium and Dickeya, related to stem and tuber rot, are major causes for downgrading and rejection of potatoes during seed potato certification. The certification is based on visual inspections in fields or on lots, ranging in Europe from 0 to 4% blackl...

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Genome Sequence of the Emerging Plant Pathogen Dickeya solani Strain RNS 08.23.3.1A

Abstract: Here we present the genome sequence of Dickeya solani strain RNS 08.23.3.1A (PRI3337), isolated from Solanum tuberosum. Dickeya solani, recently described on potato cultures in Europe, is a proposed new taxon closely related to the Dickeya dianthicola and Dickeya dadantii species.

Cited by 21 publications

References 5 publications

Common and distinctive adaptive traits expressed in Dickeya dianthicola and Dickeya solani pathogens when exploiting potato plant host

Common and distinctive adaptive traits expressed in Dickeya dianthicola and Dickeya solani pathogens when exploiting potato plant host

Complete genome anatomy of the emerging potato pathogen Dickeya solani type strain IPO 2222T

Biocontrol of the Potato Blackleg and Soft Rot Diseases Caused by Dickeya dianthicola

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