Dickeya undicola sp. nov., a novel species for pectinolytic isolates from surface waters in Europe and Asia

Oulghazi, Saïd; Pédron, Jacques; Cigna, Jérémy; Lau, Yin Yin; Moumni, Mohiéddine; Gijsegem, Frédérique Van; Chan, Kok‐Gan; Faure, Denis

doi:10.1099/ijsem.0.003497

Cited by 57 publications

(54 citation statements)

References 21 publications

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“…dadantii subsp. dieffenbachiae [12,16]), Dickeya dianthicola [12], Dickeya fangzhongdai [17], Dickeya lacustris [18], Dickeya paradisiaca [12], Dickeya solani [19], D. undicola [20] and Dickeya zeae [12] adhered into the Dickeya genus. It is worth to notice that D. solani drew much of scientific attention ever since its first appearance in Europe in 2004-2005 [19, 21-23].…”

Section: Introductionmentioning

confidence: 99%

Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

Motyka-Pomagruk

Żołędowska

Misztak

et al. 2020

Preprint

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Abstract Background: Dickeya solani was pointed as a significant trait to potato production in Europe and drew much of scientific attention due to remarkable virulence, great devastating potential and easier spread in contrast to other Dickeya spp. In a view of a high need for extensive studies on economically important soft rot Pectobacteriaceae, we performed a nearly conclusive pangenome analysis on D. solani strains to search for genetic foundations that would explain the differences in the observed virulence levels within the D. solani population.Results: High quality assemblies of 8 de novo sequenced D. solani genomes have been obtained. Whole-sequence comparison, ANIb, ANIm, Tetra and pangenome-oriented analyses performed on these genomes sequences and the sequences of 14 additional strains revealed exceptionally high level of homogeneity among the studied genetic material of D. solani strains. With the use of 22 genomes, the pangenome of D. solani, comprising 84.7% core, 7.2% accessory and 8.1% unique genes, has been almost completely determined, suggesting the presence of a nearly closed pangenome structure. Attribution of the genes included in the D. solani pangenome fractions to functional COG categories revealed that higher percentages of accessory and unique pangenome parts in contrast to the core section are encountered in phage/mobile elements- and transcription- associated groups with the genome of RNS 05.1.2A strain having the most significant impact. Also, the first D. solani large-scale genome-wide phylogeny computed on concatenated core gene alignments is herein reported.Conclusions: The almost closed status of D. solani pangenome achieved in this work points to the fact that the unique gene pool of this species should no longer expand. Such a feature is characteristic for taxa, whose representatives either occupy isolated ecological niches or lack efficient mechanisms for gene exchange and recombination, which seems rational concerning a strictly pathogenic species with clonal spread and population structure. Finally, no obvious correlations between the geographical origin of D. solani strains and their phylogeny was found, which might reflect the specificity of the international seed potato market.

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Section: Introductionmentioning

confidence: 99%

Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

Motyka-Pomagruk

Żołędowska

Misztak

et al. 2020

Preprint

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“…dadantii and D. dadantii subsp. dieffenbachiae [12,16]), Dickeya dianthicola [12], Dickeya fangzhongdai [17], Dickeya lacustris [18], Dickeya paradisiaca [12], Dickeya solani [19], D. undicola [20] and Dickeya zeae [12] are classi ed to the Dickeya genus. It is worth noting that D. solani has drawn a lot of attention ever since its rst appearance in Europe in [2004][2005] [19,[21][22][23].…”

Section: Introductionmentioning

confidence: 99%

Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

Motyka-Pomagruk

Żołędowska

Misztak

et al. 2020

Preprint

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Abstract Background: Dickeya solani is an important plant pathogenic bacterium causing severe losses in European potato production. This species draws a lot of attention due to its remarkable virulence, great devastating potential and easier spread in contrast to other Dickeya spp. In view of a high need for extensive studies on economically important soft rot Pectobacteriaceae , we performed a comparative genomics analysis on D. solani strains to search for genetic foundations that would explain the differences in the observed virulence levels within the D. solani population. Results: High quality assemblies of 8 de novo sequenced D. solani genomes have been obtained. Whole-sequence comparison, ANIb, ANIm, Tetra and pangenome-oriented analyses performed on these genomes and the sequences of 14 additional strains revealed an exceptionally high level of homogeneity among the studied genetic material of D. solani strains. With the use of 22 genomes, the pangenome of D. solani , comprising 84.7% core, 7.2% accessory and 8.1% unique genes, has been almost completely determined, suggesting the presence of a nearly closed pangenome structure. Attribution of the genes included in the D. solani pangenome fractions to functional COG categories showed that higher percentages of accessory and unique pangenome parts in contrast to the core section are encountered in phage/mobile elements- and transcription- associated groups with the genome of RNS 05.1.2A strain having the most significant impact. Also, the first D. solani large-scale genome-wide phylogeny computed on concatenated core gene alignments is herein reported. Conclusions: The almost closed status of D. solani pangenome achieved in this work points to the fact that the unique gene pool of this species should no longer expand. Such a feature is characteristic of taxa whose representatives either occupy isolated ecological niches or lack efficient mechanisms for gene exchange and recombination, which seems rational concerning a strictly pathogenic species with clonal population structure. Finally, no obvious correlations between the geographical origin of D. solani strains and their phylogeny were found, which might reflect the specificity of the international seed potato market.

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“…During the past decade, taxonomy of Dickeya species, as that of Pectobacterium, was revisited by genomics in combination with the exploitation of international culture collections and exploration of diverse ecosystems around the world [22,23]. By now, the genus Dickeya encompasses ten species: D. aquatica, D. undicola, and D. zeae [21, [24][25][26][27][28][29]. Bacteria belonging to this genus cause plant disease symptoms in temperate, tropical and subtropical climates [30].…”

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confidence: 99%

“…MLSA may exploit gene sequences obtained by PCR-sequencing of each locus and whole genome sequencing. Among the loci commonly included in MLSA, the rrs sequence is poorly informative at a species level while the gapA gene appeared as an appropriate marker to discriminate the different Dickeya and Pectobacterium species [10,18,19,26,27,32]. Taxonomy of Dickeya and Pectobacterium gained in precision and robustness with additional genome analyses that are ANI and isDDH [33].…”

mentioning

confidence: 99%

“…Comparative genomics is also used to identify species-specific DNA regions. Analysis of the functions encoded by these DNA regions allows the prediction of species-specific metabolic traits: this knowledge contributes to the understanding of both the taxonomy and ecology of the Dickeya and Pectobacterium pathogens [21, [25][26][27]34]. P. atrosepticum, P. carotovorum and P. brasiliense were described in Morocco as the main causative agents of blackleg and soft rot disease in potato crop [35][36][37][38].…”

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confidence: 99%

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Dickeya dianthicola emerged from a potato culture area exhibiting a wide diversity of pectinolytic pathogens in northern Morocco

Oulghazi¹,

Moumni²,

Khayi³

et al. 2020

Preprint

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Background: Dickeya and Pectobacterium are pectinolytic pathogens that cause damage to many plants including major crops. Emergence of D. solani and re-emergence D. dianthicola were recently observed in potato fields in several continents. The purpose of this work was to describe the species diversity of Dickeya and Pectobacterium collected from potato fields in Northern Morocco, where Dickeya potato pathogens have not been isolated until recently. Results: Along three years, 119 pathogens belonging to Pectobacterium and Dickeya genera were isolated from three potato culture areas and characterized using selective PCR and gapA gene sequencing. Out of them, 19% belonged to P. versatile, 3% to P. carotovorum, 5% to P. polaris, 56% to P. brasiliense, while 17% to D. dianthicola. The taxonomic assignations were confirmed by draft genome analyses of representative isolates belonging to the collected species. D. dianthicola were isolated from a unique area where a wide species diversity of pectinolytic pathogens was also observed. In potato maceration assay, D. dianthicola isolates were more aggressive than Pectobacterium isolates, a feature that should alert stakeholders of a potential threat linked to the emergence of D. dianthicola in this country. By combining Oxford Nanopore Technologies (ONT) and Illumina technologies, the sequence of the complete genome of D. dianthicola LAR.16.03.LID was obtained. A unique circular chromosome of 4,976,211 bp codes for 4,223 predicted proteins. Comparison of the three complete genomes of D. dianthicola strains RNS049, ME23 and LAR.16.03.LID revealed a highly conserved synteny and the occurrence of strain-specific regions associated with the presence of mobile elements. Conclusion: By combining population sampling and genomics, this study highlighted the ecological context from which D. dianthicola emerged in Morocco. Furthermore, the first complete genome of a D. dianthicola strain isolated in Northern Morocco will constitute a reference genome for investigating the dynamics of the emerging D. dianthicola pathogens in this country.

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Dickeya undicola sp. nov., a novel species for pectinolytic isolates from surface waters in Europe and Asia

Cited by 57 publications

References 21 publications

Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

Dickeya dianthicola emerged from a potato culture area exhibiting a wide diversity of pectinolytic pathogens in northern Morocco

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