The uniform structure of O-polysaccharides isolated from Dickeya solani strains of different origin

Ossowska, Karolina; Czerwicka, Małgorzata; Śledź, Wojciech; Żołędowska, Sabina; Motyka, Agata; Golanowska, Małgorzata; Condemine, Guy; Łojkowska, Ewa; Kaczyński, Zbigniew

doi:10.1016/j.carres.2017.04.001

“…Notably, this extrachromosomal genetic sequence shared complete identity (100%) with the plasmid of Burkholderia ambifaria AMMD (CP000443.1) [39]. In spite of sharing a common plasmid, there is another argument pointing to the association between D. solani and B. ambifaria, as these two species exhibited notable similarities in the Opolysaccharides (OPS) within their lipopolysaccharide (LPS) structures [78,79]. In more detail, 6-deoxy-D-altrose that was found in the OPS of D. solani and D. dadantii [78] was up to now reported only as a constituent of a disaccharide repeating unit →4)-α-d-Rhap-(1 → 3)-β-d-6dAltp-(1 → in the OPS of B. ambifaria type strain LMG 19182 [79].…”

Section: Discussionmentioning

confidence: 99%

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

Motyka-Pomagruk

¹

,

Żołędowska

²

,

Misztak

³

et al. 2020

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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. Wholesequence 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

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“…Notably, this extrachromosomal genetic sequence shared complete identity (100%) with the plasmid of Burkholderia ambifaria AMMD (CP000443.1) [32]. In spite of sharing a common plasmid, there is another argument pointing to the association between D. solani and B. ambifaria, as these two species exhibited notable similarities in the O-polysaccharides (OPS) within their lipopolysaccharide (LPS) structures [72,73]. In more detail, 6-deoxy-D-altrose that was found in the OPS of D. solani and D. dadantii [72] was up to now reported only as a constituent of a disaccharide repeating unit →4)-α-d-Rhap-(1→3)-β-d-6dAltp-(1→ in the OPS of B. ambifaria type strain LMG 19182 [73].…”

Section: Solani Genomic Assembliesmentioning

confidence: 99%

“…In spite of sharing a common plasmid, there is another argument pointing to the association between D. solani and B. ambifaria, as these two species exhibited notable similarities in the O-polysaccharides (OPS) within their lipopolysaccharide (LPS) structures [72,73]. In more detail, 6-deoxy-D-altrose that was found in the OPS of D. solani and D. dadantii [72] was up to now reported only as a constituent of a disaccharide repeating unit →4)-α-d-Rhap-(1→3)-β-d-6dAltp-(1→ in the OPS of B. ambifaria type strain LMG 19182 [73]. Interestingly, B. ambifaria was noted to possess two diverse OPS molecules, which might be related with the adaptation of these strains to various environmental niches such as plant leaves, roots and rhizospheres, forest soil or even sputum or respiratory tract of patients suffering from cystic brosis [74].…”

Section: Solani Genomic Assembliesmentioning

confidence: 99%

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

Motyka-Pomagruk

¹

,

Żołędowska

²

,

Misztak

³

et al. 2020

Preprint

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0

View full text Add to dashboard Cite

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.

show abstract

“…Notably, this extrachromosomal genetic sequence shared complete identity (100%) with the plasmid of Burkholderia ambifaria AMMD (CP000443.1) [32]. In spite of sharing a common plasmid, there is another argument pointing to the association between D. solani and B. ambifaria, as these two species exhibited notable similarities in the O-polysaccharides (OPS) within their lipopolysaccharide (LPS) structures [72,73]. In more detail, 6-deoxy-D-altrose that was found in the OPS of D. solani and D. dadantii [72] was up to now reported only as a constituent of a disaccharide repeating unit →4)-α-d-Rhap-(1→3)-βd-6dAltp-(1→ in the OPS of B. ambifaria type strain LMG 19182 [73].…”

Section: Solani Genomic Assembliesmentioning

confidence: 99%

“…In spite of sharing a common plasmid, there is another argument pointing to the association between D. solani and B. ambifaria, as these two species exhibited notable similarities in the O-polysaccharides (OPS) within their lipopolysaccharide (LPS) structures [72,73]. In more detail, 6-deoxy-D-altrose that was found in the OPS of D. solani and D. dadantii [72] was up to now reported only as a constituent of a disaccharide repeating unit →4)-α-d-Rhap-(1→3)-βd-6dAltp-(1→ in the OPS of B. ambifaria type strain LMG 19182 [73]. Interestingly, B. ambifaria was noted to possess two diverse OPS molecules, which might be related with the adaptation of these strains to various environmental niches such as plant leaves, roots and rhizospheres, forest soil or even sputum or respiratory tract of patients suffering from cystic brosis [74].…”

Section: Solani Genomic Assembliesmentioning

confidence: 99%

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

Motyka-Pomagruk

¹

,

Żołędowska

²

,

Misztak

³

et al. 2020

Preprint

Self Cite

0

View full text Add to dashboard Cite

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.

show abstract

The uniform structure of O-polysaccharides isolated from Dickeya solani strains of different origin

Cited by 14 publications

References 22 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

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

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