High genomic variability in the plant pathogenic bacterium Pectobacterium parmentieri deciphered from de novo assembled complete genomes

Abstract

BackgroundPectobacterium parmentieri is a newly established species within the plant pathogenic family Pectobacteriaceae. Bacteria belonging to this species are causative agents of diseases in economically important crops (e.g. potato) in a wide range of different environmental conditions, encountered in Europe, North America, Africa, and New Zealand. Severe disease symptoms result from the activity of P. parmentieri virulence factors, such as plant cell wall degrading enzymes. Interestingly, we observe significant phenotypic differences among P. parmentieri isolates regarding virulence factors production and the abilities to macerate plants. To establish the possible genomic basis of these differences, we sequenced 12 genomes of P. parmentieri strains (10 isolated in Poland, 2 in Belgium) with the combined use of Illumina and PacBio approaches. De novo genome assembly was performed with the use of SPAdes software, while annotation was conducted by NCBI Prokaryotic Genome Annotation Pipeline.ResultsThe pan-genome study was performed on 15 genomes (12 de novo assembled and three reference strains: P. parmentieri CFBP 8475T, P. parmentieri SCC3193, P. parmentieri WPP163). The pan-genome includes 3706 core genes, a high number of accessory (1468) genes, and numerous unique (1847) genes. We identified the presence of well-known genes encoding virulence factors in the core genome fraction, but some of them were located in the dispensable genome. A significant fraction of horizontally transferred genes, virulence-related gene duplications, as well as different CRISPR arrays were found, which can explain the observed phenotypic differences. Finally, we found also, for the first time, the presence of a plasmid in one of the tested P. parmentieri strains isolated in Poland.ConclusionsWe can hypothesize that a large number of the genes in the dispensable genome and significant genomic variation among P. parmentieri strains could be the basis of the potential wide host range and widespread diffusion of P. parmentieri. The obtained data on the structure and gene content of P. parmentieri strains enabled us to speculate on the importance of high genomic plasticity for P. parmentieri adaptation to different environments.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5140-9) contains supplementary material, which is available to authorized users.

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

“…In contrastto D. solani, another member of the Pectobacteriaceae family, namely Pectobacterium parmentieri, was reported to possess an open pangenome [91]. In that work, computation with the use of Roary on 15 P. parmentieri genomes disclosed a notably lesser contribution of core (52.8%) and higher of accessory (20.9%) and unique (26.3%) pangenome fractions in comparison to D. solani.…”

“…In that work, computation with the use of Roary on 15 P. parmentieri genomes disclosed a notably lesser contribution of core (52.8%) and higher of accessory (20.9%) and unique (26.3%) pangenome fractions in comparison to D. solani. The authors associated the overrepresentation of the dispensable pangenome part with high genomic plasticity of P. parmentieri [91], suggesting a less clonal population structure with respect to that of D. solani [19,21,23,59]. Thus, the closely related P. parmentieri species adhered to the categories of non-specialized species or opportunistic pathogens that often exhibit open pangenomes [86,92] along with, for instance, Escherichia coli [93], Streptococcus agalactiae [94], Listeria monocytogenes [95], Legionella pneumophila [96] or Salmonella typhi [97].…”

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

“…In contrast to D. solani, another member of the Pectobacteriaceae family, namely Pectobacterium parmentieri, was reported to possess an open pangenome [91]. In that work, computation with the use of Roary on 15 P. parmentieri genomes disclosed a notably lesser contribution of core (52.8%) and higher of accessory (20.9%) and unique (26.3%) pangenome fractions in comparison to D. solani.…”

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

“…Contrarily to D. solani, another member of the Pectobacteriaceae family, namely Pectobacterium parmentieri, was reported to possess an open pangenome[91]. In that work, computation with the use of Roary on 15 P. parmentieri genomes, disclosed notably lesser contribution of core (52.8%) and higher of accessory (20.9%) and unique (26.3%) pangenome fractions in comparison to D. solani.…”