Browsing by Subject "soft rot"

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  • Ekmark, Risto (Helsingin yliopisto, 2020)
    Soft rot diseases of potato (Solanum tuberosum) cause significant economic losses worldwide as S. tuberosum is the fourth most important food crop in the world and extensively cultivated. S. tuberosum is susceptible to diseases during storage, where the two most important soft rot causing bacterial genera Pectobacterium and Dickeya can efficiently cause rotting in humid conditions with limited oxygen concentration. The focus of this study was in two Pectobacterium isolates that exhibit orange pigmentation during their infection of S. tuberosum tubers. The genomes of the isolates were sequenced and then assembled into contigs with SPAdes genome assembler. The draft genomes were compared to reference genomes of Pectobacterium species by average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) methods. The isolates were determined to be of Pectobacterium versatile species by ANI score of 97.6%, analyzed by pyANI, and dDDH similarity of 78.6%, analyzed by Type (Strain) Genome Server of DSMZ-German Collection of Micro-organisms and Cell Cultures GmbH. The genomes of the isolates were annotated with the Automated Annotation Server of Kyoto Encyclopedia of Genes and Genomes. The characteristic features of Pectobacteria, Quorum Sensing and Bacterial Secretion Systems, were among the most numerous genes along with essential genes for metabolism and biosynthesis. To support the taxonomic analyses, pangenomic analysis was carried out with Rapid large-scale prokaryote pangenome analysis software Roary with annotation data provided by rapid prokaryotic genome annotation software PROKKA. The genomes of the isolates and reference genomes were used as an input for PROKKA. The pangenomic analysis grouped the Pectobacterium versatile reference genomes and the isolates to the same branch as expected. Comparing reference Pectobacterium versatile genomes with the isolates also showed that the Pectobacterium core genome consists only of 56% of the total number of genes in the genomes. The role of the orange pigmentation still remains unclear and requires extensive further study. However, the isolates were shown to contain genes that were homologous to a previously published gene cluster responsible for the production of an orange pigment by Pectobacterium carotovorum isolate SCRI193. It is hypothesized that the homologous genes present in the characterized isolates are responsible for the pigmentation of infected S. tuberosum tissue.
  • Pasanen, Miia; Waleron, Malgorzata; Schott, Thomas; Cleenwerck, Ilse; Misztak, Agnieszka; Waleron, Krzysztof; Pritchard, Leighton; Bakr, Ramadan; Degefu, Yeshitila; van der Wolf, Jan; Vandamme, Peter; Pirhonen, Minna (2020)
    Pectobacterium strains isolated from potato stems in Finland, Poland and the Netherlands were subjected to polyphasic analyses to characterize their genomic and phenotypic features. Phylogenetic analysis based on 382 core proteins showed that the isolates clustered closest to Pectobacterium polaris but could be divided into two clades. Average nucleotide identity (ANI) analysis revealed that the isolates in one of the clades included the P. polaris type strain, whereas the second Glade was at the border of the species P. polaris with a 96 % ANI value. In silico genome-to-genome comparisons between the isolates revealed values below 70%, patristic distances based on 1294 core proteins were at the level observed between closely related Pectobacterium species, and the two groups of bacteria differed in genome size, G+C content and results of amplified fragment length polymorphism and Biolog analyses. Comparisons between the genomes revealed that the isolates of the atypical group contained SPI-1-type Type III secretion island and genes coding for proteins known for toxic effects on nematodes or insects, and lacked many genes coding for previously characterized virulence determinants affecting rotting of plant tissue by soft rot bacteria. Furthermore, the atypical isolates could be differentiated from P. polaris by their low virulence, production of antibacterial metabolites and a citrate-negative phenotype. Based on the results of a polyphasic approach including genome-to-genome comparisons, biochemical and virulence assays, presented in this report, we propose delineation of the atypical isolates as a novel species Pectobacterium parvum, for which the isolate s0421(T) (CFBP 8630(T)=LMG 30828(T)) is suggested as a type strain.
  • van den Bosch, Tijs J. M.; Niemi, Outi; Welte, Cornelia U. (2020)
    Plants of the Brassicales order, including Arabidopsis and many common vegetables, produce toxic isothiocyanates to defend themselves against pathogens. Despite this defence, plant pathogenic microorganisms like Pectobacterium cause large yield losses in fields and during storage of crops. The bacterial gene saxA was previously found to encode isothiocyanate hydrolase that degrades isothiocyanates in vitro. Here we demonstrate in planta that saxA is a virulence factor that can overcome the chemical defence system of Brassicales plants. Analysis of the distribution of saxA genes in Pectobacterium suggests that saxA from three different phylogenetic origins are present within this genus. Deletion of saxA genes representing two of the most common classes from P. odoriferum and P. versatile resulted in significantly reduced virulence on Arabidopsis thaliana and Brassica oleracea. Furthermore, expressing saxA from a plasmid in a potato-specific P. parmentieri strain that does not naturally harbour this gene significantly increased the ability of the strain to macerate Arabidopsis. These findings suggest that a single gene may have a significant role in defining the host range of a plant pathogen.