Browsing by Author "Ekmark, Risto"

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.