Browsing by Subject "Solanum tuberosum"

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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.
  • Hiltunen, Lea H.; Tarvainen, Oili; Kelloniemi, Jani; Tanskanen, Jaakko; Karhu, Jouni; Valkonen, Jari P. T. (2021)
    Disease suppressive soils are important for managing soil-borne diseases that cannot be controlled with chemicals. One such disease is the potato common scab caused by Streptomyces species. Suppressiveness against common scab can develop spontaneously in fields where potato is grown for years without interruption, and this has been attributed to non-pathogenic Streptomyces strains. Streptomyces spp. have been used as inoculants in biological control, but their long-term effects have gained less attention. In our previous studies, a nonpathogenic Streptomyces strain (Str272) isolated from a potato common scab lesion suppressed common scab in field trials lasting over 5 years. In this study, bacterial communities in the tuberosphere i.e. in the soil adjacent to potato tubers, were analysed by next generation sequencing (NGS). The aim was to compare bacterial communities in untreated control plots to those in which seed tubers were treated with Str272 in one or several growing seasons. Str272 applications increased soil bacterial diversity and affected the bacterial composition in the potato tuberosphere. The most pronounced differences were observed between the untreated control and the treatments in which the antagonist had been applied in three or four consecutive years. The differences remained similar until the following growing season. Bacterial composition after repeated antagonist applications was associated with lower common scab severity. The antagonist applications had no or only slight effect on the number or abundance of OTUs belonging to Actinobacteria or Streptomyces, and no differences in quantities of pathogenic Streptomyces populations were detected by qPCR. This indicates that suppression of common scab by Str272 may not be based on direct effect on the common scab pathogens but is more likely to be associated with the alterations of the soil bacterial community. The most abundant bacteria phyla in the potato tuberosphere were Actinobacteria, Proteobacteria and Acidobacteria. However, the OTUs responding greatest to the antagonist treatments belonged to Bacterioidetes and Gemmatimonadetes. Results indicate that repeated applications of Str272 can change the bacterial community in the potato tuberosphere and lead to development of soil that is suppressive against potato common scab for several growing seasons after the last application.
  • Chiunga, Evangelista (Helsingfors universitet, 2013)
    Potato leaf roll virus (PLRV), Potato virus Y (PVY), Potato virus X (PVX), Potato virus S (PVS), Potato virus A (PVA), and Potato virus M (PVM) are widely distributed in potato (Solanum tuberosum) all over the world. This study was conducted to establish if these viruses also infect potato in Mbeya region, Tanzania. A total of 219 potato leaf samples from 13 farmers’ fields were collected. Of these, 20 samples were pressed on FTA cards. Samples were screened for viruses by Double Antibody Sandwich Enzyme Linked Immunosorbent Assay (DAS-ELISA). Those which were pressed on FTA cards were further analysed by Reverse Transcription Polymerase Chain Reaction (RT-PCR). Virus-like symptoms such as yellowish-green mosaic, leaf rolling and vein necrosis were observed and recorded at the time of field sample collection. DAS-ELISA results suggested the occurrence of all six viruses in samples from Mbeya region. RT-PCR analysis confirmed the presence of these viruses except PVY. PVS and PLRV were the most prevalent viruses. Complete coat proteins (CP) encoding sequence of five viruses (PLRV, PVX, PVA, PVS and PVM) were sequenced. Blast searches detected presence of sequences in the GenBank sharing nucleotide sequence identities of 94%-100% with isolates of viruses sequenced in this study. The complete CP sequences of the aforementioned viruses from the current study were closely related with virus isolates from different countries. The Tanzania isolates of PLRV, PVX, PVA, PVS and PVM were each suggested to belong to the one group as well as one isolate. These results are important in seed potato multiplication systems in Tanzania for improving seed quality in the local seed potato chain, an important service currently lacking to potato farmers in Tanzania.