Species' identification and microarray-based comparative genome analysis of Streptomyces species isolated from potato scab lesions in Norway

Authors

  • MERETE W. DEES,

    1. Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, PO Box 5003, N-1432 Ås, Norway
    2. Bioforsk, Norwegian Institute for Agricultural and Environmental Research, Plant Health and Plant Protection Division, N-1432 Ås, Norway
    3. Department of Agricultural Sciences, PO Box 27, FI-00014 University of Helsinki, Finland
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  • PANU SOMERVUO,

    1. Department of Agricultural Sciences, PO Box 27, FI-00014 University of Helsinki, Finland
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  • ERIK LYSØE,

    1. Bioforsk, Norwegian Institute for Agricultural and Environmental Research, Plant Health and Plant Protection Division, N-1432 Ås, Norway
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  • MARJA AITTAMAA,

    1. Department of Agricultural Sciences, PO Box 27, FI-00014 University of Helsinki, Finland
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  • JARI P. T. VALKONEN

    Corresponding author
    1. Department of Agricultural Sciences, PO Box 27, FI-00014 University of Helsinki, Finland
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: Email: jari.valkonen@helsinki.fi

SUMMARY

Streptomyces strains were isolated from scab lesions on potatoes collected from different parts of Norway. Twenty-eight plant-pathogenic strains, as tested on seedlings of radish and on potato, were identified on the basis of physiological and molecular criteria. Polymerase chain reaction (PCR) analysis, using species-specific primers, and sequencing of the 16S rRNA gene identified 14 nonmelanin-producing strains to S. turgidiscabies. Fourteen melanin-producing strains were detected with primers specific to S. scabies, but whole-genome microarray analysis, based on 12 766 probes designed for 8848 predicted open reading frames (ORFs) of S. scabies, showed that the 14 strains were different from S. scabies. They were subsequently identified to be S. europaeiscabiei based on the internal transcribed spacer (ITS) sequences of the rRNA genes. This is the first report of the occurrence of S. turgidiscabies and S. europaeiscabiei in Norway. The putative 762 genes exhibiting the highest sequence differences between strains of S. europaeiscabiei and S. scabies according to microarray analysis were concentrated in relatively few gene ontology (GO) categories, including ‘symbiosis and mutualism through parasitism’, ‘cell death’ and ‘responses to biotic stimulus’, whereas genes related to primary metabolism appeared to be more conserved. Microarray data and 16S rRNA gene phylogeny showed, consistently, that there were two genetically distinguishable groups of S. europaeiscabiei on the basis of differences in 131 genes. The results provide novel information about the genetic variability of S. europaeiscabiei and the gene-specific variability between the genomes of S. europaeiscabiei and S. scabies. The usefulness of a custom-designed, whole-genome oligonucleotide microarray in a survey of bacterial plant pathogens was demonstrated.

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