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Microarray-based species identification of Streptomyces spp. isolated from potato scab lesions in Norway

ABSTRACT: Microarray-based species identification of Streptomyces spp. isolated from potato scab lesions in Norway

PROVIDER: PRJNA125179 | ENA |

REPOSITORIES: ENA

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Microarray-based species identification of Streptomyces spp. isolated from potato scab lesions in Norway

2010-05-01 | GSE20487 | GEO

Microarray-based species identification of Streptomyces spp. isolated from potato scab lesions in Norway

Project description:28 Streptomyces strains isolated from common scab lesions of potato tubers from a wide geographic range in Norway, were selected for microarray analysis. The selected strains were subjected to species identification by microarray, 16S phylogenetic analysis and PCR; and microarray-based comparative genome analysis. To our knowledge, this is the first report of S. turgidiscabies and S. europaeiscabiei in Norway. 28 Norwegian Streptomyces strains were hybridized in duplicates, one S.turgidiscabies strain (St32) and one S.scabies strain (ATCC49173) were hybridized in 4 replicates. Two out of 64 hybridizations failed (replicate hybridizations of Norwegian strains 33 and 44), for a total of 62 samples. Normalization was based on log-ratios against reference strain.

2010-04-30 | E-GEOD-20487 | biostudies-arrayexpress

Multi-omics reveals mechanisms of potato resistance to powdery scab

Project description:The potato powdery scab agent Spongospora subterranea causes damage on the skin of tubers and induces root gall formation, precipitating considerable yield and quality losses. Currently, there are no effective chemical treatments for the control of powdery scabs. Understanding the inducible defence responses in roots of potato plants in the resistant and susceptible host environment, particularly during colonisation of the root by S. subterranea is required for the breeding of novel resistant cultivars. Here, we integrated transcriptomics, proteomics and metabolomics datasets to uncover the mechanisms underlying of the potato resistance to powdery scab. This multi-omics approach identified upregulation of glutathione metabolism at the levels of RNA, protein and metabolite in the resistant cultivar but not in the susceptible cultivar. Upregulation of the lignin metabolic process was also specific to in the resistant cultivar at the transcriptome level. In addition, Tthe inositol phosphate pathway was differentially expressed between two cultivars in response to S. subterranea infection, where it was upregulated in the susceptible cultivar but downregulated in the resistant cultivar. We provide, for the first time, large-scale multi-omics data of Spongospora-potato interaction, thereby suggesting the signaling role of glutathione metabolism in the potato resistance against powdery scab

2022-08-12 | PXD029381 | Pride

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

Project description: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.

| S-EPMC6638902 | biostudies-literature

Comparison of genetic differences between Streptomyces scabies and turgidiscabies strains

2010-02-01 | GSE18665 | GEO

Streptomyces spp.

Project description:Genome sequences of three non-pathogenic Streptomyces strains isolated from potato common scab lesions

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Project description:Identification of scab resistant genes in apple varieties. The research was funded by SERB.

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Comparison of genetic differences between Streptomyces scabies and turgidiscabies strains

Project description:Bacteria isolated from potato scab lesions in Finland or northern Sweden were analyzed using microarrays, PCR, and sequencing. Data indicate wide genetic variability in pathogenicity islands among S.turgidiscabies and S.scabies strains. Thirteen Streptomyces scabies and turgidiscabies strains from two different growings, Streptomyces reticulisabiei reference strain DSM41804 and Streptomyces scabies reference strain ATCC49173 were hybridized. Data were analyzed in single channel mode.

2010-06-18 | E-GEOD-18665 | biostudies-arrayexpress

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