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PMID: 19018999 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Distinguishing bacterial pathogens of potato using a genome-wide microarray approach.

Molecular plant pathology ·Vol. 9 ·No. 5 ·2008-09-00 ·Pages 705-17

Aittamaa M, Somervuo P, Pirhonen M, Mattinen L, Nissinen R, Auvinen P, Valkonen JP

Abstract

A set of 9676 probes was designed for the most harmful bacterial pathogens of potato and tested in a microarray format. Gene-specific probes could be designed for all genes of Pectobacterium atrosepticum, c. 50% of the genes of Streptomyces scabies and c. 30% of the genes of Clavibacter michiganensis ssp. sepedonicus utilizing the whole-genome sequence information available. For Streptomyces turgidiscabies, 226 probes were designed according to the sequences of a pathogenicity island containing important virulence genes. In addition, probes were designed for the virulence-associated nip (necrosis-inducing protein) genes of P. atrosepticum, P. carotovorum and Dickeya dadantii and for the intergenic spacer (IGS) sequences of the 16S-23S rRNA gene region. Ralstonia solanacearum was not included in the study, because it is a quarantine organism and is not presently found in Finland, but a few probes were also designed for this species. The probes contained on average 40 target-specific nucleotides and were synthesized on the array in situ, organized as eight sub-arrays with an identical set of probes which could be used for hybridization with different samples. All bacteria were readily distinguished using a single channel system for signal detection. Nearly all of the c. 1000 probes designed for C. michiganensis ssp. sepedonicus, c. 50% and 40% of the c. 4000 probes designed for the genes of S. scabies and P. atrosepticum, respectively, and over 100 probes for S. turgidiscabies showed significant signals only with the respective species. P. atrosepticum, P. carotovorum and Dickeya strains were all detected with 110 common probes. By contrast, the strains of these species were found to differ in their signal profiles. Probes targeting the IGS region and nip genes could be used to place strains of Dickeya to two groups, which correlated with differences in virulence. Taken together, the approach of using a custom-designed, genome-wide microarray provided a robust means for distinguishing the bacterial pathogens of potato.

MeSH Terms
Bacteria/classification,genetics Genome, Bacterial/genetics Oligonucleotide Array Sequence Analysis/methods Pectobacterium/genetics RNA, Ribosomal, 16S/genetics RNA, Ribosomal, 23S/genetics Ralstonia solanacearum/genetics Solanum tuberosum/microbiology Streptomyces/genetics
Chemicals
RNA, Ribosomal, 16S RNA, Ribosomal, 23S
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Aittamaa M
Department of Applied Biology, PO Box 27, FIN-00014 University of Helsinki, Finland.
Somervuo P
Pirhonen M
Mattinen L
Nissinen R
Auvinen P
Valkonen J P T
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Article Info
Journal
Molecular plant pathology
Abbr.
Mol Plant Pathol
ISSN
1364-3703
DOI
10.1111/j.1364-3703.2008.00482.x
Published
2008-09-00
Pages
705-17
Language
English
Region
England
NLM ID
100954969
PMCID
PMC6640225
Subset
IM
External Links
PubMed source DOI: 10.1111/j.1364-3703.2008.00482.x PMC Full Text View journal details
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