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United States Department of Agriculture

Agricultural Research Service

Research Project: BIOLOGY AND MANAGEMENT OF SOILBORNE DISEASES OF HORTICULTURAL CROPS Title: Comparative genomic analysis reveals new aspects of the biology and secondary metabolism of biological control strains of Pseudomonas spp.

Authors
item Loper, Joyce
item Hassan, Karl -
item Davis, Edward
item Lim, Chee -
item Paulsen, Ian -

Submitted to: Phytopathology
Publication Type: Abstract Only
Publication Acceptance Date: March 30, 2011
Publication Date: June 1, 2011
Citation: Loper, J.E., Hassan, K.A., Davis, E.W., Lim, C.K., Paulsen, I.T. 2011. Comparative genomic analysis reveals new aspects of the biology and secondary metabolism of biological control strains of Pseudomonas spp.. Phytopathology. 101(6S):231.

Technical Abstract: To explore the genomic diversity of biocontrol strains of Pseudomonas spp., we derived high quality draft sequences of seven strains that suppress plant disease. The strains were isolated from the phyllosphere of pear (P. fluorescens A506), the rhizosphere of wheat (three strains of P. fluorescens and two strains of P. chlororaphis), or the rhizosphere of peach (P. synxantha BG33R). Genome size varies from ca. 5.9 Megabases with 5500 ORFs (P. fluorescens A506) to 7.0 Megabases with 6300 ORFs (P. chlororaphis O-6). Along with three previously-sequenced strains of P. fluorescens (Pf-5, Pf0-1 and SBW25), these bacteria share 2831 genes that represent a core genome, with each strain having approximately 300 to 900 genes that are not found in the other genomes. Phylogenetic analysis of the ten strains defined three distinct clades. Within each clade, the strains share 75 to 90% of their proteomes, whereas a smaller proportion of the proteome, typically 60 to 70%, is shared between strains in different clades. Bioinformatic analysis revealed genes with potential roles in the biology of each strain and its multitrophic interactions on plant surfaces, including genes for the production of toxins, antibiotics, and siderophores not previously associated with these strains. The many orphan gene clusters in the genomes provide avenues for the future discovery of novel natural products, including those contributing to biocontrol of plant disease.

Last Modified: 10/23/2014
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