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United States Department of Agriculture

Agricultural Research Service

Research Project: PSEUDOMONAS SYSTEMS BIOLOGY

Location: Plant-Microbe Interactions Research

Title: Genomic plasticity enables phenotypic variation of Pseudomonas syringae pv. tomato DC3000

Authors
item Swingle, Bryan
item Bao, Zhongmeng -
item Stodghill, Paul
item Myers, Christopher -
item Lam, Hanh -
item Markel, Eric
item Collmer, Alan -
item Cartinhour, Samuel
item Schweitzer, Peter -

Submitted to: Molecular Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 6, 2013
Publication Date: February 6, 2014
Citation: Swingle, B.M., Bao, Z., Stodghill, P., Myers, C.R., Lam, H., Markel, E.J., Collmer, A., Cartinhour, S.W., Schweitzer, P. 2014. Genomic plasticity enables phenotypic variation of Pseudomonas syringae pv. tomato DC3000. Molecular Microbiology. 9(2):e86628. DOI: 10.1371/Journal.pone.0086628.

Interpretive Summary: Plant diseases are an ever-present threat to agriculture and directly impact production of food, fiber and fuel. Modern agricultural systems rely heavily on pesticides and plant breading to help protect crops from being destroyed by disease. The problem is, that development of these strategies is very costly and the microbes that cause disease in plants adapt quickly to overcome the new control measures. We have very little understanding of what enables these microbes to change so quickly and make worthless all of the effort that went into development of the control strategy. In this report, we describe an example of how the DNA of a destructive plant pathogen can change and how this effects the behavior of the microbe. We used state of the art methods to examine a plant pathogen and found a specific segment of its genome duplicated spontaneously. Our finding demonstrates that microbial genomes are able to quickly mutate, providing ways to help them meet the demands of their immediate environment, thus allowing these microbes to grow faster and become more virulent. This means that changes in the DNA, could cause the microbe to become more aggressive and destructive. This information is relevant to anyone working towards building a healthy, productive and sustainable agriculture.

Technical Abstract: Whole genome sequencing revealed the presence of a genomic anomaly in the region of 4.7 to 4.9 Mb of the Pseudomonas syringae pv. tomato (Pst) DC3000 genome. The average read depth coverage of Pst DC3000 suggested that a 165 kb segment of the chromosome had doubled in copy number. PCR and analysis of deletion derivatives confirmed that the 165 kb region had been duplicated and that the two copies are positioned as a tandem duplication. Additionally, comparison of this locus to the progenitor strain suggested that the 165 kb duplication likely formed in two steps since Pst DC3000 diverged from Pst NCPPB1106: first by transposition of an ISPsy5 insertion sequence (IS) followed by unequal crossing over between ISPsy5 elements at each end of the duplicated region. Deletion of one copy of the 165 kb region revealed that the duplication facilitates enhanced growth in some culture conditions, but does not affect pathogenic growth in host tomato plants. These types of duplications are predicted to be unstable and we have observed at least one example of the 165 kb duplication collapsing to single copy and then subsequently reforming. These data results demonstrate the role of IS elements in recombination events that facilitate genomic reorganization and the dynamic nature of bacterial genomes. These rearrangements provide a mechanism for phenotypic adaptation without the introduction of foreign DNA sequences. Additionally, we present an automated method for identifying copy number polymorphisms in bacterial genomes using whole genome sequence data.

Last Modified: 11/28/2014
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