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Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens

Mark W Silby1, Ana M Cerdeño-Tárraga2, Georgios S Vernikos2, Stephen R Giddens3, Robert W Jackson34, Gail M Preston3, Xue-Xian Zhang5, Christina D Moon123, Stefanie M Gehrig3, Scott AC Godfrey133, Christopher G Knight143, Jacob G Malone153, Zena Robinson3, Andrew J Spiers163, Simon Harris2, Gregory L Challis6, Alice M Yaxley7, David Harris2, Kathy Seeger2, Lee Murphy2, Simon Rutter2, Rob Squares2, Michael A Quail2, Elizabeth Saunders8, Konstantinos Mavromatis9, Thomas S Brettin8, Stephen D Bentley2, Joanne Hothersall10, Elton Stephens10, Christopher M Thomas10, Julian Parkhill2, Stuart B Levy1, Paul B Rainey115 and Nicholas R Thomson2*

  • * Corresponding author: Nicholas R Thomson nrt@sanger.ac.uk

  • † Equal contributors

Author Affiliations

1 Centre for Adaptation Genetics and Drug Resistance and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA

2 Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK

3 Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK

4 School of Biological Sciences, The University of Reading, Whiteknights, Reading RG6 6AJ, UK

5 New Zealand Institute for Advanced Study, Massey University, Private Bag 102 904, North Shore Mail Centre, Auckland, New Zealand

6 Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK

7 Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK

8 DOE Joint Genome Institute, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA

9 Genome Biology Program, Department of Energy's Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA

10 Department of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK

11 Allan Wilson Centre for Molecular Ecology and Evolution, Massey University Auckland, Private Bag 102 904, North Shore Mail Centre, Auckland, New Zealand

12 Current address: AgResearch Limited, Grasslands Research Centre, Private Bag 11008, Palmerston North, New Zealand

13 Current address: School of Life Sciences, University of the West of England, Bristol, Frenchay Campus, Coldharbour Lane, Bristol BS16 1QY, UK

14 Current address: Faculty of Life Sciences, The University of Manchester, Oxford Road, Manchester M13 9PT, UK

15 Current address: Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland

16 Current address: SIMBIOS Centre, Level 5, Kydd Building, University of Abertay Dundee, Bell Street, Dundee DD1 1HG, UK

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Genome Biology 2009, 10:R51  doi:10.1186/gb-2009-10-5-r51

Published: 11 May 2009

Abstract

Background

Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species.

Results

Comparisons of three P. fluorescens genomes (SBW25, Pf0-1, Pf-5) revealed considerable divergence: 61% of genes are shared, the majority located near the replication origin. Phylogenetic and average amino acid identity analyses showed a low overall relationship. A functional screen of SBW25 defined 125 plant-induced genes including a range of functions specific to the plant environment. Orthologues of 83 of these exist in Pf0-1 and Pf-5, with 73 shared by both strains. The P. fluorescens genomes carry numerous complex repetitive DNA sequences, some resembling Miniature Inverted-repeat Transposable Elements (MITEs). In SBW25, repeat density and distribution revealed 'repeat deserts' lacking repeats, covering approximately 40% of the genome.

Conclusions

P. fluorescens genomes are highly diverse. Strain-specific regions around the replication terminus suggest genome compartmentalization. The genomic heterogeneity among the three strains is reminiscent of a species complex rather than a single species. That 42% of plant-inducible genes were not shared by all strains reinforces this conclusion and shows that ecological success requires specialized and core functions. The diversity also indicates the significant size of genetic information within the Pseudomonas pan genome.