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dc.contributor.authorSilby, Mark W.
dc.contributor.authorCerdeno-Tarraga, Ana M.
dc.contributor.authorVernikos, Georgios S.
dc.contributor.authorGiddens, Stephen R.
dc.contributor.authorJackson, Robert W.
dc.contributor.authorPreston, Gail M.
dc.contributor.authorZhang, Xue-Xian
dc.contributor.authorMoon, Christina D.
dc.contributor.authorGehrig, Stefanie M.
dc.contributor.authorGodfrey, Scott A. C.
dc.contributor.authorKnight, Christopher G.
dc.contributor.authorMalone, Jacob G.
dc.contributor.authorRobinson, Zena
dc.contributor.authorSpiers, Andrew J.
dc.contributor.authorHarris, Simon
dc.contributor.authorChallis, Gregory L
dc.contributor.authorYaxley, Alice M.
dc.contributor.authorHarris, David
dc.contributor.authorSeeger, Kathy
dc.contributor.authorMurphy, Lee
dc.contributor.authorRutter, Simon
dc.contributor.authorSquares, Rob
dc.contributor.authorQuail, Michael A.
dc.contributor.authorSaunders, Elizabeth
dc.contributor.authorMavromatis, Konstantinos
dc.contributor.authorBrettin, Thomas S.
dc.contributor.authorBentley, Stephen D.
dc.contributor.authorHothersall, Joanne
dc.contributor.authorStephens, Elton
dc.contributor.authorThomas, Christopher M.
dc.contributor.authorParkhill, Julian
dc.contributor.authorLevy, Stuart B.
dc.contributor.authorRainey, Paul B.
dc.contributor.authorThomson, Nicholas R.
dc.date.accessioned2010-10-07T21:30:01Z
dc.date.accessioned2016-03-06T22:26:03Z
dc.date.accessioned2016-09-07T13:57:46Z
dc.date.availableNO_RESTRICTIONen_US
dc.date.available2010-10-07T21:30:01Z
dc.date.available2016-03-06T22:26:03Z
dc.date.available2016-09-07T13:57:46Z
dc.date.issued2009-05-11
dc.identifier.citationSilby, M. W., Cerdeno-Tarraga, A. M., Vernikos, G. S., Giddens, S. R., Jackson, R. W., Preston, G. M., et al. (2009). Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biology, 10(R51). doi: 10.1186/gb-2009-10-5-r51en_US
dc.identifier.issn1474-760X
dc.identifier.urihttp://hdl.handle.net/10179/9706
dc.description.abstractBackground: 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.en_US
dc.language.isoenen_US
dc.publisherBiomed Centralen_US
dc.relation.isformatofhttp://genomebiology.com/2009/10/5/R51en_US
dc.relation.isbasedonGenome Biologyen_US
dc.relation.isbasedonBiomed Centralen_US
dc.rights© 2009 Silby et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.subjectPseudomonas fluorescensen_US
dc.subjectSoil bacteriaen_US
dc.subjectGenomeen_US
dc.subject.otherFields of Research::270000 Biological Sciences::270200 Geneticsen_US
dc.titleGenomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescensen_US
dc.typeJournal Articleen_US
dc.identifier.harvestedMassey_Dark
dc.identifier.harvestedMassey_Dark


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