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

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dc.contributor.authorSilby MW
dc.contributor.authorCerdeno-Tarraga AM
dc.contributor.authorVernikos GS
dc.contributor.authorGiddens SR
dc.contributor.authorJackson RW
dc.contributor.authorPreston GM
dc.contributor.authorZhang XX
dc.contributor.authorMoon CD
dc.contributor.authorGehrig SM
dc.contributor.authorGodfrey SAC
dc.contributor.authorKnight CG
dc.contributor.authorMalone JG
dc.contributor.authorRobinson Z
dc.contributor.authorSpiers AJ
dc.contributor.authorHarris S
dc.contributor.authorChallis GL
dc.contributor.authorYaxley AM
dc.contributor.authorHarris D
dc.contributor.authorSeeger K
dc.contributor.authorMurphy L
dc.contributor.authorRutter S
dc.contributor.authorSquares R
dc.contributor.authorQuail MA
dc.contributor.authorSaunders E
dc.contributor.authorMavromatis K
dc.contributor.authorBrettin TS
dc.contributor.authorBentley SD
dc.contributor.authorHothersall J
dc.contributor.authorStephens E
dc.contributor.authorThomas CM
dc.contributor.authorParkhill J
dc.contributor.authorLevy SB
dc.contributor.authorRainey PB
dc.contributor.authorThomson NR
dc.date.accessioned2010-10-07T21:30:01Z
dc.date.accessioned2016-03-06T22:26:03Z
dc.date.availableNO_RESTRICTION
dc.date.available2010-10-07T21:30:01Z
dc.date.available2016-03-06T22:26:03Z
dc.date.issued2009
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.
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-r51
dc.identifier.harvestedMassey_Dark
dc.identifier.harvestedMassey_Dark
dc.identifier.issn1474-760X
dc.identifier.urihttps://hdl.handle.net/10179/1761
dc.language.isoen
dc.publisherBIOMED CENTRAL LTD
dc.relation.isbasedonGenome Biology
dc.relation.isbasedonBiomed Central
dc.relation.isformatofhttp://genomebiology.com/2009/10/5/R51
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 fluorescens
dc.subjectSoil bacteria
dc.subjectGenome
dc.subject.otherFields of Research::270000 Biological Sciences::270200 Genetics
dc.titleGenomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens
dc.typeJournal article
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