The Library
Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens
Tools
(2009) Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biology (Online), Vol.10 (No.5). R51. doi:10.1186/gb-2009-10-5-r51 ISSN 1474-760X.
|
PDF
WRAP_Challis_gb-2009-10-5-r51.pdf - Requires a PDF viewer. Download (3383Kb) |
Official URL: http://dx.doi.org/10.1186/gb-2009-10-5-r51
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.
Item Type: | Journal Article | ||||
---|---|---|---|---|---|
Subjects: | S Agriculture > SB Plant culture Q Science > QR Microbiology |
||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) > Biological Sciences ( -2010) Faculty of Science, Engineering and Medicine > Science > Chemistry |
||||
Library of Congress Subject Headings (LCSH): | Pseudomonas fluorescens, Bacterial genetics -- Research, Gram-negative bacteria, Plant-microbe relationships | ||||
Journal or Publication Title: | Genome Biology (Online) | ||||
Publisher: | BioMed Central Ltd. | ||||
ISSN: | 1474-760X | ||||
Official Date: | 11 May 2009 | ||||
Dates: |
|
||||
Volume: | Vol.10 | ||||
Number: | No.5 | ||||
Number of Pages: | 16 | ||||
Page Range: | R51 | ||||
DOI: | 10.1186/gb-2009-10-5-r51 | ||||
Status: | Peer Reviewed | ||||
Access rights to Published version: | Open Access (Creative Commons) | ||||
Funder: | Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC), Wellcome Trust (London, England), United States. Dept. of Energy. Office of Biological and Environmental Research, Lawrence Livermore Laboratory (LLL), Lawrence Berkeley National Laboratory (LBNL), Los Alamos National Laboratory (LANL), United States. Dept. of Agriculture, Foundation for Research, Science & Technology (N.Z.) (FRST) | ||||
Grant number: | 104/P16729 (BBSRC), P15257 (BBSRC), W-7405-Eng-48 (LLL), DE-AC03-76SF00098 (LBNL), W-7405-ENG-36 (LANL), 2006-35604-16673 (USDA) |
Data sourced from Thomson Reuters' Web of Knowledge
Request changes or add full text files to a record
Repository staff actions (login required)
View Item |
Downloads
Downloads per month over past year