ArticleGenome biology2009
Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens.
Article in Genome biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 210 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
210 citing papers in PubMed.
- Cloning of human DING: Developmental expression and downregulation by EtOH in-utero.Archives of internal medicine research · 2026Article
- Compensatory evolution facilitates loss of prfB autoregulation in Pseudomonas fluorescens SBW25.Molecular biology and evolution · 2026Article
- Article
- Article
- Jumbo phage-mediated transduction of genomic islands.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Genetic Drivers of Plant Root Colonisation by the Biocontrol Agent Pseudomonas protegens Pf-5.Environmental microbiology reports · 2025Article
- Polyyne production is regulated by the transcriptional regulators PgnC and GacA inApplied and environmental microbiology · 2025Article
- Diversity and functional features of the root-associated bacteriome are dependent on grapevine susceptibility to Plasmopara viticola.Environmental microbiome · 2025Article
- A more significant role for insertion sequences in large-scale rearrangements in bacterial genomes.mBio · 2025Article
- An extreme mutational hotspot in nlpD depends on transcriptional induction of rpoS.PLoS genetics · 2025Article
- Comparative analysis of thermal adaptations of extremophilic prolyl oligopeptidases.Biophysical journal · 2024Article
- Molecular mechanism of the one-component regulator RccR on bacterial metabolism and virulence.Nucleic acids research · 2024Article
- The genotype of barley cultivars influences multiple aspects of their associated microbiota via differential root exudate secretion.PLoS biology · 2024Article
- Large-scale duplication events underpin population-level flexibility in tRNA gene copy number in Pseudomonas fluorescens SBW25.Nucleic acids research · 2024Article
- Total substitution and partial modification of the set of non-ribosomal peptide synthetases clusters lead to pyoverdine diversity in theFrontiers in microbiology · 2024Article
- Expanding theFrontiers in microbiology · 2024Article
- Insights into the diversity and survival strategies of soil bacterial isolates from the Atacama Desert.Frontiers in microbiology · 2024Article
- Polar accumulation of pyoverdin and exit from stationary phase.microLife · 2024Article
- Mutational hotspots lead to robust but suboptimal adaptive outcomes in certain environments.Microbiology (Reading, England) · 2023Article
- Evolutionary innovation through transcription factor rewiring in microbes is shaped by levels of transcription factor activity, expression, and existing connectivity.PLoS biology · 2023Article
150 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
34 authors.
Funding
Abstract
backgroundPseudomonas 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.
resultsComparisons 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.
conclusionsP. 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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.