ArticlePLoS computational biology2010
Conditions for the evolution of gene clusters in bacterial genomes.
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 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
38 citing papers in PubMed, 64 citations in OpenAlex.
- Predicting rhizosphere-competence-related catabolic gene clusters in plant-associated bacteria with rhizoSMASH.Nature communications · 2025Article
- Evolution of gene order in prokaryotes is driven primarily by gene gain and loss.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Evolution of gene order in prokaryotes is driven primarily by gene gain and loss.bioRxiv : the preprint server for biology · 2025Article
- Exploring the microbial communities in coastal cenote and their hidden biotechnological potential.Microbial genomics · 2025Article
- Microbial community structure is affected by phage-resistance associated increases in host density.FEMS microbiology ecology · 2025Article
- A new selective force driving metabolic gene clustering.mSystems · 2024Article
- Noncontiguous operon atlas for themicroLife · 2024Article
- Genome-guided prediction of acid resistance mechanisms in acidophilic methanotrophs of phylogenetically deep-rooted Verrucomicrobia isolated from geothermal environments.Frontiers in microbiology · 2022Article
- Phylogenetic analysis of the bacterial Pro-Pro-endopeptidase domain reveals a diverse family including secreted and membrane anchored proteins.Current research in microbial sciences · 2021Review
- Mining genomes to illuminate the specialized chemistry of life.Nature reviews. Genetics · 2021Review
- Treat Me Well or Will Resist: Uptake of Mobile Genetic Elements Determine the Resistome ofInternational journal of molecular sciences · 2021Review
- Plant Metabolic Gene Clusters: Evolution, Organization, and Their Applications in Synthetic Biology.Frontiers in plant science · 2021Review
- Article
- Host-glycan metabolism is regulated by a species-conserved two-component system in Streptococcus pneumoniae.PLoS pathogens · 2020Article
- Advances in microbial culturing conditions to activate silent biosynthetic gene clusters for novel metabolite production.Journal of industrial microbiology & biotechnology · 2019Review
- The predominance of nucleotidyl activation in bacterial phosphonate biosynthesis.Nature communications · 2019Article
- Motion, fixation probability and the choice of an evolutionary process.PLoS computational biology · 2019Article
- Article
- Article
- FLIM-MAP: Gene Context Based Identification of Functional Modules in Bacterial Metabolic Pathways.Frontiers in microbiology · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genes encoding proteins in a common pathway are often found near each other along bacterial chromosomes. Several explanations have been proposed to account for the evolution of these structures. For instance, natural selection may directly favour gene clusters through a variety of mechanisms, such as increased efficiency of coregulation. An alternative and controversial hypothesis is the selfish operon model, which asserts that clustered arrangements of genes are more easily transferred to other species, thus improving the prospects for survival of the cluster. According to another hypothesis (the persistence model), genes that are in close proximity are less likely to be disrupted by deletions. Here we develop computational models to study the conditions under which gene clusters can evolve and persist. First, we examine the selfish operon model by re-implementing the simulation and running it under a wide range of conditions. Second, we introduce and study a Moran process in which there is natural selection for gene clustering and rearrangement occurs by genome inversion events. Finally, we develop and study a model that includes selection and inversion, which tracks the occurrence and fixation of rearrangements. Surprisingly, gene clusters fail to evolve under a wide range of conditions. Factors that promote the evolution of gene clusters include a low number of genes in the pathway, a high population size, and in the case of the selfish operon model, a high horizontal transfer rate. The computational analysis here has shown that the evolution of gene clusters can occur under both direct and indirect selection as long as certain conditions hold. Under these conditions the selfish operon model is still viable as an explanation for the evolution of gene clusters.
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.