ArticleGenome biology and evolution2012
The infinitely many genes model for the distributed genome of bacteria.
Article in Genome biology and evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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57 citing papers in PubMed.
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- Persistent, Private, and Mobile Genes: A Model for Gene Dynamics in Evolving Pangenomes.Molecular biology and evolution · 2025Article
- CELEBRIMBOR: core and accessory genes from metagenomes.Bioinformatics (Oxford, England) · 2024Article
- Emergence of potentially disinfection-resistant, naturalized Escherichia coli populations across food- and water-associated engineered environments.Scientific reports · 2024Article
- Detecting co-selection through excess linkage disequilibrium in bacterial genomes.NAR genomics and bioinformatics · 2024Article
- A distinct, high-affinity, alkaline phosphatase facilitates occupation of P-depleted environments by marine picocyanobacteria.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Quantification and modeling of turnover dynamics of de novo transcripts in Drosophila melanogaster.Nucleic acids research · 2024Article
- Accurate and fast graph-based pangenome annotation and clustering with ggCaller.Genome research · 2023Article
- Isolation, biochemical characterization, and genome sequencing of two high-quality genomes of a novel chitinolytic Jeongeupia species.MicrobiologyOpen · 2023Article
- A multidrug-resistantMicrobial genomics · 2023Article
- Tackling the Pangenome Dilemma Requires the Concerted Analysis of Multiple Population Genetic Processes.Genome biology and evolution · 2023Article
- Challenges in prokaryote pangenomics.Microbial genomics · 2023Review
- Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe.Genome research · 2023Article
- Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes.BMC ecology and evolution · 2022Article
- Diversity and Evolution of Pigment Types in Marine Synechococcus Cyanobacteria.Genome biology and evolution · 2022Article
- Horizontal gene transfer and adaptive evolution in bacteria.Nature reviews. Microbiology · 2022Review
- Article
- Producing polished prokaryotic pangenomes with the Panaroo pipeline.Genome biology · 2020Article
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3 authors.
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Abstract
The distributed genome hypothesis states that the gene pool of a bacterial taxon is much more complex than that found in a single individual genome. However, the possible fitness advantage, why such genomic diversity is maintained, whether this variation is largely adaptive or neutral, and why these distinct individuals can coexist, remains poorly understood. Here, we present the infinitely many genes (IMG) model, which is a quantitative, evolutionary model for the distributed genome. It is based on a genealogy of individual genomes and the possibility of gene gain (from an unbounded reservoir of novel genes, e.g., by horizontal gene transfer from distant taxa) and gene loss, for example, by pseudogenization and deletion of genes, during reproduction. By implementing these mechanisms, the IMG model differs from existing concepts for the distributed genome, which cannot differentiate between neutral evolution and adaptation as drivers of the observed genomic diversity. Using the IMG model, we tested whether the distributed genome of 22 full genomes of picocyanobacteria (Prochlorococcus and Synechococcus) shows signs of adaptation or neutrality. We calculated the effective population size of Prochlorococcus at 1.01 × 10(11) and predicted 18 distinct clades for this population, only six of which have been isolated and cultured thus far. We predicted that the Prochlorococcus pangenome contains 57,792 genes and found that the evolution of the distributed genome of Prochlorococcus was possibly neutral, whereas that of Synechococcus and the combined sample shows a clear deviation from neutrality.
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