ArticleProceedings of the National Academy of Sciences of the United States of America2016
Theory of prokaryotic genome evolution.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers.
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86 citing papers in PubMed, 179 citations in OpenAlex.
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- The heterogeneous selection landscape of genome evolution in prokaryotes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Deep-branching Chloroflexota lineages illuminate the eco-evolutionary foundation of cross-ecosystem colonization.Nature communications · 2026Article
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- Wave succession in the pandemic clone of Vibrio parahaemolyticus driven by gene loss.Nature ecology & evolution · 2026Article
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- Rare metabolic gene essentiality is a determinant of microniche adaptation in Eschherichia coli.PLoS pathogens · 2025Article
- De novo origin of numerous microproteins in enterobacteria.Nucleic acids research · 2025Article
- Staphylococcus aureus promotes strain-dependent immunopathology during cutaneous leishmaniasis through induction of IL-1β.Cell reports · 2025Article
- Laboratory evolution of the bacterial genome structure through insertion sequence activation.Nucleic acids research · 2025Article
- Land conversion to cropland homogenizes variation in soil biota, gene assemblages, and ecological strategies on local and regional scales.The ISME journal · 2025Article
- Applying the Classic Test dN/dS to Detect Selection in Archaea.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Higher frequency of prokaryotic low complexity regions in core and orthologous genes.Frontiers in bioinformatics · 2025Article
- Principles of Molecular Evolution: Concepts from Non-equilibrium Thermodynamics for the Multilevel Theory of Learning.Journal of molecular evolution · 2024Article
26 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacteria and archaea typically possess small genomes that are tightly packed with protein-coding genes. The compactness of prokaryotic genomes is commonly perceived as evidence of adaptive genome streamlining caused by strong purifying selection in large microbial populations. In such populations, even the small cost incurred by nonfunctional DNA because of extra energy and time expenditure is thought to be sufficient for this extra genetic material to be eliminated by selection. However, contrary to the predictions of this model, there exists a consistent, positive correlation between the strength of selection at the protein sequence level, measured as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size. Here, by fitting the genome size distributions in multiple groups of prokaryotes to predictions of mathematical models of population evolution, we show that only models in which acquisition of additional genes is, on average, slightly beneficial yield a good fit to genomic data. These results suggest that the number of genes in prokaryotic genomes reflects the equilibrium between the benefit of additional genes that diminishes as the genome grows and deletion bias (i.e., the rate of deletion of genetic material being slightly greater than the rate of acquisition). Thus, new genes acquired by microbial genomes, on average, appear to be adaptive. The tight spacing of protein-coding genes likely results from a combination of the deletion bias and purifying selection that efficiently eliminates nonfunctional, noncoding sequences.
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