ArticleBMC genomics2017
The nucleotide composition of microbial genomes indicates differential patterns of selection on core and accessory genomes.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
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- Molecular diversity and evolutionary dynamics of phage receptor binding proteins in Staphylococcus aureus: implications for phage therapy and resistance.Scientific reports · 2026Article
- Pan-genome insights into genetic diversity, evolutionary dynamics, and pathogenic traits of Staphylococcus agnetis.BMC genomics · 2026Article
- Genome-wide comparative and taxonomic characterization of prophages in Stenotrophomonas maltophilia.Archives of microbiology · 2026Article
- Extracellular vesicles drive stress-induced antibiotic resistance spread in soil.Environmental science and ecotechnology · 2026Article
- Characterizing the ecological niche of insertion sequences within prokaryotic genomes.The ISME journal · 2026Article
- DL-GapFilling: a novel deep learning framework for improved plant genome gap filling.Briefings in bioinformatics · 2026Article
- Pangenome Analysis of the Plant Pathogen Pseudomonas syringae Reveals Unique Natural Products for Niche Adaptation.Angewandte Chemie (International ed. in English) · 2025Article
- A 69.9-kb long inverted repeat increases genome instability in a strain ofNAR genomics and bioinformatics · 2025Article
- Homologous recombination shapes the architecture and evolution of bacterial genomes.Nucleic acids research · 2025Article
- Article
- First genome sequence and functional profiling ofFrontiers in microbiology · 2025Article
- The GC% landscape of the Nucleocytoviricota.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2024Article
- Development of a loop-mediated isothermal amplification method for the rapid detection of Clostridium botulinum serotypes E and F.Molecular biology reports · 2024Article
- Microplastic diversity increases the abundance of antibiotic resistance genes in soil.Nature communications · 2024Article
- Compression rates of microbial genomes are associated with genome size and base composition.Genomics & informatics · 2024Article
- Solving genomic puzzles: computational methods for metagenomic binning.Briefings in bioinformatics · 2024Review
- The role of DNA in the pathogenesis of SLE: DNA as a molecular chameleon.Annals of the rheumatic diseases · 2024Review
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5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe core genome consists of genes shared by the vast majority of a species and is therefore assumed to have been subjected to substantially stronger purifying selection than the more mobile elements of the genome, also known as the accessory genome. Here we examine intragenic base composition differences in core genomes and corresponding accessory genomes in 36 species, represented by the genomes of 731 bacterial strains, to assess the impact of selective forces on base composition in microbes. We also explore, in turn, how these results compare with findings for whole genome intragenic regions.
resultsWe found that GC content in coding regions is significantly higher in core genomes than accessory genomes and whole genomes. Likewise, GC content variation within coding regions was significantly lower in core genomes than in accessory genomes and whole genomes. Relative entropy in coding regions, measured as the difference between observed and expected trinucleotide frequencies estimated from mononucleotide frequencies, was significantly higher in the core genomes than in accessory and whole genomes. Relative entropy was positively associated with coding region GC content within the accessory genomes, but not within the corresponding coding regions of core or whole genomes.
conclusionThe higher intragenic GC content and relative entropy, as well as the lower GC content variation, observed in the core genomes is most likely associated with selective constraints. It is unclear whether the positive association between GC content and relative entropy in the more mobile accessory genomes constitutes signatures of selection or selective neutral processes.
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