ArticleGenome biology and evolution2015
Prokaryotic nucleotide composition is shaped by both phylogeny and the environment.
Article in Genome biology and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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55 citing papers in PubMed.
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- Metagenomic sequencing and binning reveal carbon cycling microorganisms and gene functions in park environments.BMC microbiology · 2026Article
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- Prospective identification of extracellular triacylglycerol hydrolase with conserved amino acids inBiotechnology reports (Amsterdam, Netherlands) · 2025Article
- Homologous recombination shapes the architecture and evolution of bacterial genomes.Nucleic acids research · 2025Article
- G-quadruplex structures in 16S rRNA regions correlate with thermal adaptation in prokaryotes.Nucleic acids research · 2025Article
- Laws of Genome Nucleotide Composition.Genomics, proteomics & bioinformatics · 2024Article
- Compression rates of microbial genomes are associated with genome size and base composition.Genomics & informatics · 2024Article
- Homologous Recombination Shapes the Architecture and Evolution of Bacterial Genomes.bioRxiv : the preprint server for biology · 2024Article
- Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae.Nature communications · 2023Article
- Genomic Legacies of Ancient Adaptation Illuminate GC-Content Evolution in Bacteria.Microbiology spectrum · 2023Article
- Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis.NPJ biofilms and microbiomes · 2023Article
- A simple stochastic model describing the evolution of genomic GC content in asexually reproducing organisms.Scientific reports · 2022Article
- Evolutionary jumps in bacterial GC content.G3 (Bethesda, Md.) · 2022Article
- Exploring the Distinct Distribution of Archaeal Communities in Sites Contaminated with Explosives.Biomolecules · 2022Article
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- Hydrological properties predict the composition of microbial communities cycling methane and nitrogen in rivers.ISME communications · 2022Article
- CompoDynamics: a comprehensive database for characterizing sequence composition dynamics.Nucleic acids research · 2022Article
- Common Features in lncRNA Annotation and Classification: A Survey.Non-coding RNA · 2021Review
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Abstract
The causes of the great variation in nucleotide composition of prokaryotic genomes have long been disputed. Here, we use extensive metagenomic and whole-genome data to demonstrate that both phylogeny and the environment shape prokaryotic nucleotide content. We show that across environments, various phyla are characterized by different mean guanine and cytosine (GC) values as well as by the extent of variation on that mean value. At the same time, we show that GC-content varies greatly as a function of environment, in a manner that cannot be entirely explained by disparities in phylogenetic composition. We find environmentally driven differences in nucleotide content not only between highly diverged environments (e.g., soil, vs. aquatic vs. human gut) but also within a single type of environment. More specifically, we demonstrate that some human guts are associated with a microbiome that is consistently more GC-rich across phyla, whereas others are associated with a more AT-rich microbiome. These differences appear to be driven both by variations in phylogenetic composition and by environmental differences-which are independent of these phylogenetic composition differences. Combined, our results demonstrate that both phylogeny and the environment significantly affect nucleotide composition and that the environmental differences affecting nucleotide composition are far subtler than previously appreciated.
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