GC content

Edge evidence

• genomic DNA carries GC content

  Genomic DNA is the substrate on which the GC content phenotype is measured.

  • DOI:10.1038/nrg2358 GC content Supports GC content as a property of the genomic DNA sequence.
• GC/AT mutation bias causes GC content biolink:causes

  Asymmetric GC/AT mutation bias shapes the equilibrium genome-wide GC content.

  • DOI:10.1186/1471-2148-10-374 mutation bias Supports mutation bias as a primary driver of bacterial GC content.
• GC-biased gene conversion causes GC content biolink:causes

  GC-biased gene conversion elevates GC content at recombination hotspots and across the genome.

  • DOI:10.1186/1471-2148-10-374 GC-biased gene conversion Supports GC-biased gene conversion as a recombination-driven contributor to GC content.
• selection on codon usage contributes to GC content RO:0002326

  Selection on synonymous codon usage contributes to genome-wide GC content patterns.

  • DOI:10.1038/nrg2358 codon usage Supports translational selection on codon usage as a contributor to GC composition.
• GC high is a GC content rdfs:subClassOf

  GC high is a quantitative bin of the GC-content phenotype.

  • DOI:10.1038/nrg2358 GC content Supports the binned phenotype as a value within the GC-content distribution.
• GC low is a GC content rdfs:subClassOf

  GC low is a quantitative bin of the GC-content phenotype.

  • DOI:10.1038/nrg2358 GC content Supports the binned phenotype as a value within the GC-content distribution.
• GC mid1 is a GC content rdfs:subClassOf

  GC mid1 is a quantitative bin of the GC-content phenotype.

  • DOI:10.1038/nrg2358 GC content Supports the binned phenotype as a value within the GC-content distribution.
• GC mid2 is a GC content rdfs:subClassOf

  GC mid2 is a quantitative bin of the GC-content phenotype.

  • DOI:10.1038/nrg2358 GC content Supports the binned phenotype as a value within the GC-content distribution.
• cytosine deamination decreases GC content RO:0002212

  Cytosine deamination introduces GC-to-AT changes, reducing genome-wide GC content.

  • DOI:10.1128/spectrum.02145-22 cytosine deamination reduces the GC content Strong mechanistic statement from bacterial comparative study; general mutation-bias edge.
• guanine oxidation (8-oxoG) decreases GC content RO:0002212

  Guanine oxidation (8-oxoG) promotes G:C to A:T mispairing, biasing composition toward lower GC.

  • DOI:10.1128/spectrum.02145-22 guanine oxidation (8OG) causes A mis-pairing Source-backed oxidative-damage mechanism shifting the mutational spectrum toward AT.
• DNA replication and repair (DRR) system change causes GC content biolink:causes

  Changes in the DNA replication and repair system drive mutational biases that shape GC-content evolution.

  • DOI:10.1128/spectrum.02145-22 ancient adaptations transformed the DRR system, producing mutational biases that shaped GC-content evolution Core, directly stated high-level mechanistic edge for the mutation-bias module.
• error-prone translesion synthesis increases GC content RO:0002213

  Error-prone translesion synthesis polymerases are causally linked to increases in genomic GC content.

  • DOI:10.1128/spectrum.02145-22 Error-prone polymerases are causally linked to increases in genomic GC Direction explicit in comparative study; complements existing mutation-bias drivers.