identifier: METPO:1000127
label: GC content
definition: A quality that is describing the percentage of guanine and cytosine nucleotides
  in genomic DNA, calculated as the ratio of GC base pairs to total base pairs.
definition_source: DOI:10.1038/nrg2358
trait_category: GENOMICS
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000188
created_by: Luke Wang
evidence:
- reference: DOI:10.1038/nrg2358
  snippet: GC content
  notes: Bacterial-genome review supports GC content as a fundamental genome-composition
    descriptor varying widely across prokaryotic lineages.
- reference: DOI:10.1186/1471-2148-10-374
  snippet: GC-biased gene conversion
  notes: Bacterial-GC-content evolution review supports GC-biased gene conversion
    and mutation bias as the mechanistic drivers of genomic GC composition.
causal_graphs:
- graph_id: gc_content_composition_drivers
  title: GC content composition drivers
  description: DOI-backed graph linking mutation bias, GC-biased gene conversion,
    and selection on codon usage to the genome-wide GC content phenotype, with `is
    a` edges to the four METPO GC-content bins.
  nodes:
  - node_id: gc_content_trait
    label: GC content
    node_type: TRAIT
    grounding: METPO:1000127
    description: Percentage of guanine and cytosine nucleotides in genomic DNA.
  - node_id: genomic_dna
    label: genomic DNA
    node_type: CELLULAR_LOCALIZATION
    description: Bacterial or archaeal chromosomal DNA on which GC composition is
      measured.
  - node_id: mutation_bias
    label: GC/AT mutation bias
    node_type: BIOLOGICAL_PROCESS
    description: Asymmetric substitution rates between GC and AT base pairs across
      the genome.
  - node_id: gc_biased_gene_conversion
    label: GC-biased gene conversion
    node_type: BIOLOGICAL_PROCESS
    description: Recombination-associated process favoring fixation of GC alleles
      at heterozygous sites.
  - node_id: codon_usage_selection
    label: selection on codon usage
    node_type: BIOLOGICAL_PROCESS
    description: Translational and gene-expression selection shaping synonymous-codon
      GC content.
  - node_id: gc_high_bin
    label: GC high
    node_type: TRAIT
    grounding: METPO:1000432
    description: METPO GC-high bin (synonym GC_<=42.65; see record).
  - node_id: gc_low_bin
    label: GC low
    node_type: TRAIT
    grounding: METPO:1000429
    description: METPO GC-low bin (synonym GC_42.65_57.0; see record).
  - node_id: gc_mid1_bin
    label: GC mid1
    node_type: TRAIT
    grounding: METPO:1000430
    description: METPO GC-mid1 bin (synonym GC_>66.3; see record).
  - node_id: gc_mid2_bin
    label: GC mid2
    node_type: TRAIT
    grounding: METPO:1000431
    description: METPO GC-mid2 bin (synonym GC_57.0_66.3; see record).
  - node_id: cytosine_deamination
    label: cytosine deamination
    node_type: BIOLOGICAL_PROCESS
    description: Hydrolytic deamination of cytosine to uracil/thymine, a GC-to-AT
      mutational lesion.
  - node_id: guanine_oxidation
    label: guanine oxidation (8-oxoG)
    node_type: BIOLOGICAL_PROCESS
    description: Oxidative damage forming 8-oxoguanine that mispairs and biases the
      mutational spectrum toward AT.
  - node_id: dna_repair_replication_system
    label: DNA replication and repair (DRR) system change
    node_type: BIOLOGICAL_PROCESS
    description: Evolutionary change in DNA replication/repair machinery producing
      mutational biases that shape GC composition.
  - node_id: translesion_synthesis
    label: error-prone translesion synthesis
    node_type: BIOLOGICAL_PROCESS
    description: Error-prone DNA synthesis past lesions by specialized polymerases,
      causally linked to increased genomic GC.
    grounding: GO:0042276
  edges:
  - subject: genomic_dna
    predicate: carries
    object: gc_content_trait
    description: Genomic DNA is the substrate on which the GC content phenotype is
      measured.
    evidence:
    - reference: DOI:10.1038/nrg2358
      snippet: GC content
      notes: Supports GC content as a property of the genomic DNA sequence.
  - subject: mutation_bias
    predicate: causes
    object: gc_content_trait
    description: Asymmetric GC/AT mutation bias shapes the equilibrium genome-wide
      GC content.
    evidence:
    - reference: DOI:10.1186/1471-2148-10-374
      snippet: mutation bias
      notes: Supports mutation bias as a primary driver of bacterial GC content.
    predicate_id: biolink:causes
  - subject: gc_biased_gene_conversion
    predicate: causes
    object: gc_content_trait
    description: GC-biased gene conversion elevates GC content at recombination hotspots
      and across the genome.
    evidence:
    - reference: DOI:10.1186/1471-2148-10-374
      snippet: GC-biased gene conversion
      notes: Supports GC-biased gene conversion as a recombination-driven contributor
        to GC content.
    predicate_id: biolink:causes
  - subject: codon_usage_selection
    predicate: contributes to
    object: gc_content_trait
    description: Selection on synonymous codon usage contributes to genome-wide GC
      content patterns.
    evidence:
    - reference: DOI:10.1038/nrg2358
      snippet: codon usage
      notes: Supports translational selection on codon usage as a contributor to GC
        composition.
    predicate_id: RO:0002326
  - subject: gc_high_bin
    predicate: is a
    object: gc_content_trait
    description: GC high is a quantitative bin of the GC-content phenotype.
    evidence:
    - reference: DOI:10.1038/nrg2358
      snippet: GC content
      notes: Supports the binned phenotype as a value within the GC-content distribution.
    predicate_id: rdfs:subClassOf
  - subject: gc_low_bin
    predicate: is a
    object: gc_content_trait
    description: GC low is a quantitative bin of the GC-content phenotype.
    evidence:
    - reference: DOI:10.1038/nrg2358
      snippet: GC content
      notes: Supports the binned phenotype as a value within the GC-content distribution.
    predicate_id: rdfs:subClassOf
  - subject: gc_mid1_bin
    predicate: is a
    object: gc_content_trait
    description: GC mid1 is a quantitative bin of the GC-content phenotype.
    evidence:
    - reference: DOI:10.1038/nrg2358
      snippet: GC content
      notes: Supports the binned phenotype as a value within the GC-content distribution.
    predicate_id: rdfs:subClassOf
  - subject: gc_mid2_bin
    predicate: is a
    object: gc_content_trait
    description: GC mid2 is a quantitative bin of the GC-content phenotype.
    evidence:
    - reference: DOI:10.1038/nrg2358
      snippet: GC content
      notes: Supports the binned phenotype as a value within the GC-content distribution.
    predicate_id: rdfs:subClassOf
  - subject: cytosine_deamination
    predicate: decreases
    object: gc_content_trait
    description: Cytosine deamination introduces GC-to-AT changes, reducing genome-wide
      GC content.
    evidence:
    - reference: DOI:10.1128/spectrum.02145-22
      snippet: cytosine deamination reduces the GC content
      notes: Strong mechanistic statement from bacterial comparative study; general
        mutation-bias edge.
    predicate_id: RO:0002212
  - subject: guanine_oxidation
    predicate: decreases
    object: gc_content_trait
    description: Guanine oxidation (8-oxoG) promotes G:C to A:T mispairing, biasing
      composition toward lower GC.
    evidence:
    - reference: DOI:10.1128/spectrum.02145-22
      snippet: guanine oxidation (8OG) causes A mis-pairing
      notes: Source-backed oxidative-damage mechanism shifting the mutational spectrum
        toward AT.
    predicate_id: RO:0002212
  - subject: dna_repair_replication_system
    predicate: causes
    object: gc_content_trait
    description: Changes in the DNA replication and repair system drive mutational
      biases that shape GC-content evolution.
    evidence:
    - reference: DOI:10.1128/spectrum.02145-22
      snippet: ancient adaptations transformed the DRR system, producing mutational
        biases that shaped GC-content evolution
      notes: Core, directly stated high-level mechanistic edge for the mutation-bias
        module.
    predicate_id: biolink:causes
  - subject: translesion_synthesis
    predicate: increases
    object: gc_content_trait
    description: Error-prone translesion synthesis polymerases are causally linked
      to increases in genomic GC content.
    evidence:
    - reference: DOI:10.1128/spectrum.02145-22
      snippet: Error-prone polymerases are causally linked to increases in genomic
        GC
      notes: Direction explicit in comparative study; complements existing mutation-bias
        drivers.
    predicate_id: RO:0002213
curation_history:
- timestamp: '2026-05-05T01:35:46.811180+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-13T13:00:00-07:00'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added DOI-backed causal graph linking mutation bias, GC-biased gene conversion,
    and codon-usage selection to the GC-content phenotype, with is-a edges to the
    four METPO GC-content bins.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:30Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (rdfs:subClassOf×4, RO:0002326×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:13:18Z'
  curator: claude
  action: RENAME_PREDICATE_LABELS
  changes: 'Renamed 2 causal-edge predicate label(s) to align with existing groundings:
    shapes → causes ×2.'
  llm_assisted: true
- timestamp: '2026-05-24T04:13:21Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:causes×2).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 4 evidence-backed generic edges (4 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:11Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002212×2, biolink:causes×1, RO:0002213×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:32Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0042276×1).
  llm_assisted: true