identifier: METPO:1000431 label: GC mid2 definition: A GC-content phenotype with genome-wide GC composition between approximately 57.0% and 66.3% (the METPO `GC_57.0_66.3` bin). definition_source: DOI:10.1038/nrg2358 trait_category: GENOMICS term_kind: CLASS mapping_status: REVIEWED parent_traits: - METPO:1000127 synonyms: - synonym_text: GC_57.0_66.3 synonym_type: RELATED_SYNONYM source: metpo.owl evidence: - reference: DOI:10.1186/1471-2148-10-374 snippet: GC-biased gene conversion notes: Bacterial-GC-content evolution review supports moderate GC-biased gene conversion as the mechanism producing mid-high GC content. causal_graphs: - graph_id: gc_mid2_mid_high_gc_bin title: GC-mid2 (METPO 57.0–66.3%) mid-high GC bin description: DOI-backed graph linking moderate GC-biased gene conversion to a GC content of ~57.0–66.3% (the threshold encoded by the METPO synonym GC_57.0_66.3 on this record). nodes: - node_id: gc_mid2_trait label: GC mid2 node_type: TRAIT grounding: METPO:1000431 description: GC content ~57.0–66.3% (per METPO synonym GC_57.0_66.3). - node_id: gc_content label: GC content node_type: TRAIT grounding: METPO:1000127 description: Percentage of guanine and cytosine nucleotides in genomic DNA. - node_id: moderate_gbgc label: moderate GC-biased gene conversion node_type: BIOLOGICAL_PROCESS description: Recombination-associated GC-favoring activity sufficient to elevate GC content into the mid-high range. - node_id: homologous_recombination label: homologous recombination node_type: BIOLOGICAL_PROCESS description: Template-directed exchange/repair pathway that drives GC-biased gene conversion. grounding: GO:0035825 - node_id: mutation_bias_at label: mutation bias toward AT node_type: BIOLOGICAL_PROCESS description: Universal excess of G/C->A/T mutations in bacteria opposing high genomic GC. - node_id: cytosine_deamination label: cytosine deamination node_type: BIOLOGICAL_PROCESS description: Spontaneous/chemically promoted C->T transition source contributing to AT enrichment. - node_id: guanine_oxidation label: guanine oxidation / 8-oxoG damage node_type: BIOLOGICAL_PROCESS description: Oxidative lesion process yielding G->T/C->A transversions and compositional bias. - node_id: dna_repair_efficiency label: DNA repair efficiency node_type: BIOLOGICAL_PROCESS description: Efficiency/specificity of repair pathways affecting which mutational biases are fixed. - node_id: assembly_gc_bias label: sequencing/assembly GC bias node_type: EXPERIMENTAL_FACTOR description: Technical bias where observed assembly GC shifts with true GC%, depth, and error rate. edges: - subject: moderate_gbgc predicate: produces object: gc_mid2_trait description: Moderate GC-biased gene conversion yields mid-high genome-wide GC composition. evidence: - reference: DOI:10.1186/1471-2148-10-374 snippet: GC-biased gene conversion notes: Supports GC-biased gene conversion as the driver of mid-high GC bins. predicate_id: METPO:2000202 - subject: gc_mid2_trait predicate: is a object: gc_content description: GC mid2 is a quantitative bin of the GC-content phenotype. evidence: - reference: DOI:10.1038/nrg2358 snippet: GC content notes: Supports the 57.0–66.3% bin as a value within the GC-content distribution. predicate_id: rdfs:subClassOf - subject: homologous_recombination predicate: positively influences object: moderate_gbgc description: Recombination increases fixation of AT->GC mutations via GC-biased gene conversion. evidence: - reference: DOI:10.1101/011023 notes: 'gBGC: recombination tends to increase fixation of AT->GC mutations.' - subject: mutation_bias_at predicate: negatively influences object: gc_mid2_trait description: Universal AT-biased mutation opposes maintenance of mid-high genomic GC. evidence: - reference: DOI:10.1101/011023 notes: Universal excess of G/C->A/T mutations; mutation universally biased towards AT. - subject: cytosine_deamination predicate: positively influences object: mutation_bias_at description: Cytosine deamination (C->T) drives A+T enrichment. evidence: - reference: DOI:10.63635/mrj.v1i4.188 notes: Cytosine deamination (C->T) drives A+T enrichment. - subject: guanine_oxidation predicate: positively influences object: mutation_bias_at description: Guanine oxidation to 8-oxo-guanine (G->T) contributes to AT-biased composition. evidence: - reference: DOI:10.63635/mrj.v1i4.188 notes: Guanine oxidation to 8-oxo-guanine (G->T). - subject: dna_repair_efficiency predicate: influences object: gc_mid2_trait description: Variation in repair efficiency affects fixation of changes and long-term G+C content. evidence: - reference: DOI:10.63635/mrj.v1i4.188 notes: Variations in DNA repair efficiency influence fixation and thus long-term G+C content. - subject: assembly_gc_bias predicate: can distort measurement of object: gc_mid2_trait description: Assembly conditions can bias observed GC% in a direction dependent on true GC%. evidence: - reference: DOI:10.1186/s12864-023-09910-4 notes: In low-GC genomes factors inflate assembly GC; in high-GC genomes they decrease it. curation_history: - timestamp: '2026-05-05T01:35:46.817814+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 definition (derived from METPO synonym GC_57.0_66.3) and causal graph linking moderate GC-biased gene conversion to this GC bin. llm_assisted: true - timestamp: '2026-05-20T03:35:30Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×1, rdfs:subClassOf×1). llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report. 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:0035825×1). llm_assisted: true