identifier: traitmech:000100
label: ploidy
definition: A genomics trait describing the number of complete genome copies per cell;
  many bacteria and archaea are polyploid, maintaining many chromosome copies that
  support survival, repair, and large cell size.
definition_source: DOI:10.1159/000368855
trait_category: GENOMICS
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000188
synonyms:
- synonym_text: polyploidy
  synonym_type: RELATED_SYNONYM
  source: DOI:10.1159/000368855
evidence:
- reference: DOI:10.1159/000368855
  notes: Soppa reviews polyploidy in archaea and bacteria and its links to desiccation
    resistance, giant cell size, and long-term survival.
- reference: DOI:10.1073/pnas.0707522105
  notes: Mendell et al. document extreme polyploidy (tens of thousands of genome copies)
    in the large bacterium Epulopiscium.
canonical_examples:
- taxon_id: NCBITaxon:354
  taxon_label: Azotobacter vinelandii
  note: "Model of bacterial polyploidy (accumulates up to ~100 genome copies per cell in stationary phase)."
  reference: PMID:8021173
causal_graphs:
- graph_id: ploidy_repair_survival
  title: Polyploidy supports DNA repair and long-term survival
  description: Evidence-backed causal sketch linking multiple genome copies to homologous-recombination
    repair templates and survival under desiccation and starvation.
  nodes:
  - node_id: ploidy_trait
    label: ploidy
    node_type: TRAIT
    grounding: traitmech:000100
    description: Number of complete genome copies per cell.
  - node_id: dna_recombinational_repair
    label: recombinational repair of damaged DNA
    node_type: BIOLOGICAL_PROCESS
    grounding: GO:0000725
    description: Homologous recombination using sister chromosome as repair template.
  - node_id: long_term_survival
    label: long-term survival
    node_type: QUALITY
    description: Persistence under desiccation, starvation, and damage.
  - node_id: phosphate_starvation
    label: phosphate starvation
    node_type: ENVIRONMENTAL_FACTOR
    description: Absence or limitation of environmental phosphate.
  - node_id: genome_copy_number
    label: genome copy number per cell
    node_type: QUALITY
    description: Number of chromosomal genome copies maintained per cell.
  - node_id: dna_phosphate_storage
    label: genomic DNA as phosphate storage polymer
    node_type: MOLECULAR_FUNCTION
    description: Use of genomic DNA copies as an intracellular phosphate reservoir.
  - node_id: growth_without_phosphate
    label: growth in absence of environmental phosphate
    node_type: CAPACITY
    description: Ability to grow when external phosphate is unavailable.
  - node_id: segregational_drift
    label: segregational drift
    node_type: BIOLOGICAL_PROCESS
    description: Stochastic segregation of alleles on polyploid replicons during cell
      division.
  - node_id: beneficial_allele_loss
    label: loss of beneficial resistance alleles
    node_type: BIOLOGICAL_PROCESS
    description: Stochastic loss of beneficial alleles carried on multicopy replicons.
  edges:
  - subject: ploidy_trait
    predicate: enables
    object: dna_recombinational_repair
    description: Extra genome copies provide templates for recombinational repair
      of DNA damage.
    evidence:
    - reference: DOI:10.1159/000368855
      notes: Soppa reviews polyploidy supporting damage tolerance via redundant chromosomes.
    predicate_id: RO:0002327
  - subject: ploidy_trait
    predicate: contributes to
    object: long_term_survival
    description: Polyploidy underpins desiccation resistance and large cell sizes
      observed in extreme polyploid lineages.
    evidence:
    - reference: DOI:10.1073/pnas.0707522105
      notes: Mendell et al. document extreme polyploidy in Epulopiscium supporting
        giant cell size.
    predicate_id: RO:0002326
  - subject: phosphate_starvation
    predicate: decreases
    object: genome_copy_number
    description: Polyploid prokaryotes reduce chromosomal copy number under phosphate
      starvation.
    evidence:
    - reference: DOI:10.3390/microorganisms11092267
      notes: All five characterized polyploid prokaryotic species grow without environmental
        phosphate by reducing genome copy numbers.
    predicate_id: RO:0002212
  - subject: genome_copy_number
    predicate: enables
    object: growth_without_phosphate
    description: Consuming extra genome copies as a phosphate source enables growth
      in the absence of external phosphate; monoploid E. coli cannot.
    evidence:
    - reference: DOI:10.3390/microorganisms11092267
      notes: Multiple polyploid prokaryotes grow without external phosphate by reducing
        intracellular genome copy number; monoploid E. coli showed no growth without
        phosphate.
    predicate_id: RO:0002327
  - subject: genome_copy_number
    predicate: has function
    object: dna_phosphate_storage
    description: Genomic DNA copies act as a phosphate storage polymer that can be
      consumed under starvation.
    evidence:
    - reference: DOI:10.3390/microorganisms11092267
      notes: Genomic DNA acts as a phosphate storage polymer in polyploid prokaryotes.
    predicate_id: RO:0000085
  - subject: ploidy_trait
    predicate: increases
    object: segregational_drift
    description: Higher ploidy increases stochastic segregation of alleles on polyploid
      replicons during division.
    evidence:
    - reference: DOI:10.1371/journal.pgen.1010829
      notes: Alleles on polyploid replicons segregate stochastically during cell division,
        termed segregational drift; shown with experiments and modeling.
    predicate_id: RO:0002213
  - subject: segregational_drift
    predicate: causes
    object: beneficial_allele_loss
    description: Segregational drift drives frequent loss of beneficial resistance
      alleles on multicopy replicons.
    evidence:
    - reference: DOI:10.1371/journal.pgen.1010829
      notes: Resistance alleles in polyploid elements are lost frequently versus monoploid
        elements due to segregational drift.
    predicate_id: biolink:causes
curation_history:
- timestamp: '2026-06-05T00:00:00Z'
  curator: claude
  action: PROPOSED_FROM_RESEARCH
  changes: Proposed candidate GENOMICS trait (ploidy / polyploidy) from literature
    research.
  llm_assisted: true
- timestamp: '2026-06-08T14:00:00Z'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added evidence-backed causal graph (ploidy / repair / survival) with GO
    node grounding and RO predicate groundings; promoted PROPOSED to REVIEWED.
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 5 evidence-backed generic edges (6 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:11Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002212×1, RO:0002327×1, RO:0000085×1, RO:0002213×1, biolink:causes×1).
  llm_assisted: true