identifier: traitmech:000092
label: transposable element
definition: A genomics trait describing possession of transposable elements — such
  as insertion sequences and transposons — that move within the genome and drive genome
  rearrangement, gene inactivation, and plasticity.
definition_source: DOI:10.1111/1574-6976.12067
trait_category: GENOMICS
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- traitmech:000089
synonyms:
- synonym_text: insertion sequence
  synonym_type: RELATED_SYNONYM
  source: DOI:10.1111/1574-6976.12067
- synonym_text: transposon
  synonym_type: RELATED_SYNONYM
  source: DOI:10.1111/1574-6976.12067
evidence:
- reference: DOI:10.1111/1574-6976.12067
  notes: Siguier, Gourbeyre & Chandler review bacterial insertion sequences and their
    genomic impact and diversity.
- reference: DOI:10.1038/nrmicro1235
  notes: Frost et al. include transposons among the mobile genetic elements driving
    genome evolution.
canonical_examples:
- taxon_id: NCBITaxon:562
  taxon_label: Escherichia coli
  note: "insertion sequences and Tn transposons"
  reference: PMID:21224843
- taxon_id: NCBITaxon:303
  taxon_label: Pseudomonas putida
  note: "catabolic transposons"
  reference: PMID:16352819
causal_graphs:
- graph_id: te_transposition_rearrangement
  title: Transposable elements drive DNA transposition and genome rearrangement
  description: Evidence-backed causal sketch linking TE possession to DNA transposition
    activity and resulting genome rearrangement and plasticity.
  nodes:
  - node_id: te_trait
    label: transposable element
    node_type: TRAIT
    grounding: traitmech:000092
    description: Possession of insertion sequences or transposons.
  - node_id: dna_transposition
    label: DNA transposition
    node_type: BIOLOGICAL_PROCESS
    grounding: GO:0006313
    description: Movement of a DNA segment to a new genomic location.
  - node_id: genome_rearrangement
    label: genome rearrangement
    node_type: QUALITY
    description: Insertions, deletions, and inversions of chromosomal segments.
  - node_id: transposase
    label: transposase
    node_type: GENE_OR_PROTEIN
    description: DDE-family enzyme encoded by the element that catalyzes its movement.
    grounding: UniProtKB:A0A023WVD3
  - node_id: te_insertion
    label: transposable element insertion
    node_type: BIOLOGICAL_PROCESS
    description: Integration of a transposable element at a target genomic site.
  - node_id: target_site_duplication
    label: target site duplication
    node_type: QUALITY
    description: Short direct repeats flanking the element created upon insertion.
  - node_id: gene_disruption
    label: gene disruption
    node_type: BIOLOGICAL_PROCESS
    description: Inactivation of a gene by insertion of a transposable element into
      it.
  - node_id: homologous_recombination_is
    label: homologous recombination between IS copies
    node_type: BIOLOGICAL_PROCESS
    description: Recombination between identical IS copies at distinct loci.
  edges:
  - subject: te_trait
    predicate: enables
    object: dna_transposition
    description: TEs encode transposases that catalyze transposition.
    evidence:
    - reference: DOI:10.1111/1574-6976.12067
      notes: Siguier et al. review insertion-sequence transposase machinery and activity.
    predicate_id: RO:0002327
  - subject: dna_transposition
    predicate: causes
    object: genome_rearrangement
    description: Transposition events generate insertions and rearrangements.
    evidence:
    - reference: DOI:10.1038/nrmicro1235
      notes: Frost et al. cite transposons among MGEs driving genome evolution.
    predicate_id: biolink:causes
  - subject: te_trait
    predicate: has participant
    object: transposase
    description: The defining effector of a TE is a transposase required for movement.
    evidence:
    - reference: DOI:10.1128/MMBR.00119-22
      notes: IS element encodes a single ORF, a DDE-family transposase required for
        movement (Harmer & Hall 2024).
  - subject: transposase
    predicate: enables
    object: dna_transposition
    description: Transposase activity is causal for element movement/transposition.
    evidence:
    - reference: DOI:10.1128/MMBR.00119-22
      notes: tnp26 encodes a transposase required for movement (Harmer & Hall 2024).
    predicate_id: RO:0002327
  - subject: te_insertion
    predicate: causes
    object: target_site_duplication
    description: Element insertion typically generates short flanking target site
      duplications.
    evidence:
    - reference: DOI:10.1038/s41467-023-39964-7
      notes: Insertion sequences typically create target site duplications (TSDs)
        upon insertion (Sheng et al. 2023).
    predicate_id: biolink:causes
  - subject: te_insertion
    predicate: causes
    object: gene_disruption
    description: Insertion into a coding region disrupts gene function.
    evidence:
    - reference: DOI:10.1038/s41467-023-39964-7
      notes: Element movement causes gene disruption (Sheng et al. 2023).
    predicate_id: biolink:causes
  - subject: homologous_recombination_is
    predicate: causes
    object: genome_rearrangement
    description: Recombination between identical IS copies produces genome rearrangements.
    evidence:
    - reference: DOI:10.1038/s41467-023-39964-7
      notes: Homologous recombination between identical IS copies can produce genome
        rearrangements (Sheng et al. 2023).
    predicate_id: biolink:causes
curation_history:
- timestamp: '2026-06-05T00:00:00Z'
  curator: claude
  action: PROPOSED_FROM_RESEARCH
  changes: Proposed candidate GENOMICS trait (transposable element); sub-variant of
    mobile genetic element.
  llm_assisted: true
- timestamp: '2026-06-08T14:00:00Z'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added evidence-backed causal graph (transposition / genome rearrangement)
    with GO node grounding and RO/biolink 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 (5 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
    (biolink:causes×3, RO:0002327×1).
  llm_assisted: true
- timestamp: '2026-06-26T07:15:18Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A023WVD3×1).
  llm_assisted: true