identifier: traitmech:000093 label: genomic island definition: A genomics trait describing possession of a genomic island — a horizontally acquired chromosomal region (e.g. a pathogenicity, symbiosis, or metabolic island) that often retains mobility signatures such as flanking repeats and atypical nucleotide composition. definition_source: DOI:10.1038/nrmicro884 trait_category: GENOMICS term_kind: CLASS mapping_status: REVIEWED parent_traits: - traitmech:000089 synonyms: - synonym_text: pathogenicity island synonym_type: NARROW_SYNONYM source: DOI:10.1038/nrmicro884 evidence: - reference: DOI:10.1038/nrmicro884 notes: Dobrindt et al. review genomic islands in pathogenic and environmental microorganisms. - reference: DOI:10.1111/j.1574-6976.2008.00136.x notes: Juhas et al. review genomic islands as tools of bacterial horizontal gene transfer and evolution. canonical_examples: - taxon_id: NCBITaxon:28901 taxon_label: Salmonella enterica note: "Salmonella pathogenicity islands (SPI)" reference: PMID:17715824 - taxon_id: NCBITaxon:666 taxon_label: Vibrio cholerae note: "Vibrio pathogenicity island (VPI)" reference: PMID:33123494 causal_graphs: - graph_id: gi_hgt_accessory_function title: Genomic islands acquired by HGT carry accessory functions description: Evidence-backed causal sketch linking horizontal gene transfer to acquisition of genomic islands that confer accessory phenotypes (pathogenicity, symbiosis, metabolism). nodes: - node_id: gi_trait label: genomic island node_type: TRAIT grounding: traitmech:000093 description: Possession of a horizontally acquired chromosomal island. - node_id: horizontal_gene_transfer label: horizontal gene transfer node_type: BIOLOGICAL_PROCESS description: Transfer of genetic material between organisms outside vertical descent. grounding: GO:0009292 - node_id: accessory_function label: accessory function node_type: QUALITY description: Pathogenicity, symbiosis, or metabolic capability encoded by the island. - node_id: mobility_module label: integrase/recombinase/transposase mobility module node_type: GENE_OR_PROTEIN description: DDE transposases or tyrosine/serine recombinases that mediate island integration and mobility. - node_id: integrative_conjugative_element label: integrative conjugative element (ICE) node_type: BIOLOGICAL_PROCESS description: Self-transmissible genomic island subclass that excises, transfers by conjugation, and reintegrates. - node_id: conjugation label: conjugation node_type: BIOLOGICAL_PROCESS description: Contact-dependent transfer of DNA between cells. - node_id: type_iv_secretion_system label: type IV secretion system (T4SS) node_type: GENE_OR_PROTEIN description: Secretion apparatus that mediates conjugative DNA transfer. - node_id: integrative_mobilizable_element label: integrative mobilizable element (IME) node_type: BIOLOGICAL_PROCESS description: Genomic island subclass that lacks its own conjugation apparatus and spreads using a helper ICE or conjugative plasmid. edges: - subject: horizontal_gene_transfer predicate: causes object: gi_trait description: Genomic islands are integrated into host chromosomes via HGT. evidence: - reference: DOI:10.1111/j.1574-6976.2008.00136.x notes: Juhas et al. review genomic islands as tools of bacterial HGT. predicate_id: biolink:causes - subject: gi_trait predicate: contributes to object: accessory_function description: Genomic islands deliver pathogenicity, symbiosis, or metabolic modules to the host. evidence: - reference: DOI:10.1038/nrmicro884 notes: Dobrindt et al. review genomic islands carrying virulence and metabolic functions in pathogens and environmental microbes. predicate_id: RO:0002326 - subject: gi_trait predicate: carries object: mobility_module description: Genomic islands often encode a dedicated mobility module (DDE transposase or tyrosine/serine recombinase). evidence: - reference: DOI:10.1093/nar/gkad644 notes: Intracellular mobility is often mediated by dedicated DDE transposases or integrases belonging to serine or tyrosine recombinases. - subject: integrative_conjugative_element predicate: disseminates by object: conjugation description: ICE-type genomic islands spread by conjugation. evidence: - reference: DOI:10.1093/nar/gkad644 notes: ICEs disseminate by conjugation. - subject: integrative_conjugative_element predicate: requires object: type_iv_secretion_system description: ICE conjugative transfer requires a type IV secretion system. evidence: - reference: DOI:10.1093/nar/gkad644 notes: ICEs disseminate by conjugation using a type IV secretion system (T4SS). - subject: integrative_mobilizable_element predicate: uses object: conjugation description: IME-type islands lack their own apparatus and spread via the conjugative apparatus of a helper ICE or conjugative plasmid. evidence: - reference: DOI:10.1093/nar/gkad644 notes: IMEs spread via the conjugative apparatus encoded by a helper ICE or conjugative plasmid. curation_history: - timestamp: '2026-06-05T00:00:00Z' curator: claude action: PROPOSED_FROM_RESEARCH changes: Proposed candidate GENOMICS trait (genomic island); 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 (HGT-acquired genomic island accessory function) with RO/biolink predicate groundings; promoted PROPOSED to REVIEWED. llm_assisted: true - timestamp: '2026-06-14T06:55:38Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009292×1). llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 4 evidence-backed generic edges (5 new nodes) from the deep-research report. llm_assisted: true