identifier: traitmech:000656
label: synnema formation
definition: A morphological phenotype in which fungal hyphae aggregate into an erect,
  stalk-like asexual reproductive structure, with conidiogenous elements borne from
  the stalk in its fertile form.
definition_source: DOI:10.1016/j.simyco.2017.09.001
trait_category: MORPHOLOGY
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- METPO:1000059
evidence:
- reference: DOI:10.1016/j.simyco.2017.09.001
  snippet: Hyphae of stipe parallel, 2–2.5 μm wide, pale-brown, slightly thick-walled.
  notes: Woudenberg et al. (2017), PMID:29158610, PMC5679026. Direct full-text Taxonomy,
    Cephalotrichum lignatile description; the snippet describes this species, not
    universal dimensions or pigmentation. Actual Figure 7D-F shows synnemata, G the
    stalk apex, and H-I conidiophores and conidiogenous cells. Methods describes microscopic
    structures from SNA cultures after 14 days at 25 C in darkness; Figure 7A-C instead
    shows colonies on OA, MEA and DG18. The paper also reports loosely attached stipe
    hyphae in C. domesticum, so tight fusion is not imposed on the class.
- reference: DOI:10.3390/ijms21186660
  snippet: deletion of the brlA gene blocked conidiation but not the formation of
    synnemata formed by aggregation of hyphal mycelia.
  notes: 'Zetina-Serrano et al. (2020), PMID:32932988, PMC7555563, Introduction''s
    summary of the authors'' experiment. Direct Results 2.2.3 and actual Figure 4
    were also inspected: after 30 days on apples at 25 C in darkness, the engineered
    Penicillium expansum brlA-null strain formed sporeless hyphal stalks lacking mature
    conidiophores; the wild-type strain formed conidiophores in coremia. This supports
    separating stalk formation from completed conidiation, not a universal BrlA requirement
    for synnemata. The mutant is qualified evidence, not a natural canonical example.'
- reference: DOI:10.1099/00221287-87-2-292
  snippet: Coremia of Penicillium claviforme develop in three stages; primordium formation,
    elongation, and sporulation.
  notes: Watkinson (1975), PMID:1141857, scientific abstract retrieved directly from
    Europe PMC. The publisher abstract agrees on the three stages but uses a colon
    where this indexed version has a semicolon. Only abstract-level developmental
    evidence is used; full text and figures were not inspected. Nutrient responses
    in this study do not define all synnemata. The historical species name is retained
    without a new taxon mapping or exact coremium/synnema synonym assertion.
canonical_examples:
- taxon_id: NCBITaxon:2041050
  taxon_label: Cephalotrichum lignatile
  reference: DOI:10.1016/j.simyco.2017.09.001
  note: Ex-type culture CBS 209.63. The primary taxonomic description and Figure 7
    directly document synnemata; microscopic descriptions use SNA after 14 days at
    25 C in darkness. Specimen examined and Table 1 at https://pmc.ncbi.nlm.nih.gov/articles/PMC5679026/
    identify Hennebert's 1959 isolate from timber in a cave at Han-sur-Lesse, Belgium.
    This is primary isolate provenance, not an inferred wild-type or GMO status. Synnemata
    production can vary with culture history; it is not asserted for every life stage
    or growth condition.
discussions:
- discussion_id: synnema-formation-scope-and-hierarchy
  prompt: Review a fungal reproductive morphology parent and terminology.
  kind: CURATION_TODO
  status: OPEN
  rationale: Retain phenotype METPO:1000059. Sporulation METPO:1000870 and spore forming
    METPO:1000871 explicitly concern bacterial endospores; mycelial growth traitmech:000074
    explicitly concerns bacterial hyphae. Hyphal anastomosis traitmech:000605 requires
    cytoplasmic continuity, not mere bundling. Pseudohyphal growth traitmech:000653
    concerns chains of budding yeast cells. None is an exact duplicate or appropriate
    parent. Zetina-Serrano uses coremia for conidiophore clusters and synnemata for
    sporeless hyphal stalks; Watkinson uses coremia across developmental stages. Do
    not force these usages into an exact synonym. No exact external mapping or organism-level
    disjointness is asserted.
  posed_by: codex
  posed_date: '2026-10-07'
- discussion_id: synnema-formation-development-and-mechanism
  prompt: Resolve stage-specific mechanisms before adding a causal graph.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: The fertile-form qualifier preserves the documented sporeless synnemata
    of the brlA-null P. expansum strain. Formation does not require already mature
    conidiophores or conidia, a universal shape, size, color, spore wetness, growth
    medium or nutritional trigger. BrlA perturbation separates developmental stages
    in that experiment; it does not establish a universal stalk-formation gene or
    a mechanism in Cephalotrichum. Defer a causal graph pending organism-specific
    perturbations and accession-level review. Gene possession alone does not establish
    this phenotype. Use the 2017 paper's directly examined CBS 209.63 material, not
    older sequences attributed to CBS 159.66 that the authors identify as erroneous.
  posed_by: codex
  posed_date: '2026-10-07'
curation_history:
- timestamp: '2026-10-07T02:43:42Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Added synnema formation with three DOI-backed snippets, a qualified Cephalotrichum
    lignatile example and developmental scope boundaries. Ignored-and-hidden searches
    and structured METPO review found no exact record. Reserved METPO:1060900 in v532;
    existing records unchanged.
  llm_assisted: true