fungal sclerotium formation

traitmech:000660 · CLASS · PROPOSED

A morphological phenotype in which a fungus forms compact mycelial resting bodies called sclerotia.

Trait evidence (5)

  • DOI:10.1128/AEM.00565-08
    Aspergillus flavus differentiates to produce asexual dispersing spores (conidia) or overwintering survival structures called sclerotia.

    Horowitz Brown et al. (2008), PMID:18658287, PMC2547031; scientific abstract retrieved through Europe PMC and checked against publisher/PMC HTML. The XML endpoint failed; full text was read as HTML. Introduction, growth/density Methods, first Results subsection, Table 1 and actual Figure 1 were inspected. NRRL 3357 was tested at 29 C for seven days in darkness on glucose minimal medium with sorbitol. Figure 1A reports log10 sclerotial dry mass per plate, not raw body counts despite the abstract's number wording. Density association does not identify the proposed quorum factor. Other figures, supplements and natural strain provenance were not inspected; no additional canonical example or universal LOX mechanism is inferred.

  • DOI:10.3390/jof9070737
    WT and ΔSSA-178C formed black mature sclerotia on the colonies and at the rim of the Petri dishes

    Wang et al. (2023), PMID:37504726, PMC10381867; full-text XML, Results 3.3. Methods 2.1/2.6, Discussion and actual Figures 3-4 were inspected. WT 1980 was observed on PDA at 20 C after 10/15 days and on autoclaved carrot slices after 20 days. Colony photographs are Figure 3A; the Results' Figure 3B pointers for maturation are misplaced because 3B plots growth. Figure 4C/D report bodies and total air-dried mass per flask, not mass per body. Delayed maturation is not complete loss of formation; do not infer rescue of every cortex measurement or survival duration. Other figures and supplements were not inspected.

  • DOI:10.1016/j.micres.2019.126326
    there are no structural differences in the three stages of formation of melanized and non-melanized sclerotium.

    2019 microscopy study, PMID:31493702; directly retrieved Europe PMC scientific abstract only. The authors report development on PDA and compare melanized/non-melanized Sclerotinia sclerotiorum structures by microscopy and histochemistry. This supports not requiring melanization in the definition; the quoted observation is not a claim of identical composition or preserved function in every respect. Full text, figures, supplements, the treatment producing non-melanized structures and strain provenance were not inspected. No canonical example or transcript-inferred biochemical pathway is asserted.

  • DOI:10.1128/spectrum.02084-21
    There are different types of sclerotia-like fungal structures, such as the true sclerotia, the pseudosclerotia, the small sclerotia, and the microsclerotia.

    2022 primary study, PMID:35080446, PMC8791194; Introduction read directly as full-text XML. This passage is a terminology classification, not a new experimental observation. The authors distinguish tissue organization, host-material incorporation and developmental origins across these forms. Preserve that attributed distinction rather than imposing one size, three-layer anatomy or pure-fungal composition on every usage. Detailed equivalence/subclass mapping remains unresolved. Experimental Results, figures, supplements and strain provenance were not inspected; no universal ROS mechanism or additional canonical example is claimed.

  • DOI:10.2478/s11658-007-0047-5
    Sclerotization only took place when the plasmodia were starved and very slowly dried.

    Krzywda et al. (2008; online 2007), PMID:17965965, PMC6275577; scientific abstract read directly in full-text XML. Fuligo septica forms a dormant plasmodial state also called a sclerotium. This nonfungal usage motivates the explicit fungal scope; it is not a mycelial exemplar or an exact synonym of this trait. The reported dehydration conditions and pigment/viability observations are not transferred to fungi. Methods, figures and natural-isolate provenance were not inspected.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1128/AEM.00565-08

Parent traits (1)

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Canonical examples (1)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

  • Sclerotinia sclerotiorum NCBITaxon:5180 DOI:10.3390/jof9070737 Wild-type strain 1980 in Wang et al. (2023), Methods 2.1/2.6, Results 3.3 and actual Figures 3A/4, forms sclerotia under the tested PDA/carrot conditions. NCBI Taxonomy confirms the species label and rank. Independent primary Methods at https://doi.org/10.1128/AEM.67.1.75-81.2001 (PMID:11133430, PMC92519) explicitly identify isolate 1980 as originating from dry bean culls in western Nebraska, supplied by J. R. Steadman. That passage was read directly in PMC HTML; its cited original 1990 study was not retrieved. This URL supports provenance, not an extra formation observation. The example is not an SSA disruption/complementary mutant and does not assert the phenotype for every strain or condition.

Discussions and Knowledge Gaps (2)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

Reconcile legacy labels and the scope of sclerotial structures.

CURATION TODO OPEN fungal-sclerotium-identity-and-mapping · raised by codex · 2026-10-07

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

The explicit fungal label excludes the dormant plasmodial usage in Fuligo. Retain phenotype METPO:1000059 rather than plant pathogen, black pigmented, fungal conidiation traitmech:000657 or chlamydospore formation traitmech:000658. The pinned ontology contains only deprecated bare-label sclerotia classes METPO:0000117, METPO:000118 and METPO:1000398, without definitions or replacement links. Their original scope is unresolved; do not silently reactivate them or assert equivalence to this organismal formation phenotype. Upstream review must reconcile that legacy. QuickGO resolves GO:1990045 as sclerotium development, a biological process rather than an exact organismal phenotype; no xref or SSSOM mapping is asserted. The 2022 source distinguishes true, small, pseudo- and microsclerotial structures. Whether these need separate subclasses or mappings requires further primary morphology review; no exact synonyms, universal size threshold, three-layer requirement or host-material exclusion is imposed.

Separate formation from maturation, survival and mechanism.

KNOWLEDGE GAP OPEN fungal-sclerotium-formation-and-function · raised by codex · 2026-10-07

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

Initiation, maturation, persistence and germination are distinct readouts. Formation of a named resting body does not establish a particular dormancy duration, survival after stress or later germinability. Size, pigmentation, nutrient regime and density responses are not universal defining requirements. Do not infer plant pathogenicity, aflatoxin production or a sexual/asexual reproductive mode from formation alone. The SSA study separates delayed maturation from a complete block, and total mass per flask from body number. A causal graph awaits taxon-specific perturbation/complementation assessment, remaining figures/supplements and authority-verified protein accessions. Candidate gene possession or expression of ROS, pigmentation or signaling genes is not itself the formation phenotype.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Added fungal sclerotium formation with five directly checked source snippets, a provenance-qualified strain 1980 example and explicit legacy-identity, morphology and functional limits. Ignored-and-hidden searches found deprecated bare labels but no live exact formation trait. Reserved METPO:1061300 in v536; existing records unchanged and protein-level mechanism deferred.

Recorded curation sessions

  • · claude-code
    • CREATE — Add fungal sclerotium formation with explicit identity and developmental scope

      Added traitmech:000660, a PROPOSED MORPHOLOGY phenotype under METPO:1000059, with five directly checked source snippets and a provenance-qualified wild-type strain 1980 example. Ignored-and-hidden duplicate searches distinguish three deprecated bare sclerotia labels from the new organismal phenotype; legacy identity and GO process mapping remain unresolved. Reserved METPO:1061300 in proposal v536. Formation, maturation, count versus mass and functional readouts are distinguished; no causal graph, xrefs or exact synonyms are asserted. Twenty focused writer tests and dry-run validation passed before application; broader generated-artifact, corpus and online checks follow in the PR receipt. Existing trait records are unchanged.

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  • · codex
    • AUDIT — Correct session actor attribution without rewriting history

      Correction to history/records/fungal_sclerotium_formation/2026-10-07T064956Z-claude-code-77563e.yaml: the actual curation actor was codex, using model gpt-5 and agent_tool codex, not the scaffolder default claude-code recorded in session.actors.name. The original append-only record is preserved. No TraitRecord content changes in this audit. The add-trait skill now warns that --model and --agent-tool do not override --actor-name and requires inspecting the emitted session actors. README morphology prose is reconciled with the live 14 PROPOSED morphology records. Tracked by issue #1776.

    Read this curation session