identifier: traitmech:000614 label: primary homothallism definition: A homothallic fungal phenotype enabling self-fertile sexual reproduction through compatible mating-type determinants co-resident in one genome, without requiring mating-type switching. definition_source: DOI:10.1371/journal.pgen.1006110 trait_category: PHYSIOLOGY term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000609 evidence: - reference: DOI:10.1371/journal.pgen.1006110 snippet: co-occurrence in the genome of a single individual of all the MAT alleles required to trigger sexual development notes: 'David-Palma et al. (2016), PMID:27327578, PMC4915694. Exact Introduction sec001 clause defining primary homothallism, not an abstract quote. Abstract sections, Introduction, all Results and Methods sec011/sec014/sec015 were read. Actual Figures 1, 3 and 4, Table 1 and supplementary Table S3 were inspected. Methods/tables/images identify CBS 6938; prose also says CBS 6838, a retained source inconsistency. Single receptor deletions retain sporulation; double deletion blocks it and rescue restores it. HD2 deletion retains vestigial sporulation; an obligatory HD1/HD2 heterodimer is not established. Figure 3''s caption swaps C/D: the actual C is the count plot. Table S3''s Figure 2 E/G pointers correspond to actual Figure 1 E/F. SPO11-mutant basidia counts are not significantly reduced; spore viability is. Other figures, supplements and unread Methods/Discussion remain uninspected. Functional genetics supports the model, not MAT sequence presence alone.' - reference: DOI:10.5598/imafungus.2015.06.01.13 snippet: combined expression of MAT1-1 and MAT1-2 genes in a single genome notes: 2015 terminology review, PMID:26203424, PMC4500084. Exact contiguous phrase from section s2a Primary homothallism, read end-to-end in full-text XML. This is terminology authority, not experimental replication. Its MAT1-1/MAT1-2 formulation describes the ascomycete framework; do not impose that nomenclature on basidiomycetes. The section permits linked or unlinked loci and distinguishes other routes to self-fertility. Its Aspergillus example does not require eight uninucleate spores in every primary-homothallic fungus. Actual Figure 1 remains uninspected. - reference: DOI:10.1016/j.cub.2007.07.012 snippet: self-fertilization does not bypass requirements for outcrossing sex but instead requires activation of these pathways within a single individual. notes: Paoletti et al. (2007), PMID:17669651. Exact contiguous clause from the directly retrieved Europe PMC scientific abstract. In Aspergillus nidulans, alpha- and HMG-domain MAT gene expression is required for normal sexual development and ascospore production; balanced overexpression and an mpkB mutant test distinct perturbations. This does not establish universal dependence on every MAT gene in other fungi. Full text, methods, figures, supplements and original strain provenance remain uninspected; no canonical example is inferred. - reference: DOI:10.1128/EC.00019-10 snippet: produced the same number of perithecia as the WT, containing mature, viable ascospores at day 7 of development. notes: Klix et al. (2010), PMID:20435701, PMC2901639. Exact first Results subsection clause, whose subjects are the SmtA-1 and SmtA-3 deletion strains. Author-institution published PDF at https://www.uni-goettingen.de/de/document/download/a343d8aa3ca6ea7528fe002c2281f0fb.pdf/60.pdf was read after Europe PMC full-text failure; NCBI efetch returned front matter only. Abstract, Introduction, first two Results subsections, strain/culture and microscopy Methods were read; actual Figures 1/2 were inspected. On SWG at 24 C, SmtA-2 deletion instead arrests development at protoperithecia; rescue restores fertility. Thus all MAT genes are not individually essential. The abstract calls SmtA-3 an alpha-domain protein, whereas Introduction/Figure 1 report no known functional domain; do not infer an HMG domain from its MAT1-1-3 relationship. Other experiments, Discussion, supplements and natural provenance of S48977 remain unverified. canonical_examples: - taxon_id: NCBITaxon:264483 taxon_label: Phaffia rhodozyma reference: DOI:10.1371/journal.pgen.1006110 note: 'Qualified example: wild-type CBS 6938, not engineered derivatives. Natural provenance is reported in Table 1 at https://pmc.ncbi.nlm.nih.gov/articles/PMC5103461/: UCD 77-61, sap of Betula stumps in Finland; this is provenance, not independent trait replication. The reproductive study''s Methods, Table 1 and figure images support 6938 despite 6838 in parts of the prose. Figure 1D shows basidia and basidiospores; sec014 assays DWR (2.5% agar, 0.5% ribitol) at 18 C for 10 days. Figure 4B reports 32 of 41 wild-type basidiospores germinated. Keep basidia counts and spore viability distinct. NCBI 264483 resolves to this species on 2026-10-04; do not generalize the assay to every strain.' discussions: - discussion_id: primary-homothallism-scope-and-hierarchy prompt: Distinguish functional self-fertility from co-occurring MAT sequences. kind: CURATION_TODO status: OPEN rationale: This narrows operational homothallism (traitmech:000609) and agrees with the older evidence note's primary-homothallism umbrella placement. Like pseudohomothallism (traitmech:000612), it includes single-founder self-fertility, but combines determinants within one genome rather than packaging compatible nuclei in a spore. Mating-type switching (traitmech:000611) and same-type outcrossing within unisexual reproduction (traitmech:000613) do not alone imply that operational phenotype; their broader phenotype parents are not inconsistent with this narrower placement. MAT inventory alone is insufficient, as the parent's Chromocrea evidence illustrates. Do not require linked loci, one domain architecture, every MAT gene's indispensability, fixed spore counts or absence of outcrossing. These capabilities are not asserted disjoint. Resolve true-homothallism terminology and external mappings before adding synonyms or xrefs. PHYSIOLOGY is a filesystem category; the standalone METPO proposal uses released phenotype METPO:1000059 pending acceptance of homothallism METPO:1056300, not an unlabeled placeholder parent. posed_by: codex posed_date: '2026-10-04' - discussion_id: primary-homothallism-mechanism-and-readouts prompt: Resolve taxon-specific interactions and native proteins before graphing. kind: CURATION_TODO status: OPEN rationale: Complete unread experiments and supplements before extending mechanistic claims. Phaffia receptor compatibility follows deletion/complementation, not direct ligand-binding assays; HD heterodimerization remains tentative. Different draft scaffolds do not prove genetic unlinkage. Sordaria mutant noncomplementation does not distinguish failed fusion from a same-nucleus requirement. Separate MAT expression, sexual structures, viable spores and meiotic evidence. Preserve source strain/domain/panel discrepancies instead of silently harmonizing them. Resolve native protein accessions and dependencies before causal edges; do not use NONMECHANISTIC to bypass grounding. Manual full-text matches are not abstract-resolver VERIFIED verdicts. posed_by: codex posed_date: '2026-10-04' curation_history: - timestamp: '2026-10-05T05:50:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: Added primary homothallism with four DOI-backed snippets and qualified CBS 6938 after primary source, actual figure/table, natural provenance and NCBI checks. Kept self-fertility distinct from MAT inventory and retained strain/domain/panel discrepancies. Ignored-and-hidden novelty and allocation searches found no exact record or ID collision. Reserved METPO:1056800 in v491 under released phenotype pending the local homothallism parent's upstream acceptance. Deferred lexical mappings and protein graphs. llm_assisted: true