db: MATss, MATpf, MATbz families and five tier-3 candidate records (S. schoenii, P. fabianii, B. californica)

db/Ascomycota/order.yml

@@ -792,3 +792,79 @@ loci:
       # sla2: sla2_homolog by precedent; optional so that contigs ending inside the locus (MH260578 is one) are not demoted.
       - {name: sla2, role: flanking_conserved, gene_class: sla2_homolog, optional: true}
       - {name: tgl1, role: flanking_conserved, optional: true}
+  - locus_name: "MATss"
+    vocabulary_type: "enum"
+    # NEW FAMILY, curator decision 2026-10-30 (candidate records for the SLA2-type genera, results/2026-10-29_near_tie/
+    # CANDIDATE_RECORDS.md): Saccharomycopsis (Ascoideales, Saccharomycopsidaceae) has its own scope-only family, named MATss
+    # after the genus as MATkp, MATog and MATpk are named after theirs; the code is the curator's to change.
+    # ARCHITECTURE (Kriti et al., G3 2026, PMID 41849659, doi 10.1093/g3journal/jkag067; Dost et al., Microbiol Res 2024, PMID 38492364):
+    # S. schoenii is HOMOTHALLIC and carries an expanded MAT system, SLA2-MAT cassettes (MATa1, MATa2, MATalpha1, MATalpha2) on every
+    # chromosome, with SLA2 as the anchor and the MAT genes co-transcribed with it (189-247 bp splice junctions between the MAT genes
+    # and SLA2). DIC1 is scattered, not linked. The active locus is on chromosome IV: an alpha-dominant sub-cluster (470,610-475,000)
+    # and a palindromic cassette (528,044-537,777, an SLA2 anchor flanked by mirrored MATa1/MATa2 arrays). Neither MATsc (three
+    # cassettes, HO switching) nor MTL (PAP1/OBP1/PIK1 inside the idiomorph) describes it: the replay of v0.7.0 called these loci MTL
+    # in 22 of 27 cases with SLA2 inside the call and no PIK1/OBP1/PAP1 (results/2026-10-29_near_tie/).
+    # `cassette_report` stays off: which cassette is expressed is not determined and one genome holds several per idiomorph.
+    # `two_idiomorphs_report` stays off (a homothallic species carries both idiomorphs by design).
+    idiomorph_values: ["MATa", "MATalpha"]
+    idiomorph_class: {MATalpha: unassigned, MATa: unassigned}
+    # SCOPE = THE SPECIES Saccharomycopsis schoenii (taxid 44080; genus Saccharomycopsis 4943, family Saccharomycopsidaceae 34366, order
+    # Ascoideales 2926619; NCBI Taxonomy efetch 2026-10-30). Curator decision 2026-10-30: narrowed from the genus. Only S. schoenii has a record
+    # and it is homothallic with an expanded SLA2-MAT cassette system; the genus is NOT uniform: S. lassenensis is heterothallic (Dost et al. 2024,
+    # PMID 38492364), so a heterothallic species of the genus is EXPECTED to carry a single locus with one idiomorph per genome, a different
+    # architecture from the one recorded here. Other Saccharomycopsis genomes stay in phylum fallback (and, as before, can still be called by
+    # MATsc or MTL until a record of a second species exists).
+    taxonomic_scope: [44080]
+    fallback_subphylum: 147537  # Saccharomycotina
+    fallback_searchable: false
+    flank_carried_window_bp: 20000
+    genes:
+      # Gene models of the records are OUR OWN (tier 3): the authors' GTF is not public (results/2026-10-29_ss_records/README.md).
+      # Gene NAMES rest on the MATa1, MATalpha2 and MATa2 profiles of results/2026-10-30_mat_hmms (supporting evidence, a score
+      # difference, not referenced by any rule). MATa1 and MATalpha2 are homeodomain proteins: no class (the schema has none).
+      - {name: MATa1, role: core_MAT, present_in_idiomorphs: ["MATa"]}
+      # MATa2: optional (HMG-box, divergent; no Pfam HMG_box hit above GA, a2 profile 78 bits on the chromosome IV ORF).
+      - {name: MATa2, role: core_MAT, optional: true, present_in_idiomorphs: ["MATa"]}
+      # MATalpha1: alpha_box (Pfam PF04769 54 bits, GA 28.1, on the chromosome IV ORF), the same bar as MATkp, MATog and MATpk.
+      - {name: MATalpha1, role: core_MAT, gene_class: alpha_box, present_in_idiomorphs: ["MATalpha"]}
+      - {name: MATalpha2, role: core_MAT, optional: true, present_in_idiomorphs: ["MATalpha"]}
+      # sla2: the anchor of every cassette; sla2_homolog by precedent. Optional so that truncated copies are not demoted.
+      - {name: sla2, role: flanking_conserved, gene_class: sla2_homolog, optional: true}
+      - {name: dic1, role: flanking_conserved, optional: true}
+  # NEW FAMILY, curator decision 2026-10-30 (candidate records for the SLA2-type genera): Petasospora (Cyberlindnera) fabianii has its own
+  # scope-only family, named after the species as MATpk. SCOPE = THE SPECIES (taxid 36022), the same restraint as MATpk and MATog: one
+  # species is curated. HETEROTHALLIC with one idiomorph per genome in the four assemblies checked; no second cassette found. Gene models are
+  # OUR OWN predictions (tier 3: AUGUSTUS and miniprot, no RNA-seq exists for the species); see results/2026-10-30_petasospora/README.md.
+  - locus_name: "MATpf"
+    vocabulary_type: "enum"
+    idiomorph_values: ["MATa", "MATalpha"]
+    idiomorph_class: {MATalpha: unassigned, MATa: unassigned}
+    taxonomic_scope: [36022]
+    fallback_subphylum: 147537  # Saccharomycotina
+    fallback_searchable: false
+    flank_carried_window_bp: 20000
+    genes:
+      - {name: MATa1, role: core_MAT, present_in_idiomorphs: ["MATa"]}                       # homeodomain (Pfam Homeodomain 64 bits)
+      - {name: MATa2, role: core_MAT, present_in_idiomorphs: ["MATa"]}                       # HMG-box; no Pfam hit above GA, MATa2 Saccharomycotina profile 76.8 bits
+      - {name: MATalpha1, role: core_MAT, gene_class: alpha_box, present_in_idiomorphs: ["MATalpha"]}  # PF04769 36 bits
+      - {name: MATalpha2, role: core_MAT, present_in_idiomorphs: ["MATalpha"], optional: true}        # none found in either alpha allele
+      - {name: dic1, role: flanking_conserved, optional: true}
+      - {name: sla2, role: flanking_conserved, gene_class: sla2_homolog, optional: true}
+  # NEW FAMILY, curator decision 2026-10-30: Barnettozyma (Phaffomycetales) has its own scope-only family, named after the genus; scope = the genus
+  # (taxid 599802). One record, B. californica PB4207, from OUR OWN tier-3 models (no RNA-seq for the genus; the paper, Hession et al. 2025,
+  # PMID 41359681, gives no coordinates); see results/2026-10-30_barnettozyma/README.md. MATalpha2 is a partial fragment (113 aa), hence optional.
+  - locus_name: "MATbz"
+    vocabulary_type: "enum"
+    idiomorph_values: ["MATa", "MATalpha"]
+    idiomorph_class: {MATalpha: unassigned, MATa: unassigned}
+    taxonomic_scope: [599802]
+    fallback_subphylum: 147537
+    fallback_searchable: false
+    flank_carried_window_bp: 20000
+    genes:
+      - {name: MATa1, role: core_MAT, present_in_idiomorphs: ["MATa"]}
+      - {name: MATa2, role: core_MAT, optional: true, present_in_idiomorphs: ["MATa"]}      # divergent HMG-like; no Pfam HMG_box hit
+      - {name: MATalpha1, role: core_MAT, gene_class: alpha_box, present_in_idiomorphs: ["MATalpha"]}
+      - {name: MATalpha2, role: core_MAT, optional: true, present_in_idiomorphs: ["MATalpha"]}   # partial fragment in PB4207
+      - {name: sla2, role: flanking_conserved, gene_class: sla2_homolog, optional: true}
+      - {name: dic1, role: flanking_conserved, optional: true}

db/candidates/Ascomycota/36022_joy008_MATpf_MATa/metadata.yaml

@@ -0,0 +1,169 @@
+record_id: 36022_joy008_MATpf_MATa
+record_version: 1
+taxonomy:
+  taxid: 36022
+  lineage: k__Fungi;p__Ascomycota;subphylum__Saccharomycotina;c__Saccharomycetes;o__Phaffomycetales;f__Wickerhamomycetaceae;g__Petasospora;s__Petasospora_fabianii
+  lineage_resolved_date: '2026-10-30'
+organism:
+  species: Petasospora fabianii
+  strain:
+    name: JOY008
+    known: true
+    culture_collection_ids:
+    - JOY008
+    differs_from_sequenced: false
+mating_type:
+  locus_name: MATpf
+  idiomorphs:
+  - MATa
+  system: heterothallic
+locus:
+  coordinate_provenance: curator_derived
+  excluded_from_coordinate_benchmark: false
+  assembly_accession: GCA_022641835.1
+  assembly_accession_basis: sequence_link
+  assembly_location:
+    contig: CP048715.1
+    start: 628449
+    end: 644871
+    identity: 100.0
+  core:
+    completeness: complete
+    reference_orientation: DIC1->MATa2->MATa1->(six conserved genes)->SLA2
+    definition_note: 'MATa idiomorph of P. fabianii isolate JOY008 (ecotype Missouri,
+      St. Louis College of Pharmacy), complete genome GCA_022641835.1, CP048715.1
+      (BioSample SAMN14051719). The type strain JCM 3601 (GCA_001599195.1, BCGI01000001.1:641,150-657,563)
+      carries the same MATa locus with 99-100% identical proteins (MATa1 and MATa2
+      one substitution each). The v0.7.0 MATsc call (CP048715.1:630,345-685,843, 55
+      kb) is wider than the locus: the genes are DIC1 628,452-629,375 to SLA2 641,746-644,871.
+      GENE MODELS ARE OURS (tier 3, manual annotation; curator decision 2026-10-30).
+      No RNA-seq exists for the species in ENA/SRA (checked 2026-10-30), so the models
+      are AUGUSTUS ab initio predictions (species models S. cerevisiae S288C, C. guilliermondii,
+      P. stipitis, K. lactis) chosen where several agree and where homology supports
+      them; MATa2 is also supported by the Saccharomycotina MATa2 profile (76.8 bits,
+      above the 52.4 bits of P. kudriavzevii). Coordinates include the stop codon.
+      Intron signals: MATa2 72 bp GTAGGT..TACTAAC..TAG (strong); MATa1 97 bp GTACCA..AAAG
+      (weak donor; an upstream exon is required because the homeodomain open frame
+      has no start codon, but the splice sites are unconfirmed). The MATalpha1 model
+      is a single exon of 305 aa; the depositor''s ONH67106 (254 aa, strain 65) is
+      the same C-terminal 185 aa plus a 69 aa exon joined across a 1,263 bp intron
+      (GTCCTT..CCCCAG) that has no support here: the N-terminus is unresolved. GENE
+      NAMES by homology and position: MATa1 is the homeodomain protein (Pfam Homeodomain
+      64 bits, 66 bits to Komagataella MATa1), MATa2 the HMG-box protein (divergent;
+      no Pfam HMG_box hit above GA), MATalpha1 the alpha-box protein (PF04769 36 bits,
+      407 bits to ONH67106). No MATalpha2 homeodomain gene was found in either alpha
+      allele (only a 57 aa Homeobox_KN fragment at 12-18 bits about 1.2 kb upstream
+      of MATalpha1). LAYOUT: DIC1 (minus) - 0.5 kb (MATa) or 5.0 kb (MATalpha) - MAT
+      genes - six conserved non-MAT ORFs (409, 173, 589, 219, 465, 622 aa; identical
+      in both alleles, not recorded) - SLA2 (plus); SLA2 is therefore about 9.5 kb
+      from the MAT genes. The alpha allele also carries an 800 aa MutS_III-domain
+      ORF between DIC1 and MATalpha1 that has no counterpart in the MATa allele (not
+      recorded). No second MAT cassette: miniprot of the MAT proteins finds no other
+      MAT gene in any of the four assemblies, so the species looks heterothallic with
+      one idiomorph per genome. GENETIC CODE: standard (table 1). Details: results/2026-10-30_petasospora/README.md.'
+    segments:
+    - segment_index: 0
+      sequence_source:
+        type: insdc_nucleotide
+        accession: CP048715.1
+        seq_region: CP048715.1
+      start: 628449
+      end: 644871
+      contig_edge_distance: null
+      sequence_checksum: null
+  extended_flank: []
+genes:
+- gene_index: 0
+  name: dic1
+  protein_accession: null
+  role: flanking_conserved
+  present: true
+  locus_tag: null
+  segment_index: 0
+  start: 628449
+  end: 629375
+  strand: '-'
+  order_in_locus: 0
+  exons:
+  - start: 628449
+    end: 629375
+- gene_index: 1
+  name: MATa2
+  protein_accession: null
+  role: core_MAT
+  present: true
+  locus_tag: null
+  segment_index: 0
+  start: 629850
+  end: 630863
+  strand: '-'
+  order_in_locus: 1
+  exons:
+  - start: 630492
+    end: 630863
+  - start: 629850
+    end: 630419
+- gene_index: 2
+  name: MATa1
+  protein_accession: null
+  role: core_MAT
+  present: true
+  locus_tag: null
+  segment_index: 0
+  start: 631437
+  end: 632136
+  strand: +
+  order_in_locus: 2
+  exons:
+  - start: 631437
+    end: 631737
+  - start: 631835
+    end: 632136
+- gene_index: 3
+  name: sla2
+  protein_accession: null
+  role: flanking_conserved
+  present: true
+  locus_tag: null
+  segment_index: 0
+  start: 641746
+  end: 644871
+  strand: +
+  order_in_locus: 3
+  exons:
+  - start: 641746
+    end: 644871
+evidence:
+  locus_existence:
+    tier: 3
+    experimental_method: 'manual annotation: homology (curated Saccharomycotina MAT
+      proteins, Pfam, MATa2 profile) and AUGUSTUS ab initio models on the deposited
+      assembly; no RNA-seq'
+    citations: &id001 []
+  boundaries:
+    tier: 3
+    experimental_method: AUGUSTUS ab initio gene models checked against homology;
+      DIC1 and SLA2 are the flanking anchors, MAT genes lie between them
+    citations: *id001
+  idiomorph_assignment:
+    tier: 3
+    experimental_method: 'gene content: MATa1 (homeodomain) with MATa2 (HMG-box) versus
+      MATalpha1 (alpha box), at the same DIC1-SLA2 position in different strains'
+    citations: *id001
+validation:
+  status: needs_review
+  rejection_reason: null
+  accession_resolved: false
+  accession_resolved_date: null
+  accession_resolved_version: null
+  sequence_match:
+    status: pass
+    per_gene: []
+    notes: ''
+  taxonomy_current: null
+curation:
+  proposed_by: claude-code-curation-agent
+  proposal_dedupe_key: manual|36022|MATpf|MATa
+  reviewed_by: null
+  reviewed_date: null
+model_provenance: null