{
  "schema_version": "1.0.0",
  "study_id": "STUDY-22-PRIMARY-PLASTID-ENDOSYMBIOSIS-TOCTIC-SERIES",
  "validation_set_id": "VAL-SET-032-PLASTID-ENDOSYMBIOSIS-TOCTIC-28COHORT",
  "generated_at": "2026-11-04T00:48:00.000Z",
  "scope": "Dry-Lab In-Silico Sequence, Synteny, Sub-Domain Partitioning & 3D Structural Bioinformatics across 68 Cyanobacteria, Archaeplastida (Glaucophyta, Rhodophyta, Viridiplantae) and Paulinella Rhizaria Taxa (2.14 Mb, 28 Cohorts)",
  "tiers": {
    "tier1_exploratory": {
      "slug": "plastid-toctic-tier1-exploratory",
      "cohorts": 10,
      "total_bp": 412400,
      "taxa_count": 28,
      "beaker_prior": 5,
      "beaker_posterior": 4,
      "peak_z_score": 4.38,
      "key_findings": {
        "toc75_omp85_potra_tm_score": 0.914,
        "toc75_potra_rmsd_angstrom": 1.18,
        "glaucophyta_murg_pbp_ftsZ_retention": "9/9 cyanobacterial peptidoglycan synthesis & FtsZ division enzymes retained in Cyanophora paradoxa vs. 5/9 cryptic moss/lycophyte plastid-division homologs and 0/9 in angiosperm plastids",
        "rbcl_form1b_vs_form1a_divergence": "Archaeplastida plastids share beta-cyanobacterial Form IB RbcL + Gloeomargarita-affiliated rRNA/rp16 core (98.8% UFBoot), whereas Paulinella chromatophore encodes alpha-cyanobacterial Synechococcus/Prochlorococcus Form IA RbcL + carboxysome csoS2 operon (100.0% UFBoot)"
      }
    },
    "tier2_blind_validation": {
      "slug": "plastid-toctic-blind-tier2",
      "cohorts": 24,
      "dev_cohorts": 12,
      "reserve_cohorts": 12,
      "total_bp": 1184000,
      "taxa_count": 48,
      "beaker_prior": 5,
      "beaker_posterior": 5,
      "peak_z_score": 5.16,
      "blinded_concordance_clean_cohorts": "20/20 (100.0%, mean D_ctx = 0.038 SD)",
      "context_anomalies_flagged": [
        {
          "token": "BLIND-PLASTID-07",
          "repository_label": "Galdieria sulphuraria / Rhodophyta Plastid Outer-Membrane TOC75-Like Import Channel",
          "blinded_extrapolation": "Acidophilic red algal plastid Omp85/TOC75 ortholog carrying a 145-aa Ser/Pro/acidic inter-POTRA linker expansion (RCFV = 0.164 unpartitioned vs. 0.021 partitioned)",
          "d_ctx": 5.42
        },
        {
          "token": "BLIND-PLASTID-14",
          "repository_label": "Arabidopsis thaliana Chloroplast Inner-Envelope TIC110 Annotated Full-Length Preprotein",
          "blinded_extrapolation": "Truncated RefSeq splice isoform missing the N-terminal 62-aa stroma-facing transit-peptide recruitment SLiM and amphipathic helix (Error Type B)",
          "d_ctx": 5.18
        },
        {
          "token": "BLIND-PLASTID-19",
          "repository_label": "Paulinella micropora Plastid TOC/TIC Homolog Candidate",
          "blinded_extrapolation": "Host-derived rhizarian Sec61/ER-golgi vesicular crTP trafficking factor + intact alpha-cyanobacterial Omp85 (Synpcc7942_1468 ortholog), lacking canonical plant TOC34/TOC159 GTPase receptors and TIC20/TIC110 channels",
          "d_ctx": 5.84
        },
        {
          "token": "BLIND-PLASTID-23",
          "repository_label": "Nicotiana tabacum Chloroplast Genome Contig (Reference Plastome Paralog)",
          "blinded_extrapolation": "Nuclear integrant of plastid DNA (NUPT pseudogene, dN/dS = 0.874, 4 internal stop codons in rpoB-rbcL)",
          "d_ctx": 6.12
        }
      ]
    },
    "tier3_scientific_synthesis": {
      "slug": "plastid-endosymbiosis-archaeplastida-tier3",
      "cohorts": 28,
      "dev_cohorts": 14,
      "reserve_cohorts": 14,
      "total_bp": 2142000,
      "taxa_count": 68,
      "beaker_prior": 5,
      "beaker_posterior": 5,
      "peak_z_score": 5.48,
      "hypotheses": [
        {
          "id": "H1",
          "status": "Accepted",
          "locus": "TOC75 / Omp85 Outer-Envelope Beta-Barrel & POTRA1-3 Chaperone Gate (PDB: 5O8O)",
          "unpartitioned_rcfv": 0.164,
          "partitioned_rcfv": 0.021,
          "rcfv_reduction_pct": 87.2,
          "tm_score": 0.918,
          "rmsd_angstrom": 1.14,
          "potts_j_ij": 1.712,
          "archaeplastida_gloeomargarita_ufboot": 99.6,
          "z_score": 5.48,
          "beakers": 5
        },
        {
          "id": "H2",
          "status": "Accepted",
          "locus": "Plastid Division FtsZ GTPase Core + C-Terminal ARC6/FtsA Tethering SLiM (PDB: 1FSZ) & Glaucophyte MurG/PBP Peptidoglycan Wall",
          "unpartitioned_rcfv": 0.151,
          "partitioned_rcfv": 0.020,
          "rcfv_reduction_pct": 86.8,
          "tm_score": 0.934,
          "rmsd_angstrom": 1.04,
          "potts_j_ij": 1.664,
          "archaeplastida_gloeomargarita_ufboot": 99.4,
          "z_score": 5.22,
          "beakers": 5
        },
        {
          "id": "H3",
          "status": "Accepted",
          "locus": "RuBisCO RbcL Catalytic Barrel + C-Terminal Latch SLiM (PDB: 8RUC) & TIC20/TIC110 vs. Paulinella Host ER-Golgi crTP Import",
          "unpartitioned_rcfv": 0.158,
          "partitioned_rcfv": 0.022,
          "rcfv_reduction_pct": 86.1,
          "tm_score": 0.946,
          "rmsd_angstrom": 0.96,
          "potts_j_ij": 1.748,
          "archaeplastida_gloeomargarita_ufboot": 99.8,
          "z_score": 5.36,
          "beakers": 5
        },
        {
          "id": "H4",
          "status": "Falsified Control",
          "locus": "Constrained Polyphyletic Archaeplastida or Direct Paulinella + Viridiplantae Sisterhood without Sub-Domain Partitioning",
          "unpartitioned_rcfv": 0.164,
          "partitioned_rcfv": 0.021,
          "delta_lnl_penalty": -342.8,
          "au_test_p": 0.0001,
          "polyphyly_ufboot": 0.8,
          "z_score": 0.82,
          "beakers": 1
        }
      ],
      "sixteen_family_cross_kingdom_summary": {
        "total_families": 16,
        "total_taxa": 324,
        "total_mb": 11.90,
        "mean_rcfv_reduction_pct": 86.1,
        "crown_ufboot_range": "99.2% - 100.0%"
      }
    }
  }
}