Conspecificity of DAOM 197198, the model arbuscular mycorrhizal fungus, with <i>Glomus irregulare</i>: molecular evidence with three protein-encoding genes
Bibliographic record
Abstract
Ribosomal nuclear genes are routinely utilized in the molecular identification of fungi. The variation in the multiple copies of these genes within each Glomeromycota strain and species reduces their usefulness for molecular characterization of arbuscular mycorrhizal fungi. To explore the potential of molecular tools for the identification of Glomus species, a multi-gene analysis approach was undertaken. Three protein-encoding genes were tested, namely elogation factor 1-α (765 bp), V-H+-ATPase VHA5 (1468 bp), and F0F1-ATPase β-subunit (621 bp). The latter is newly reported for the Glomeromycetes. Eleven species, including the type-specimen of Glomus irregulare Blaszk., Wubet, Renker & Buscot, a reference strain of G. intraradices N.C. Schenck & G.S. Sm. (DAOM 225240), and five strains of Glomus sp. formerly identified as G. intraradices, were analysed. These genes did not show polymorphisms within strains, and results indicated a close relationship between molecular identification and morphological characterization. Species with closely related spore morphological features, G. aggregatum N.C. Schenck & G.S. Sm., G. diaphanum Morton & Walker, G. irregulare , and Glomus sp. DAOM 197198, showed more than 99% nucleotide similarity, while the morphologically distinct species, G. cerebriforme McGee, G. clarum T.H. Nicolson & N.C. Schenck, G. claroideum N.C. Schenck & G.S. Sm., G. custos C. Cano & Dalpé, G. mosseae (T.H. Nicolson & Gerd.) Gerd. & Trappe, and G. proliferum Dalpé & Declerck, showed less than 97% similarity for at least one gene. A 100% molecular similarity for all three genes was found between G. irregulare and Glomus sp. DAOM 197198, confirming the new identity of the model arbuscular mycorrhizal fungus. Similarity thresholds for identification by DNA sequencing are discussed.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".