The most informative loci to identify trunk disease pathogens associated with grapevine and perennial fruit and nut crops
Bibliographic record
Abstract
Trunk disease (TD) fungi are taxonomically diverse, and accurate species delimitation relies on multilocus phylogenetic analyses. However, the loci commonly employed vary among fungal groups, leading to inconsistencies in species recognition. This paper provides a comparative overview of the most informative genetic loci for species identification within the main families associated with TDs, including Botryosphaeriaceae, Cytosporaceae, Diaporthaceae, Diatrypaceae, Phaeomoniellaceae, Togniniaceae, Nectriaceae (Ascomycota), and Hymenochaetales (Basidiomycota). The internal transcribed spacer region (ITS) remains the universal primary barcode, but its discriminatory power is often limited. The most informative loci [translation elongation factor 1-α (tef1), β-tubulin (tub2), actin (act1), calmodulin (cal), histone (his3), and the RNA polymerase II second largest subunit (rpb2)] are identified, and optimal locus combinations for each fungal group are identified. This synthesis will aid selection of the most appropriate loci for robust phylogenetic inference and accurate pathogen identification, thereby improving epidemiological and management studies of TDs.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| 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) | 0.000 | 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 teacher head, 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".