De novo Genome Assembly and Annotation of 12 Fungi Associated with Fruit Tree Decline Syndrome in ON, Canada
Bibliographic record
Abstract
Apple and stone fruit trees are vital components of Ontario's agricultural landscape. However, since 2016, these trees have been facing alarming mortality rates, exhibiting symptoms collectively referred to as Fruit Tree Decline (FTD) and Rapid Apple Decline (RAD). Despite its widespread occurrence, the exact cause of FTD and RAD remains elusive, with various pathogenic fungi and viruses implicated, along with abiotic stressors such as drought, winter injury and nutrient deficiency. In this study, we sequenced, assembled and annotated the genomes of 12 fungi associated with FTD and RAD syndromes in Ontario, Canada. We present the first and only publicly available assemblies for three ascomycete species including Diplodia intermedia, Diatrype stigma, and Nothophoma quercina. Additionally, we present high-quality reference genome sequences for Diplodia seriata, Didymella pomorum and Neofusicoccum ribis. These genomic resources are valuable for understanding the molecular mechanisms behind FTD and RAD, and for developing strategies for disease prevention and management in fruit trees.
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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 | 0.001 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.003 | 0.005 |
| Science and technology studies | 0.003 | 0.001 |
| Scholarly communication | 0.002 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 0.001 |
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".