Phylogeny of Canadian ergot fungi and a detection assay by real-time polymerase chain reaction
Bibliographic record
Abstract
The ergot disease of cereals has become increasingly important in agricultural areas of Canada since 1999. Generally, this disease is considered to be caused by <i>Claviceps purpurea</i>, but the taxonomy of <i>Claviceps</i> from these areas has not been well studied. The objectives of this study were (i) to determine the phylogenetic lineages (phylogenetic species) present in agricultural areas of Canada and (ii) to develop a molecular assay that can separate the lineages on crops from other lineages. Genetic diversity of <i>Claviceps</i> collected from agriculture areas in Canada were investigated using multilocus sequence typing. The loci sequenced include nuc rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS), partial fragments of translation elongation factor 1-α (<i>TEF1</i>), RNA polymerase II second largest subunit (<i>RPB2</i>), β-tubulin (<i>tubB</i>), and two ergot alkaloid synthesis genes (<i>easA, easE</i>). Based on individual locus and concatenated alignments, phylogenetic analyses revealed seven lineages within the premolecular concept of <i>C. purpurea</i>, of which five corresponded with undescribed species (G2b and G4–7). Although lineages G2–7 had narrow host ranges, lineage G1 (= <i>C. purpurea</i> s.s.) had a broad host range that overlapped with other lineages. A molecular diagnostic quantitative polymerase chain reaction (qPCR) assay was developed and validated with 185 samples from a wide range of host plants and geographic origins, including 10 phylogenetic species in <i>C</i>. sect. <i>Claviceps</i>, 8 in <i>C</i>. sect. <i>Pusillae</i>, 1 in <i>C</i>. sect. <i>Citrinae</i>, and 1–2 species from <i>Alternaria, Fusarium</i>, and <i>Penicillium</i>. The assay can detect lineage G1 at a concentration of 7.5 pg/μL and distinguish it from other <i>Claviceps</i> species and lineages. This facilitates disease management by detecting the inocula from nonagriculture host plants.
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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 | 0.000 |
| 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) | 0.038 | 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; both teacher heads agree on what is shown here.
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".