Differentiation of European and North American genotypes of <i>Phytophthora ramorum</i> by real-time polymerase chain reaction primer extension
Bibliographic record
Abstract
Phytophthora ramorum, the organism responsible for sudden oak death, causes severe damage to oak (Quercus spp.) and tanoak (Lithocarpus densiflorus) trees in California and Oregon.There are now >100 host plants that can be affected by this pathogen in nurseries and in the wild in Europe and North America.Molecular diagnosis and genotyping are important tools to monitor and prevent spread of this pathogen, to enforce quarantines, and to support eradication programs.By amplifying and sequencing DNA in a worldwide panel of strains of P. ramorum, we discovered singlenucleotide polymorphisms (SNP) in two genes (-tubulin and cellulose binding elicitor lectin (CBEL)) that differ in the European and the North American P. ramorum isolates.Using these SNPs in diagnostic assays and distinguishing among strains of different geographic origins, we developed primer extension assays in real-time polymerase chain reaction using allele-specific oligonucleotides.All European isolates genotyped were homozygous for the SNP at position 279 in the tubulin gene (-tub279; G/G) but heterozygous at position 858 (-tub858; A/G).By contrast, all the California isolates were heterozygous for -tub279 (T/G) but homozygous for -tub858 (A/A).For CBEL, all European isolates were heterozygous for the SNPs at position 245 (CBEL245; G/C) and 412 (CBEL412; G/A), but the California samples were homozygous at both SNP loci CBEL245 (G/G) and CBEL412 (G/G).This assay was also used directly on DNA extracted from the ELISA lysates from field samples collected in British Columbia in 2005 by the Canadian Food Inspection Agency.Although most samples had the North American DNA profiles, there were several samples with the European profiles from the nurseries.This finding could provide information on the biology, epidemiology, etiology, host range, and populations of P. ramorum from North America and Europe and provide useful tools in P. ramorum surveys.
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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) | 0.000 | 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".