Uncovering the history of recombination and population structure in western Canadian stripe rust populations through mating-type alleles
Bibliographic record
Abstract
Abstract The population structure of crop pathogens such as Puccinia striiformis f. sp. tritici ( Pst ); the cause of wheat stripe rust, is of interest to researchers looking to understand these pathogens on a molecular level, as well as those with an applied focus such as disease epidemiology. Cereal rusts can reproduce sexually or asexually, and the introduction of novel genetic lineages has the potential to cause serious epidemics such as the one caused by ‘Warrior’ lineage in Europe. In a global context, Pst lineages in Canada were not well-characterized and origin of foreign incursions was not known. We used a whole-genome/transcriptome sequencing approach for the Canadian Pst population to identify lineages in a global context, origin, and evidence for foreign incursion. More importantly, for the first time ever, we identified nine alleles of the homeodomain mating-type locus in the worldwide Pst population and show that previously identified lineages generally exhibit a single pair of these alleles. In addition, we find only two pheromone receptor alleles. We show that the recent population shift from the ‘ PstS1’ lineage to the ‘ PstS1-related’ lineage is also associated with the introduction of a novel mating-type allele ( b-3 ) to the Canadian population. We also show evidence for high levels of mating-type diversity in samples associated with the Himalayan center of diversity for Pst , including a single Canadian race previously identified as ‘ PstPr’ (probable recombinant) which we identify as a foreign incursion from China circa. 2010. These data provide comprehensive details on the population biology of Canadian Pst diversity and mating-type alleles in the global Pst population which can be utilized in testing several research questions and hypotheses around sexuality and parasexuality in rust fungi.
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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 | 0.002 | 0.002 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.001 | 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".