The first single-cell sequencing of Plasmodiophora brassicae reveals genetic diversity and clonal dynamics
Bibliographic record
Abstract
Clubroot, caused by the obligate Chromist pathogen Plasmodiophora brassicae, is an important disease of brassica crops but little is known about its reproductive biology. We enzymatically removed cell walls from dormant spores to generate protoplasts, enabling the first single-cell sequencing of P. brassicae with DNA free from host and soil microbial contamination. Analysis of 4,000 protoplasts from a single root showed moderate genetic diversity, with 2–5 distinct genotypes. A more detailed analysis of the 500 cells indicated the presence of seven distinct genotypes, accounting for rare haplotypes. This level of genetic diversity in a single root supports other indications that there is a high genetic diversity in field populations of P. brassicae. These results support the hypothesis that balancing selection maintains multiple genotypes within the pathogen population. This level of diversity complicates the use of single-gene resistance sources for clubroot management and explains the short durability of clubroot resistance. The predominance of distinct genotypes in a single root is a strong indication that reproduction of P. brassicae is predominantly clonal. This is the first whole genome DNA sequencing of a single-cell of a plant pathogen.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 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".