Using RNA-Seq to identify oospore wall-specific Carbohydrate-Active Enzyme (CAZyme) coding genes of Pythium ultimum var. ultimum, an oomycete plant pathogen
Bibliographic record
Abstract
Oospores are propagules resulting from oomycete sexual recombination and act as long-term survival structures. In Pythium ultimum, and many other oomycete species, the glucan-rich walls of dormant oospores can account for 50% of the total volume of the oospore. Oospore walls can be digested quickly and used as a food source to propel oospores towards a germinable state. Whether digestion occurs by enzymes resulting from genes transcribed at this stage, or prepackaged transcripts/proenzymes released upon wall rehydration is currently unknown. Since oospore walls are composed predominantly of β-glucans, enzymatic digestion by glucanases may represent the earliest stage-specific molecular development ocurring at this point in its life cycle. We used RNA-Seq to investigate the oospore conversion process and to identify genes encoding oospore wall-specific enzyme products. Some enzymes were expressed solely during oospore conversion, and among those, some are only present in Pythium species when compared to other oomycetes.
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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 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| 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".