Comparative analysis of <i>Aegilops speltoides</i> and wheat repetitive elements and development of S genome-specific FISH painting
Bibliographic record
Abstract
Aegilops speltoides (2 n = 2 x = 14, genome SS) is a wild relative of wheat and a donor of useful traits for wheat improvement. Several whole-genome studies compared genic regions of Aegilops from the Sitopsis section and wheat and found that Ae. speltoides is most closely related to the wheat B subgenome but is not its direct progenitor. The results showed that a B subgenome ancestor diverged from Ae. speltoides more than 4 MYA and either has not yet been discovered, or is extinct. To further explore the evolutionary relationship between wheat and Ae. speltoides and develop Ae. speltoides chromosome paints, we performed comparative analysis of repetitive fractions of the S genome and three subgenomes of hexaploid wheat. The low-coverage sequence data were analyzed with RepeatExplorer pipeline to annotate repeats and estimate their content. The LTR-retrotransposons comprised about 80% of repeats in Ae. speltoides and wheat datasets and about two-third of them were LTR/Ty3-Gypsy. Ae. speltoides had 1.5 times more LTR/Ty-Copia repeats and 1.5 times less DNA transposons than wheat subgenomes. Several S genome-specific dispersed repeats were found and annotated. Their sequences were used to develop S genome-specific paints for detecting Ae. speltoides chromatin in the wheat background using fluorescent in situ hybridization.
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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 | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 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".