Balanced gene retention, transcription and methylation levels between subgenomes produced by soybean-specific paleo-tetraploidization
Bibliographic record
Abstract
Abstract BackgroundPolyploidization creates duplicated sets of genomes in a plant. Dominance by a subgenome is often observed in a polyploid species. Here, we studied the duplicated genomic regions in soybean, which was affected by a tetraploidization 13 million years ago.ResultsBy referring to eudicot relatives, we detailed that duplicated genes are retained in a balanced manner among homoeologs. Moreover, we found that duplicated genes in colinearity in extant genome are expressed at balance. Notably, the DNA methylation patterns of duplicated genes shared similar methylation levels among three different soybean lines (W931A, WR016, and ZAYOU1), suggesting that either the epigenetic information could be maintained transgenerationally for millions of years or homoeologs in this paleo-autopolyploid species have similar methylation patterns under similar environment.ConclusionsThese findings support the paleo-autotetraploidy of soybean. We proposed that, if taking maize as a model plant for studying paleo-allotetraploids, soybean is a model plant for studying paleo-autotetraploids.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.000 | 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) | 0.001 | 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".