Gene expression landscape of the <i>Brassica napus</i> seed reveals subgenome bias in both space and time
Bibliographic record
Abstract
Brassica napus (canola; AnAnCnCn) contains both complete diploid genomes from its progenitors Brassica rapa (An) and Brassica oleracea (Cn). Despite growing knowledge of the gene expression landscape of the B. napus seed, little is known about subgenome bias underpinning the development of specific cells and tissues across the seed lifecycle. Here, we present a large-scale transcriptome atlas of the B. napus seed, including both the maternal seed coat and filial embryo and endosperm subregions. We report on extensive, global Cn subgenome bias throughout development and use homoeologous gene pairs to describe how subgenomic bias differs across subregions. We find that subgenome bias is most prominent during early development and that the maternal subregions experience far more asymmetric transcript accumulation in favor of the Cn subgenome. In particular, the unexpectedly distinct transcriptome profile of the chalazal pole indicates the unique developmental processes involved within the chalaza. Furthermore, we report that genes integral to seed storage comprise a large portion of the transcriptome of mature seeds, especially within the embryo, and that gene pairs previously documented to be instrumental in seed development exhibit low transcriptional bias. This work represents an important synthesis of polyploid transcriptomics in seed biology and provides a comprehensive overview of the B. napus gene expression landscape in both space and time.
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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 | 0.000 | 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".