Construction of Brassica A and C genome-based ordered pan-transcriptomes for use in rapeseed genomic research
Bibliographic record
Abstract
This data article reports the establishment of the first pan-transcriptome resources for the Brassica A and C genomes. These were developed using existing coding DNA sequence (CDS) gene models from the now-published Brassica oleracea TO1000 and Brassica napus Darmor-bzh genome sequence assemblies representing the chromosomes of these species, along with preliminary CDS models from an updated Brassica rapa Chiifu genome sequence assembly. The B. rapa genome sequence scaffolds required splitting and re-ordering to match the expected genome organisation based on a high density SNP linkage map, but the B. oleracea assembly was used unchanged. The resulting B. rapa (A genome) pseudomolecules contained 47,656 ordered CDS models and the B. oleracea (C genome) pseudomolecules contained 54,766 ordered CDS models. Interpolation of B. napus CDS models not already represented by orthologues resulted in 52,790 and 63,308 ordered CDS models in the A and C pan-transcriptomes, an increase of 13,676 overall. Comparison of the organisation of this resource with publicly available genome sequences for B. napus showed excellent consistency for the B. napus Darmor-bzh resource, but more breakdown of collinearity for the B. napus ZS11 resource. CDS datasets comprising the pan-transcriptomes are available with this article (B. rapa) or from public repositories (B. oleracea and B. napus).
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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.004 | 0.003 |
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".