A near-complete genome assembly for northern wild rice (Zizania palustris L.)
Bibliographic record
Abstract
Northern wild rice (NWR; Zizania palustris L.), an annual aquatic plant in the Poaceae family, has high economic importance due to its nutrient-rich grains. However, the existing NWR genome assembly for this species has severe fragmentation and incomplete gene representation. A near-complete genome was assembled in this study to provide a high-quality genomic reference for NWR-associated research. The assembled genome exhibited a total contig length of 1.41 Gb and a contig N50 of 109.22 Mb. Overall, a 73.60% repetitive sequence content was identified and 47,804 genes predicted. Phylogenetic analysis indicated that Z. palustris was most closely related to Zizania latifolia , with an estimated divergence time of 4.57–8.15 Mya. Meanwhile, Z. palustris underwent a recent, species-specific long terminal repeat (LTR) expansion, associated with its larger genome size. We identified two genomic blocks in the Z. palustris and Z. latifolia genomes that exhibit strong synteny with the rice phytocassane biosynthetic gene cluster. The centromeric satellite repeats in Z. palustris identified in this study primarily comprised a 145 bp repetitive unit. The findings also revealed centromere homogenisation and rearrangement accompanied by LTR invasion in NWR. Among the genes missing in the previous NWR genome, we observed LTR insertion events that resulted in expanded gene lengths in our updated NWR genome. The present updated NWR genome provides a valuable resource for crop genetic improvement, functional gene discovery, and research on critical biological processes.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| 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 | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.005 | 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".