Chromosome-Level Assembly of Winged Bean Genome Reveals Evolutionary Insights
Bibliographic record
Abstract
Winged bean ( Psophocarpus tetragonolobus ) is an underutilized legume of high nutritional and agronomic value, yet its genomics has lagged behind major crops. Here we present and synthesize a chromosome-level assembly for winged bean and use it to chart genome organization, evolutionary history, and breeding applications. We combined long-read sequencing with Hi-C scaffolding to generate contiguous pseudomolecules, benchmarked assembly quality using standard metrics (e.g., contiguity statistics, BUSCO completeness) and validated structure with linkage consistency and read-mapping; gene models were produced through an evidence-integrated annotation pipeline and assessed for functional reliability. Chromosomal analyses revealed karyotype structure, centromeric/telomeric signatures, repeat landscapes, and spatial patterns of gene density, recombination hotspots, and A/B compartments that delineate 3D genome architecture. Comparative genomics against related legumes (e.g., soybean, cowpea) uncovered conserved syntenic blocks alongside lineage-specific rearrangements, divergence events, and the contraction/expansion of gene families linked to stress resilience, defense, and nutrient/metabolite biosynthesis, including key modules for nodulation and symbiosis. A case study identified a chromosomal inversion associated with pod size and developmental regulation, supported by synteny breaks, allelic variation, and differential expression, and we highlight markers and candidate targets for selection. Finally, we outline how this assembly enables marker-assisted selection, genomic prediction, and genome editing to accelerate improvement of nutritional quality and stress tolerance. Together, these resources establish a foundational reference for winged bean biology, clarify its evolutionary trajectory within legumes, and set practical priorities for pre-breeding and crop enhancement over the coming decade.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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 teacher head, 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".