Ruchuan  Chen , Yuping  Huang , Jingyi  Zhang

Tropical Legume Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China
Author    Correspondence author
Legume Genomics and Genetics, 2025, Vol. 16, No. 4   
Received: 07 May, 2025    Accepted: 17 Jun., 2025    Published: 05 Aug., 2025

This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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.

Winged bean (Psophocarpus tetragonolobus); Chromosome-level genome assembly; Hi-C chromatin architecture; Comparative genomics and synteny; Marker-assisted breeding