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<p>Winged bean (<i>Psophocarpus tetragonolobus</i>) is a nutritionally rich but genomically underexplored legume with potential for climate-resilient agriculture. We report a near chromosome-scale genome assembly (~ 697.69&#xa0;Mb; N50 = 85.98&#xa0;Mb; ~ 98.25% of the cytometric estimate) of the cultivar AKWB1 using a combination of PacBio HiFi, Illumina, BioNano, and Hi-C technologies. The high-quality assembly anchors 98.28% of bases to nine pseudochromosomes and includes 53,745 annotated protein-coding genes, with 97.6% BUSCO completeness. Repeat elements comprise ~ 60% of the genome, dominated by LINEs, LTRs, and DNA transposons. KEGG and GO annotations reveal diverse biosynthetic capabilities across metabolic and stress-response pathways. Comparative genomics with nine legumes demonstrates conserved chromosomal synteny with <i>Glycine max</i>, absence of recent whole-genome duplication, and a contraction-dominated gene family history. Lipid metabolism analysis identified more than 750 genes across 12 KEGG pathways, including fatty acid biosynthesis, elongation, and triacylglycerol assembly. Chromosomes 2, 3, and 5 showed enrichment of lipid biosynthetic loci, suggesting evolutionary hotspots. This high-quality reference genome establishes <i>P. tetragonolobus</i> as a valuable genomic resource for studying legume genome evolution and provides a robust foundation for molecular breeding and genome engineering aimed at improving oil content, protein quality, and climate adaptability in this underutilized crop.</p>

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Chromosome-scale assembly of winged bean (Psophocarpus tetragonolobus (L.) DC.) genome reveals lipid biosynthetic hotspots and gene family dynamics

  • 期刊论文

  • 发表日期：

    2026年7月20日

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  • Kishor U. Tribhuvan,
  • Nikhil Kumar Singh,
  • Binay Kumar Singh,
  • Avinash Pandey,
  • Sudhir Kumar,
  • Sujit Kumar Bishi,
  • K. K. Kanaka,
  • Tanmaya Kumar Sahu,
  • A. Pattanayak,
  • Vijai Pal Bhadana,
  • Sujay Rakshit

摘要

Winged bean (Psophocarpus tetragonolobus) is a nutritionally rich but genomically underexplored legume with potential for climate-resilient agriculture. We report a near chromosome-scale genome assembly (~ 697.69 Mb; N50 = 85.98 Mb; ~ 98.25% of the cytometric estimate) of the cultivar AKWB1 using a combination of PacBio HiFi, Illumina, BioNano, and Hi-C technologies. The high-quality assembly anchors 98.28% of bases to nine pseudochromosomes and includes 53,745 annotated protein-coding genes, with 97.6% BUSCO completeness. Repeat elements comprise ~ 60% of the genome, dominated by LINEs, LTRs, and DNA transposons. KEGG and GO annotations reveal diverse biosynthetic capabilities across metabolic and stress-response pathways. Comparative genomics with nine legumes demonstrates conserved chromosomal synteny with Glycine max, absence of recent whole-genome duplication, and a contraction-dominated gene family history. Lipid metabolism analysis identified more than 750 genes across 12 KEGG pathways, including fatty acid biosynthesis, elongation, and triacylglycerol assembly. Chromosomes 2, 3, and 5 showed enrichment of lipid biosynthetic loci, suggesting evolutionary hotspots. This high-quality reference genome establishes P. tetragonolobus as a valuable genomic resource for studying legume genome evolution and provides a robust foundation for molecular breeding and genome engineering aimed at improving oil content, protein quality, and climate adaptability in this underutilized crop.