Chromosome-Scale, Telomere-to-Telomere Assembly of Winged Bean (Psophocarpus tetragonolobus (L.) DC.) Genome Reveals Lipid Biosynthetic Hotspots and Gene Family Dynamics

Abstract

Winged bean (Psophocarpus tetragonolobus) is a nutritionally rich but cytologically and genomically underexplored legume with potential for climate-resilient agriculture. We report a telomere-to-telomere, 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. Cytogenetics revealed a diploid karyotype (2n = 18) with exclusively metacentric chromosomes, establishing the first chromosomal ideotype map for the species. 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 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 reference genome positions P. tetragonolobus as a valuable model for studying genome evolution and engineering underutilized legumes for oil yield, protein enrichment, and climate adaptability.