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bioRxiv · 10.1101/2025.08.04.668583

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

Tribhuvan, K. U.·Singh, N. K.·Singh, B. K.·Pandey, A.·Kumar, S.·Bishi, S. K.·K, K. K.·Sahu, T. K.·Pattanayak, A.·Badhana, V. P.·Rakshit, S.
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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.

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Tribhuvan, K. U., Singh, N. K., Singh, B. K., Pandey, A., Kumar, S., Bishi, S. K., K, K. K., Sahu, T. K., Pattanayak, A., Badhana, V. P., Rakshit, S.. 2025-08-06. Chromosome-Scale, Telomere-to-Telomere Assembly of Winged Bean (Psophocarpus tetragonolobus (L.) DC.) Genome Reveals Lipid Biosynthetic Hotspots and Gene Family Dynamics. https://doi.org/10.1101/2025.08.04.668583

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