Chloroplast genome sequencing in winged bean (Psophocarpus tetragonolobus L.) and comparative analysis with other legumes

The winged bean (Psophocarpus tetragonolobus) is a fast-growing, underutilized legume adapted to hot and humid regions and valued for its high nutritional content and symbiotic nitrogen fixation, making it suitable for crop rotation and intercropping systems. In this study, we generated high-coverage short-read sequencing data and assembled the complete chloroplast genome of winged bean. The plastome is 151,571 bp in length and comprises 130 genes, including 85 protein-coding genes, 37 tRNAs, and eight rRNAs, organized in a typical quadripartite structure. We identified 84 simple sequence repeats (SSRs), two compound SSRs, and 15 variable number tandem repeats (VNTRs). Comparative analyses with representative legume plastomes revealed strong clade-wise conservation of genome organization, gene content, and GC composition, together with localized variation at IR–SSC junctions consistent with plastome isomerism rather than fixed structural rearrangements. Phylogenomic reconstruction based on complete chloroplast gene sets robustly placed P. tetragonolobus within the Phaseoleae (Millettioid) lineage, consistent with current legume systematics. Molecular evolutionary analyses indicated pervasive purifying selection across chloroplast protein-coding genes, with limited relaxation of constraint in a small subset of loci, while codon usage patterns showed a pronounced A/U-ending bias typical of legume plastomes. Overall, this study provides the first complete chloroplast genome resource for winged bean and supports future comparative genomics, evolutionary studies, and crop improvement in legumes.