Comparative genomic analysis of underutilized legumes: insights into evolutionary relationships, genome evolution and stress tolerance

African yam bean, Mung bean, and Winged bean, which are rich sources of nutrients and bioactive compounds, offer significant potential for food and nutrition security, yet they are underutilized. A comparative genomic analysis of these legumes with cowpea was conducted to unearth their molecular architecture and uncover their rich genomic profile. Protein and genomic fasta sequences were retrieved from the GenBank of the NCBI, and orthologous genes investigated, and secondary metabolites determined using OrthoVenn3 and PlantiSMASH programs. A total of 7761 single-copy and 20,250 unique genes were identified, which revealed their genetic diversity and conservation. Phylogenetic analysis showed the closest relationship between Cowpea and Mung bean, with Winged bean diverging significantly. Cowpea and Mung bean had significant gene expansions (+1051), while African yam bean (-864) and Winged bean (-643) had substantial gene losses. GO enrichment revealed the contributions to adaptations in the different legume species to biotic and abiotic stresses, highlighting their potential as climate-resilient crops. The highest protein gene (enzyme) count for saccharide (68) and terpene (18) biosynthesis was obtained in AYB. At the same time, mung bean had the highest gene clusters for alkaloids (10) and polyketides (5), and the highest enzyme count for the biosynthesis of alkaloids (32) and polyketides (17). Underutilized legumes exhibited higher essential amino acid levels compared to cowpea. These findings provide valuable insights for breeding programs and biotechnological interventions to improve the nutritional value and acceptance of these underutilized legumes, ultimately contributing to food and nutrition security.