Genome-wide comparative analysis of selected legume crops reveals evolutionary relationships, genome evolution, and stress adaptation

Rice bean is an underutilized grain legume with high nutritional value and adaptability to diverse environments, yet its genomic architecture remains insufficiently explored. This study performed a genome-wide comparative analysis of rice bean, mung bean, cowpea, and fava bean to investigate evolutionary relationships, genome evolution, and stress-associated genomic features. Protein sequences retrieved from the National Center for Biotechnology Information (NCBI) were analyzed using OrthoVenn3, followed by phylogenetic, gene family evolution, Gene Ontology (GO) enrichment, and amino acid composition analyses. A total of 26,658 orthologous gene clusters, including 6,708 single-copy orthologs, were identified from 157,743 predicted proteins. Phylogenetic analysis revealed a close evolutionary relationship between rice bean and mung bean, while fava bean formed a distinct lineage. Gene family evolution showed extensive expansions in mung bean and cowpea, whereas fava bean exhibited the greatest contractions. GO enrichment identified conserved genes associated with abiotic and biotic stress responses, metabolism, and development. These findings provide valuable genomic resources for functional genomics, molecular breeding, and the genetic improvement of climate-resilient and nutritionally important legume crops.