Coordinated Evolutionary Rates in Oxidative Phosphorylation Complexes of Papilionoid Legumes: Cytonuclear Coevolution and Relaxed Selection

Across eukaryotes, mitochondrial (mt) and nuclear genomes coordinate the expression and interaction of gene products to maintain cellular functions. While mitonuclear coevolution has been widely explored in animals, it remains understudied in plants, despite their utility as model systems due to relatively slow mitochondrial evolutionary rates and the presence of plastids. Plants rely on oxidative phosphorylation (OXPHOS) for ATP conversion, which requires cofunctionality and likely coevolution of mitochondrial and nuclear gene products. Here, we investigated evolutionary rate covariation (ERC) between mitochondrial- and nuclear-encoded OXPHOS genes in papilionoid legumes, where plastid-nuclear coevolution and an inversion in plastid DNA have been documented previously. Using 50 legume species spanning 15 papilionoid clades, we estimated evolutionary rates for five gene sets: mt-encoded OXPHOS genes, nuclear-encoded mitochondrial-targeted (N-mt) OXPHOS genes, and three control nuclear gene sets that lack mitochondrial interactions (glycolysis, cell cycle, and cytosolic ribosomal genes). Both mt and N-mt OXPHOS genes exhibited significantly elevated nonsynonymous (dN) and synonymous substitution rates (dS) in the 50-kb inversion clade relative to other legumes, suggesting accelerated mitochondrial substitution rates. Moreover, elevated dN/dS ratios in mt and N-mt OXPHOS genes in this clade were driven by relaxed purifying, not intensified positive selection. ERCs were highest for OXPHOS complexes and genes with physical mitonuclear interactions, as predicted under mitonuclear coevolution. We discuss how these results compare to other cases of cytonuclear coevolution in plants, including plastid-nuclear coevolution in papilionoids, and why dual-targeted, nuclear-encoded genes that repair mt and plastid DNA may underly patterns of molecular evolution in both organelles. Significance StatementMitonuclear interactions are essential for cellular energy production, yet the evolutionary dynamics of these interactions remain poorly understood in plants. This study highlights papilionoid legumes as an important system for understanding how coordinated evolution between mitochondrial and nuclear genes shapes plant genomes. By identifying signatures of mitonuclear coevolution in the 50-kb inversion clade, this work demonstrates how shifts in selective pressures on mitochondrial processes can influence nuclear gene evolution. These findings advance our understanding of cytonuclear coordination in plants and provide a foundation for future studies exploring how interactions among genomic compartments contribute to plant evolution, adaptation, and resilience in agriculturally important lineages.