Mitogenome structural evolution and cytonuclear coordination in Astragalus sinicus revealed by graphical pan-mitogenomics

Plant mitochondrial genomes exhibit a striking "structure-sequence paradox," characterized by extreme sequence conservation alongside rapid and extensive structural reorganization. Resolving these complex repetitive architectures has historically been challenging, limiting our understanding of structural evolutionary patterns. Here, by leveraging High-Fidelity (HiFi) long-read sequencing and graph-based assembly, we constructed a species-level graphical pan-mitogenome for Astragalus sinicus using 11 representative accessions, complemented by population-scale genomic data from 140 individuals. Our analysis suggests an evolutionary transition from stable ancestral mitogenome structures to hyper-variable "multi-type" configurations. While sequence substitutions in core coding regions remain under extreme evolutionary constraint, plastid and mitochondrial phylogenies recovered partly discordant relationships, suggesting that the two organellar genomes may record different evolutionary histories. Furthermore, we explored bidirectional cytonuclear coordination by characterizing the genomic integration of nuclear mitochondrial DNA segments (NUMTs), highlighting an intriguing computational hypothesis for their potential to drive structural innovation in nuclear genes. Conversely, we observed putative inverse correlations between the expression of specific nuclear-encoded Pentatricopeptide Repeat (PPR) proteins and organellar RNA editing efficiencies, proposing an exploratory "competitive inhibition" hypothesis for the nuclear regulation of organellar homeostasis. Collectively, this study suggests that structural variation acts as a primary driver of mitochondrial evolution, providing a systematic framework for understanding "structure-driven evolution" and cytonuclear crosstalk.