Structural variations and phylogenetic implications of mitochondrial genomes in oaks

Despite their pivotal role in eukaryotic evolution, plant mitochondrial genomes (mitogenomes) remain enigmatic owing to their structural plasticity and limited exploration in nonmodel woody species-a critical knowledge gap that hinders a comprehensive understanding of plant diversification and adaptation mechanisms. As a keystone genus in Northern Hemisphere ecosystems, Quercus species exhibit exceptional economic value, ecological adaptability, and phylogenetic diversity, serving as a model clade for studying mitogenomes evolution and its correlation with lineage diversification. Here, we assembled and annotated complete mitogenomes from 15 phylogenetically representative Quercus species via a hybrid sequencing approach combining next-generation and long-read sequencing technologies. Our analyses revealed six distinct mitogenomes architectures with sizes ranging from 339 kb to 622 kb. These genomes encode 34–41 genes, 20–28 tRNAs, and 2–5 rRNAs, demonstrating remarkable intragenus variation in organellar gene inventories. Notably, we identified extensive horizontal gene transfer events between the mitochondrial and chloroplast genomes, involving 11–24 migrated gene fragments with transferred sequences spanning 5265 bp to 12,723 bp. Comparative repeat analysis demonstrated that dispersed repeats predominantly drive mitogenomes expansion and structural dynamism, fundamental processes underpinning organellar genome evolution. Phylogenomic analysis of 39 mitochondrial genes resolved deep evolutionary relationships in Quercus , revealing clear cytonuclear discordance with nuclear phylogenies. This indicates distinct evolutionary histories and potentially divergent selection pressures on cytoplasmic versus nuclear genomes. This study provides essential genomic resources and reveals significant evolutionary correlations that refine our understanding of how organellar genome dynamics contribute to the diversification and adaptation of oaks. • Four complementary assembly strategies were applied to reconstruct the mitogenomes. • Six structural variations were found in oak mitogenomes, with sizes ranging from 339 to 622 kilobases. • Dispersed repeats were identified as the primary drivers of mitochondrial genome expansion.