Mitochondrial genome of Quercus chenii: genomic features and evolutionary implications.

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Recent advances in high-throughput sequencing have enabled detailed characterization of plant mitochondrial genomes. Here, we assembled and analyzed the mitochondrial genome of Nakai, a key oak species in Fagaceae, using Illumina NovaSeq6000. The genome consists of a 364,958 bp linear and a 53,677 bp circular chromosome, totaling 418,635 bp with a GC content of 45.6%. Repeat-rich regions (210–250 and 300–340 kb) may facilitate structural rearrangements, while extensive RNA editing-particularly in and -likely enhances protein functionality and mitochondrial adaptability. Comparative collinearity analysis showed high structural conservation with Carruth. (90.92%) but marked divergence from L. (35.80%), suggesting lineage-specific rearrangements. Phylogenetic analysis based on the mitochondrial genome supports the same placement of within Fagaceae as that derived from the chloroplast genome. The analysis across Fagaceae mitochondrial genomes revealed strong conservation of core genes, with adaptive variations in energy metabolism-related genes, suggesting functional divergence linked to metabolic optimization under environmental stress. These findings highlight the distinct evolutionary strategies of mitochondrial and chloroplast genomes: the former optimizing energy production, while the latter fine-tunes photosynthesis and stress responses. Comparison analysis with the chloroplast genome further revealed both conserved ( and ) and divergent ( and ) genes, implying potential historical gene transfer events. Together, these findings highlight the dynamic yet conserved nature of the . mitochondrial genome and provide new insights into organellar genome evolution, structural plasticity, and adaptive mechanisms within the Fagaceae family.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1186/s12864-025-11877-3.