Despite their pivotal role in eukaryotic evolution, plant mitochondrial genomes 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 mechanisms. As a keystone genus in Northern Hemisphere ecosystems, Quercus species exhibit exceptional ecological adaptability and phylogenetic diversity, serving as a model clade for studying plant diversification and adaptation. Here, we assembled and annotated complete mitochondrial genomes from 15 phylogenetically representative Quercus species via a hybrid sequencing approach combining next-generation and long-read sequencing technologies. Our analyses revealed six distinct mitochondrial genome 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 5,265 bp to 12,723 bp. Comparative repeat analysis demonstrated that dispersed repeats predominantly drive mitochondrial genome expansion, with total repeat length showing a significant positive correlation with genome size (R2=0.64, P<0.001). Phylogenomic reconstruction based on 39 concatenated mitochondrial genes resolved deep evolutionary relationships within Quercus, revealing substantial topological discordance with nuclear genome-derived phylogenies and suggesting distinct cytoplasmic vs. nuclear inheritance histories. This study provides crucial genomic resources and evolutionary insights that refine our understanding of organellar genome dynamics in oaks while establishing a framework for resolving cytonuclear discordance in plant phylogenomics.

Despite their pivotal role in eukaryotic evolution, plant mitochondrial genomes 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 mechanisms. As a keystone genus in Northern Hemisphere ecosystems, Quercus species exhibit exceptional ecological adaptability and phylogenetic diversity, serving as a model clade for studying plant diversification and adaptation. Here, we assembled and annotated complete mitochondrial genomes from 15 phylogenetically representative Quercus species via a hybrid sequencing approach combining next-generation and long-read sequencing technologies. Our analyses revealed six distinct mitochondrial genome 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 5,265 bp to 12,723 bp. Comparative repeat analysis demonstrated that dispersed repeats predominantly drive mitochondrial genome expansion, with total repeat length showing a significant positive correlation with genome size (R2=0.64, P<0.001). Phylogenomic reconstruction based on 39 concatenated mitochondrial genes resolved deep evolutionary relationships within Quercus, revealing substantial topological discordance with nuclear genome-derived phylogenies and suggesting distinct cytoplasmic vs. nuclear inheritance histories. This study provides crucial genomic resources and evolutionary insights that refine our understanding of organellar genome dynamics in oaks while establishing a framework for resolving cytonuclear discordance in plant phylogenomics.

Putatively orthologous mitochondrial protein-coding genes (PCGs) shared among all taxa were identified using PhyloSuite v1.2.2. The taxon sampling comprised both newly assembled and publicly available sequences. After removing paralogous sequences, coding DNA sequences (CDSs) were extracted. To maintain correct reading frames and preserve evolutionary signal, the nucleotide sequences were translated into amino acids, aligned with MAFFT v7.313 under the “-auto” strategy, and then back-translated to generate codon-aligned nucleotide alignments. The nucleotide alignments were further refined with Gblocks v0.91b using relaxed parameters to minimize ambiguous alignment regions while retaining phylogenetic information: minimum number of sequences for conserved/flanking positions was set to 85% of all taxa, maximum number of contiguous nonconserved positions was 8, minimum block length was 10, and gap positions were allowed “with half”. Maximum likelihood phylogenies were reconstructed with IQ-TREE v1.6.8 under the “-m MFP” option and assessed with 50,000 ultrafast bootstrap (UFBoot) replicates and 1,000 SH-like approximate likelihood ratio test (SH-aLRT) replicates. Branches with UFBoot ≥ 95% and SH-aLRT ≥ 80% were considered strongly supported. The final trees were visualized using Interactive Tree of Life (iTOL) v6.

Putatively orthologous mitochondrial protein-coding genes (PCGs) shared among all taxa were identified using PhyloSuite v1.2.2. The taxon sampling comprised both newly assembled and publicly available sequences. After removing paralogous sequences, coding DNA sequences (CDSs) were extracted. To maintain correct reading frames and preserve evolutionary signal, the nucleotide sequences were translated into amino acids, aligned with MAFFT v7.313 under the “-auto” strategy, and then back-translated to generate codon-aligned nucleotide alignments. The nucleotide alignments were further refined with Gblocks v0.91b using relaxed parameters to minimize ambiguous alignment regions while retaining phylogenetic information: minimum number of sequences for conserved/flanking positions was set to 85% of all taxa, maximum number of contiguous nonconserved positions was 8, minimum block length was 10, and gap positions were allowed “with half”. Maximum likelihood phylogenies were reconstructed with IQ-TREE v1.6.8 under the “-m MFP” option and assessed with 50,000 ultrafast bootstrap (UFBoot) replicates and 1,000 SH-like approximate likelihood ratio test (SH-aLRT) replicates. Branches with UFBoot ≥ 95% and SH-aLRT ≥ 80% were considered strongly supported. The final trees were visualized using Interactive Tree of Life (iTOL) v6.

This dataset provides the complete chloroplast genome sequence of Quercus kongshanensis. The chloroplast DNA was sequenced, assembled, and annotated. The assembly and annotation results are valuable for studies on plant phylogenetics, population genetics, and genomic evolution within the genus Quercusand the family Fagaceae.

This dataset provides the complete chloroplast genome sequence of Quercus kongshanensis. The chloroplast DNA was sequenced, assembled, and annotated. The assembly and annotation results are valuable for studies on plant phylogenetics, population genetics, and genomic evolution within the genus Quercusand the family Fagaceae.