Unraveling the mitochondrial genome of : a step towards conservation of an endangered species.

Introduction: Compared to the large number of chloroplast genome resources in , only six mitogenomes (belonging to three sections) have been reported. To date, no mitogenome has been reported for section , a representative species whose chloroplast genome has been characterized, is an endangered tree endemic to the montane cloud forests of southern China.

Methods: In this study, we assembled and annotated the mitogenome of section () for the first time using the HiFi reads. We examined repeat sequences, codon usage bias, RNA editing events, and chloroplast to mitochondrion DNA transfer events, and performed collinearity analysis and phylogenetic analysis with other Fagaceae species.

Results: The mitogenome of revealed a multipartite structure composed of three continuous segments with 516,686 bp in length. The genome encoded 38 protein-coding genes, 23 transfer RNA genes, and three ribosomal RNA genes. Repeat analysis uncovered diverse simple sequence repeats and interspersed sequences, and codon usage showed clear biases. Nonsynonymous sites of RNA editing showed 12 different effects on amino acids. Notably, a small amount (1.20%) of DNA sequences occurred gene transfer events between organelles in . Comparative synteny analysis revealed substantial structural variation among oak mitogenomes. was closely related to in both the mitochondrial and chloroplast trees.

Discussion: This work fills a critical gap in mitochondrial genomic resources for section , and provides new insights into the structural diversity and evolutionary dynamics. It also establishes a valuable genomic foundation for phylogenetic reconstruction, adaptive evolution research, and the conservation of endangered species.