Mitochondrial Genome Assembly and Comparative Analysis of Three Closely Related Oaks

The genus Quercus is an ecological keystone and economically vital component of Northern Hemisphere forests. While genomic studies have advanced our understanding of its nuclear and chloroplast genomes, the mitochondrial genomes of oaks remain less explored due to their complex evolutionary dynamics, which include extreme size variation, frequent rearrangements, and recurrent horizontal gene transfer. This study presents the assembly, annotation, and comparative analysis of mitogenomes from three closely related Asian oaks—Q. engleriana, Q. kongshanensis, and Q. tungmaiensis—using PacBio HiFi sequencing. The assemblies revealed distinct structural organizations: the Q. engleriana and Q. kongshanensis mitogenomes each comprised one circular contig and one linear contig, whereas the Q. tungmaiensis mitogenome comprised one circular contig and two linear contigs. Comparative analyses revealed variations in codon usage bias, simple sequence repeats, and predicted RNA editing sites. Notably, RNA editing in rps12 was uniquely observed in Q. kongshanensis. Mitochondrial targeting of plastid transcripts constituted 1.39%, 1.79%, and 2.24% of the mitogenomes, respectively. Phylogenetic reconstruction based on mitochondrial PCGs robustly resolved Q. kongshanensis and Q. tungmaiensis as sister species, with all three forming a distinct clade separate from other Quercus species. This study provides comprehensive mitogenomic resources essential for elucidating Quercus evolutionary biology and supporting germplasm development.