Long-read sequencing reveals the mitochondrial genome architecture of the endangered Korean endemic <i>Deutzia paniculata</i> (Hydrangeaceae)

Plant mitochondrial genomes exhibit extensive structural variation, frequent rearrangements, and high levels of polymorphism, factors that often hinder accurate assembly with short-read sequencing alone. Consequently, long-read sequencing approaches are essential for resolving the complex genomic architectures of these genomes. Here, we report the complete mitochondrial genome of <i>Deutzia paniculata</i> Nakai (Hydrangeaceae), an endangered Korean endemic shrub, assembled using a hybrid sequencing strategy that integrates Oxford Nanopore Technologies (ONT) long reads with MGI short reads. High-molecular-weight DNA was extracted to obtain long DNA fragments suitable for reliable structural reconstruction. ONT long-read data were assembled using POLAP, a pipeline optimized for ONT-based plant organellar genome assembly, and the representative assembly was supported by short-read mapping. The assembled mitochondrial genome is 582,743 bp in length, with a GC content of 45.4%. It contains 69 genes, consisting of 40 proteincoding genes (PCGs), 26 transfer RNA (tRNA) genes, and three ribosomal RNA (rRNA) genes. Nine genes were identified as <i>cis</i>-spliced, whereas <i>nad2</i> was confirmed as a <i>trans</i>-spliced gene, reflecting the complex gene organization typical of plant mitochondrial genomes. A phylogenetic analysis based on 17 conserved mitochondrial PCGs recovered <i>D. paniculata</i> as a sister to the <i>Hydrangea</i> clade with strong bootstrap support, supporting the distinct placement of <i>Deutzia</i> within Hydrangeaceae. Overall, this study demonstrates the utility of long-read sequencing for characterizing structurally complex plant mitochondrial genomes and provides a valuable genomic resource for future phylogenetic, evolutionary, and conservation studies of East Asian Hydrangeaceae.