Assembly and structural validation of the mitochondrial genome of Abies sachalinensis reveals a branched genomic architecture in Pinaceae

Plant mitochondrial genomes (mitogenomes) exhibit complex and dynamic architectures. However, their physical structures remain unevenly resolved in many gymnosperm lineages. In Pinaceae, the limited number of structurally validated mitogenomes constrains comparative analyses of mitogenome architecture and the development of mitochondrial resources for studies of maternal lineage history and seed-mediated dispersal. To help address this gap, we assembled and structurally characterized the mitochondrial genome of Sakhalin fir ( Abies sachalinensis ) using PacBio high-fidelity (HiFi) long reads and validated contig connections using polymerase chain reaction to support the inferred genome conformation. The mitogenome comprises of 12 contigs with a length of 942.73 kbp containing 41 protein-coding genes, 3 rRNA genes, and 11 tRNA genes. Structural analysis revealed a large multi-branched genomic component together with a small circular molecule. Repeat analysis identified 479 simple sequence repeats and 678 dispersed repeats across 12 mitogenomic contigs. We identified mitochondrial plastid DNAs in the mitogenome and chloroplast genome of A. sachalinensis , as well as 1,488 potential C-to-U RNA editing sites supported by prediction and RNA-seq evidence. Phylogenetic analysis based on 26 shared mitochondrial protein-coding genes reconstructed relationships consistent with the current classifications of Pinaceae and confirmed the placement of A. sachalinensis within the genus Abies . Comparison with previously published Pinaceae mitogenomes suggested that this complex structure may exhibit a common structural pattern within the family. This structurally supported mitogenome provides a resource to support future investigations on mitochondrial genome evolution, maternal lineage structure, seed-mediated processes, and systematics in the genus Abies and across Pinaceae.