Assembly and comparative analysis of the complete mitochondrial genome of the endangered plant Fraxinus mandshurica

Abstract

Fraxinus mandshurica, a deciduous tree species in the Oleaceae family, is valued for its high-quality timber, medicinal properties, and ecological functions. It is classified as a second-class national protected wild plant in China. However, the complete sequence information of its mitochondrial genome has yet to be reported, and systematic studies on its genetic background and phylogenetic evolution remain limited. The mitochondrial genome of F. mandshurica was assembled into a linear structure, measuring 645,536 bp and 44.40% GC content. Annotation of the mitochondrial genome yielded 77 genes, including 44 protein-coding genes, 30 tRNAs, and 3 rRNAs. A total of 585 dispersed repeats, 184 simple repeats, and 21 tandem repeats were detected, and 476 RNA editing sites with C-to-U type changes were predicted. Codon usage analysis revealed a bias toward codons terminating with A/T. Furthermore, homology analysis revealed 36 chloroplast-derived fragments, spanning 55,673 bp and accounting for 8.62% of the mitochondrial genome. Collinearity analysis exposed considerable genomic rearrangements between F. mandshurica and its close relatives, reflecting structural divergence across evolution. Positive selection was observed for 14 genes, in which Ka/Ks ratios exceeded 1 in at least one pairwise comparison. Analysis of nucleotide polymorphisms showed differences in every gene, where nad4 displayed the greatest variation. Phylogenetic analyses suggested that F. mandshurica and F. excelsior are closely related. This study presents an integrated analysis of the F. mandshurica mitochondrial genome, revealing its unique structural and evolutionary characteristics. Moreover, this mitochondrial genome was compared with seven published Oleaceae mitochondrial genomes to investigate genome dynamics across the family. Our findings enrich the mitochondrial genome resources for Oleaceae species and highlight the potential of mitochondrial genes to elucidate plant evolutionary history.