Comparative mitogenomics of Dasiphora fruticosa and D. glabra: insights into genome structure, inter-organellar DNA transfer, and evolutionary dynamics

Abstract Background Dasiphora fruticosa and its close relative D. glabra are key alpine shrubs distributed across high-altitude regions, yet their mitochondrial genomes remain unexplored. Given the complex reticulate evolutionary history of the two Dasiphora species revealed by nuclear data, characterizing their mitogenomes is crucial for understanding organellar evolution and phylogenetic relationships. Results We assembled the complete mitochondrial genomes of nine D. fruticosa accessions and one D. glabra accession using PacBio HiFi reads. Together with two previously published accessions, all 12 mitogenomes ranged from 263,889 to 294,600 bp, with conserved GC content and a stable core gene set of 30 protein-coding genes, 17–18 tRNAs, and 3 rRNAs. Codon usage analysis showed a clear preference for A/U-ending codons. Repeat analyses revealed abundant SSRs and dispersed repeats, including lineage-specific reverse repeats in D. glabra . Extensive inter-organellar DNA transfer was detected, including multiple chloroplast-derived fragments and large NUMTs, with D. glabra harboring especially large mitochondrial-derived segments. Nucleotide diversity analysis identified several highly variable mitochondrial genes and plastid intergenic regions. Phylogenetic trees based on mitochondrial and plastid genomes consistently placed D. glabra within the D. fruticosa clade, and mitogenome collinearity showed high structural conservation with localized rearrangements. Conclusion This study provides the first comprehensive mitogenomic dataset for D. fruticosa and D. glabra , offering new insights into their genome structure, repeat dynamics, DNA transfer patterns, and evolutionary relationships. These results enrich genomic resources for the genus and lay a foundation for future studies on organellar evolution and high-altitude adaptation.