Mitochondrial genome of Iodes seguinii reveals repeat-mediated recombination and phylogenetic insights in Icacinaceae

The Icacinales order includes numerous genera and species, many of which have medicinal properties. Iodes seguinii, a species from this order, is traditionally used for treating rheumatic and inflammatory diseases. This study presents the first complete mitochondrial genome (mitogenome) of I. seguinii, the first characterized in the Icacinales order. A hybrid sequencing approach combining Oxford Nanopore long reads and Illumina short reads was used to assemble a 423,925 bp circular mitogenome, which includes 32 protein-coding genes, 3 rRNAs, and 23 tRNAs, as well as repeat elements that mediate homologous recombination. Additionally, RNA editing analysis revealed extensive post-transcriptional modifications, with C-to-U conversions primarily occurring in genes related to mitochondrial energy metabolism. The chloroplast genome, with a length of 150,599 bp, was also reconstructed. It contains typical features such as large and small single-copy regions and inverted repeats, with genes for photosynthesis, carbon fixation, and energy production. Mitochondrial plastid sequences suggested active inter-organelle gene transfer. Phylogenetic analysis based on mitochondrial genes positioned I. seguinii as a distinct lineage within basal eudicots, closely related to Eucommia ulmoides. Comparative mitogenome analyses revealed lineage-specific rearrangements and structural evolution. These findings provide insights into the evolution and functional dynamics of mitogenomes in Icacinales, offering a valuable genomic resource for future studies on plant mitochondrial biology and medicinal applications.