Comparative analysis of organelle genomes in three Terminalia species reveals structure evolution and phylogenetic position

Background Plant organelle genomes are critical for evolutionary biology research, yet their characteristics in the Terminalia genus (Combretaceae, ~ 200 tropical species of which some possess medicinal and edible value) remain unstudied. This study systematically analyzes the mitochondrial genomes (mitogenomes) and chloroplast genomes (plastomes) of three Terminalia species ( T. chebula , T. franchetii , T. intricata ). Results Using high-throughput sequencing, we successfully obtained sequences of plastomes and mitogenomes for three plants, enabling comparative and evolutionary genomic analysis. Plastomes of the three species shared a typical quadripartite structure, with similar sizes (159,700–159,971 bp) and gene compositions (103–107 genes), but differed in specific regions. In contrast, mitogenomes showed significant structural size variation (350,904–365,711 bp), with T. chebula and T. intricata having three circular and one linear molecule, and T. franchetii has two linear molecules, reflecting extensive recombination. Ka/Ks analysis indicated positive selection on mitogenome genes (e.g., rps1 , nad4 ) linked to adaptation. RNA editing (all C-to-U) enhanced protein hydrophobicity. Phylogenetic trees clarified Terminalia ’s position. Conclusions This study provides crucial genomic data for phylogenetic research and molecular ecology within the Terminalia , holding significant value for future research.