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

Abstract

Plant organelle genomes are important for evolutionary biology research, yet remain poorly characterized in genus Terminalia (Combretaceae). Here, we systematically analyzed the mitochondrial genomes (mtDNA) and chloroplast genomes (cpDNA) of three Terminalia species ( Terminalia chebula , Terminalia franchetii , Terminalia intricata ). Using high-throughput sequencing, we successfully obtained complete cpDNA and mtDNA for three Terminalia species, enabling comparative and evolutionary genomic analysis. The cpDNA of the three species exhibited a typical quadripartite structure, with similar genome sizes (159,700 − 159,971 bp) and gene compositions (103–107 genes), although variations were observed in specific regions. In contrast, the mtDNA showed significant structural and size variation (350,904 − 365,711 bp). Notably, T. chebula and T. intricata possessed three circular and one linear molecule, whereas T. franchetii contained two linear molecules, reflecting extensive recombination events. Ka/Ks (the ratio of nonsynonymous to synonymous substitution rates) analysis revealed signatures of positive selection in several mtDNA genes (e.g., rps1 , nad4 ), potentially associated with adaptive evolution. RNA editing (all C-to-U) enhanced protein hydrophobicity. Phylogenetic analysis further clarified the evolutionary position of Terminalia . This study systematically characterized the organellar genomes of three Terminalia species, revealed contrasting evolutionary patterns between cpDNA and mtDNA, and provides valuable genomic resources for future phylogenetic and evolutionary studies of the Terminalia .