Mitochondrial Genomes of Three Terminalia Species Reveal Surprising Structural Chaos and Evolutionary Clues

The humble club myrobalan, Terminalia chebula, has been a fixture of traditional medicine across Asia for centuries, but its genome has remained largely terra incognita. Now a team of Chinese and British researchers has pulled back the curtain, sequencing and assembling the complete chloroplast and mitochondrial genomes of three Terminalia species—T. chebula, T. franchetii and T. intricata—and uncovering a striking evolutionary paradox. While the chloroplast genomes of these trees are nearly interchangeable, their mitochondrial genomes have diverged dramatically in size, architecture and molecular form, offering some of the clearest evidence yet of how the two energy-producing organelles of a single plant lineage can follow radically different evolutionary trajectories.

The study, published in BMC Genomics, began with a straightforward technical goal: use high-throughput sequencing to recover complete organellar genomes from the three species, which represent an important but poorly characterized genus within the Combretaceae family. Achieving that goal proved anything but simple for the mitochondrial compartment. Whereas the chloroplast genomes assembled into the familiar quadripartite architecture seen across most flowering plants—a large single-copy region, a small single-copy region and a pair of inverted repeats—the mitochondrial genomes refused to conform to any single template. T. chebula and T. intricata each yielded a set of three circular molecules plus one linear molecule, while T. franchetii presented two linear molecules, an arrangement the authors attribute to extensive recombination events that have repeatedly reshuffled the mitochondrial DNA.

The size disparity is equally dramatic. The chloroplast genomes of the three species spanned a narrow range of just 159,700 to 159,971 base pairs and carried between 103 and 107 genes, with variations confined to specific regions. The mitochondrial genomes, by contrast, ranged from 350,904 to 365,711 base pairs—an expansion of roughly 120,000 base pairs relative to the chloroplast compartment and a degree of variation that dwarfs the differences observed in the chloroplast genomes. This pattern, in which the chloroplast genome remains remarkably conserved while the mitochondrial genome undergoes structural upheaval, mirrors what has been documented in other angiosperm lineages but is documented here in exceptional detail for Terminalia.

To probe the functional consequences of these structural differences, the researchers turned to Ka/Ks analysis—the ratio of nonsynonymous to synonymous substitution rates—which serves as a molecular detective for natural selection. Several mitochondrial genes, including rps1 and nad4, showed signatures of positive selection, suggesting that these proteins may have been recruited into adaptive roles, potentially related to the physiological demands of the species’ environments. The finding is particularly intriguing because mitochondrial genes in plants are typically regarded as evolutionarily staid, accumulating mutations slowly and with little evidence of directional pressure. The identification of positively selected sites in Terminalia hints that the organelle’s proteins may be more evolutionarily labile than conventional wisdom suggests, at least in this genus.

Equally revealing was the analysis of RNA editing, the post-transcriptional process by which specific cytidine residues in mitochondrial transcripts are converted to uridine. In all three species, the researchers found that every observed editing event was a C-to-U conversion, and that these changes systematically enhanced the hydrophobicity of the encoded proteins. This is consistent with the view that RNA editing in plant mitochondria acts as a corrective mechanism, fine-tuning protein sequences to preserve or improve the functional properties of membrane-associated enzymes in the electron transport chain. The uniformity of the C-to-U pattern across the three species suggests that this editing machinery is an ancient and deeply conserved feature of the Terminalia mitochondrial system, even as the underlying genome architecture has been repeatedly rearranged.

The contrast between the two genomes extends to their repetitive landscapes and mutational dynamics. Simple sequence repeats and longer repetitive elements, catalogued in the study’s supplementary tables, provide insight into the mechanisms generating genome size variation, particularly in the mitochondrial compartment where recombination between repeats can generate the alternative molecular conformations—circles and linear molecules—observed in the assemblies. Nucleotide diversity analysis, reported as Pi values across the organellar genomes, identified specific regions of elevated variation, offering potential molecular markers for future population genetic and phylogeographic work in the genus. Meanwhile, analysis of relative synonymous codon usage revealed patterns of codon bias that reflect the underlying mutational and selection pressures acting on each compartment.

Beyond structural characterization, the study tackled a question of broader systematic importance: where exactly does Terminalia sit in the flowering plant tree of life? Using protein-coding genes from both organellar compartments, the researchers performed maximum-likelihood phylogenetic analyses that clarified the evolutionary position of the genus within the Combretaceae and its relationships to related lineages. The inclusion of mitochondrial data proved particularly valuable, as the structural lability of plant mitochondrial genomes has historically complicated their use in phylogenetics. By demonstrating that, despite their architectural chaos, the mitochondrial genomes of these three species retain sufficient phylogenetically informative signal, the authors have bolstered the case for incorporating mitochondrial sequences into future systematic studies of Terminalia and its relatives.

One of the more fascinating aspects of plant organellar biology captured in this study is the phenomenon of mitochondrial plastid DNAs, or MTPTs—fragments of chloroplast DNA that have migrated into the mitochondrial genome over evolutionary time. Such transfers are a hallmark of endosymbiotic gene evolution and can shed light on the frequency and directionality of intercompartmental DNA exchange. Their presence and distribution in the Terminalia mitochondrial genomes provide a molecular record of past genetic conversations between the two organelles, and their characterization in this study adds to a growing body of comparative data across angiosperms. The locally collinear block analysis used to compare genome structures across species further illuminated how syntenic regions have been preserved or disrupted by recombination, painting a dynamic picture of genome evolution in motion.

The practical implications of this work reach beyond pure evolutionary biology. Terminalia species are economically and medicinally significant, particularly T. chebula, whose fruits are used in traditional medicine systems and whose genomic resources have been scarce. The complete organellar genomes now available provide a foundation for DNA barcoding, species authentication and conservation genetics in a genus where morphological identification can be challenging. The hyper-variable regions identified through nucleotide diversity analysis are likely to prove especially useful as markers for distinguishing species and tracing the geographic origins of medicinal plant material, a growing concern in the herbal products trade.

Funded by China’s National Key R&D Program, the Strategic Priority Research Program of the Chinese Academy of Sciences and the National Natural Science Foundation of China, among other sources, the study also reflects the increasing accessibility of complete organellar genome assembly as a standard tool in plant comparative genomics. What sets this contribution apart is the paired treatment of both compartments within the same three species, allowing the authors to draw direct, controlled comparisons between a genome that is structurally frozen and one that is structurally fluid. The result is a vivid illustration of the decoupled evolutionary tempos of the plant cell’s two endosymbiotic residents—and a reminder that even within a single lineage, different genomes can write very different evolutionary stories. For Terminalia, that story is only just beginning to be told.

Subject of Research: Comparative analysis of chloroplast and mitochondrial genomes in three Terminalia species

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

Article References: Liu, X., Zhang, Y., Luo, P., Yang, Z., Zuo, Y., Crabbe, M. J. C., Li, G., & Zhang, T. (2026). Comparative analysis of organelle genomes in three Terminalia species reveals structure evolution and phylogenetic position. BMC Genomics. https://doi.org/10.1186/s12864-026-13381-8

Image Credits: AI Generated

DOI: 10.1186/s12864-026-13381-8

Keywords: Terminalia, organelle genome, mitochondrial genome, chloroplast genome, comparative genomics, genome evolution, RNA editing, positive selection, phylogenetics, Combretaceae, recombination, molecular evolution