Chloroplast genomes reveal unexpected diversity within four Actinidia species

Comparative analysis of chloroplast genomes from eight accessions representing four Actinidia species found that the genomes were remarkably similar in organization and gene composition but contained enough structural and sequence variation to illuminate both species identification and evolutionary relationships. The study examined A. arguta, A. melanandra, A. kolomikta and A. polygama, members of the economically important genus Actinidia and the section Leiocarpae. Researchers assembled and annotated the chloroplast genomes, mapped variable regions, examined repeat sequences and codon usage, and reconstructed phylogenetic relationships. Together, these analyses identified a candidate molecular marker and showed that accessions assigned to the same species do not always form a single evolutionary lineage.

All eight chloroplast genomes ranged from 156,661 to 157,614 base pairs and shared a uniform GC content of 37.20%. Despite variation in total length, the genomes showed remarkable conservation in structural organization and gene composition. Long repeat sequences consisted mainly of forward, palindromic and reverse repeats, while complementary repeats were absent. The researchers also detected numerous simple sequence repeats, with mononucleotide repeats the most abundant. This combination of broad genomic stability and localized variation provides a practical foundation for comparing chloroplast sequences among closely related plants, although the analysis was limited to the four species and eight accessions examined.

Comparative analysis identified seven variable regions: rps12-psbB, trnN-ndhF, rbcL-accD, petA-psbJ, ndhF, ycf1 and ycf2. These regions are potentially useful because they contain differences that may help distinguish closely related taxa. Among them, the rbcL-accD region received experimental attention. PCR validation showed that this region could distinguish the four studied species, supporting its potential as a novel marker for selected Actinidia species. The result demonstrates discrimination within this particular sample rather than establishing diagnostic performance across the genus, other plant families or a wider range of natural populations.

The genome analysis also characterized patterns in how the chloroplast genes use genetic code. Codon-usage analysis revealed a preference for codons ending in A or T across the eight genomes. This is an observed feature of the assembled sequences, not a demonstration that it directly causes any species-level trait. More broadly, the study illustrates how chloroplast genome resources can support species identification, germplasm characterization and phylogenetic research by combining sequence conservation with markers of divergence. It also adds to genomic reference resources for Actinidia, a genus containing economically and nutritionally valuable plants, while leaving questions about relationships beyond the sampled species unresolved.

Phylogenetic analysis based on the chloroplast genomes resolved the accessions into two major clades associated with section Leiocarpae and non-Leiocarpae taxa. SNP-based principal component analysis, a haplotype network and population-structure analysis independently supported the division between those broader groups. A more complex pattern appeared within the sampled lineages: different accessions of the same species, especially the newly sequenced A. arguta samples, were placed on distinct branches rather than clustering as a single uniform group. The authors described this intraspecific divergence as evidence of a complex evolutionary history within Leiocarpae. They proposed that shared paternal ancestry or historical introgression among closely related species might account for it, but the supplied findings do not establish either mechanism as a cause. Chloroplast genomes alone also cannot fully resolve the evolutionary history of these populations, making the study strongest as a comparative resource and marker-discovery analysis rather than a definitive account of the genus’s phylogeny.

Subject of Research: Comparative chloroplast genomics and phylogeny of four Actinidia species

Article Title: Comparative chloroplast genomics of four Actinidia species: structure, variation, and phylogeny

Article References: Li, C., Bai, R., Gao, Z., Zhang, Z., Zhang, Q., Li, Y., Sun, L., Wang, R., Lin, M., & Qi, X. (2026). Comparative chloroplast genomics of four Actinidia species: structure, variation, and phylogeny. BMC Plant Biology. https://doi.org/10.1186/s12870-026-09906-8

Image Credits: AI Generated

DOI: 10.1186/s12870-026-09906-8

Keywords: Actinidia, chloroplast genomes, comparative genomics, phylogenetics, species identification, molecular markers, intraspecific diversity, simple sequence repeats, genome evolution, Comparative, chloroplast, genomics