Complete A. venetum mitogenome reveals chloroplast-derived DNA

Researchers have produced the first complete mitochondrial genome assembly for Apocynum venetum, a stress-tolerant subshrub whose mitogenome had previously remained uncharacterized. Using PacBio HiFi sequencing, the team generated and annotated a 477,173-base-pair circular genome containing 61 genes, extensive repeat DNA and 19 chloroplast-derived fragments containing 11 functional genes. The single-species reference provides a foundation for comparative mitochondrial-genomics studies in the Apocynaceae family, where such data remain scarce.

Annotation identified 38 protein-coding genes and 439 predicted RNA-editing sites. The protein-coding genes exhibited codon-usage bias, with GCU favored for alanine at a relative synonymous codon usage value of 1.65. Among the mitochondrial genes examined, nad4 contained the highest number of predicted editing sites, with 37. These results characterize the sequence features of the new reference assembly rather than demonstrating functional effects in living plants, and the RNA-editing sites remain computational predictions.

The assembly also revealed a highly repetitive mitochondrial structure. Researchers detected 333 dispersed repeats, comprising 187 palindromic repeats, 145 forward repeats and one reverse repeat. Two larger repeat sequences measured 5,554 and 2,076 base pairs. The investigators proposed that these two sequences could mediate mitochondrial recombination, but the genomic analysis alone does not establish how frequently recombination occurs or how the repeats affect mitochondrial function.

Of particular interest are 19 chloroplast-derived fragments totaling 12,540 base pairs and containing 11 functional genes. Their presence provides evidence of intracellular gene transfer from chloroplasts into the mitochondrion. The finding documents a particular transfer signal in the A. venetum assembly; it does not establish the frequency of similar transfer across Apocynaceae or the biological consequences of the retained chloroplast-derived genes in this stress-tolerant lineage.

Phylogenetic analysis of 34 angiosperm species placed A. venetum in its closest relationship with Trachelospermum jasminoides, a result also supported by conserved synteny blocks. Because the comparison involved one complete mitogenome from A. venetum and a limited set of other flowering-plant sequences, the analysis provides a reference point rather than a resolution of the family’s complete evolutionary history. Taken together, the genome assembly supplies previously unavailable information on gene content, RNA-editing predictions, repeat organization, chloroplast-to-mitochondrion gene transfer and mitochondrial sequence conservation, offering a basis for subsequent comparisons across plant lineages.

Subject of Research: Comparative mitochondrial genomics of Apocynum venetum and the Apocynaceae

Article Title: The complete mitochondrial genome of Apocynum venetum: a high-quality reference assembly for comparative genomics in Apocynaceae

Article References: Yuan, N., Zou, B., Hu, Q., Yuan, X., & Chen, X. (2026). The complete mitochondrial genome of Apocynum venetum: a high-quality reference assembly for comparative genomics in Apocynaceae. BMC Genomics. https://doi.org/10.1186/s12864-026-13448-6

Image Credits: AI Generated

DOI: 10.1186/s12864-026-13448-6

Keywords: Apocynum venetum, mitochondrial genome, Apocynaceae, PacBio HiFi sequencing, intracellular gene transfer, RNA editing, chloroplast fragments, plant genomics, genome repeats, phylogenetics, complete, mitochondrial