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

Apocynum venetum is an ecologically and medicinally important subshrub with notable stress tolerance, yet its mitochondrial genome (mitogenome) remains uncharacterized. A reference mitogenome is needed to support evolutionary and comparative genomic studies in the Apocynaceae family, where mitogenomic data are currently scarce. Using PacBio HiFi sequencing, we generated the first complete mitochondrial genome assembly of A. venetum , which was subsequently annotated to reveal a 477,173 bp circular molecule with distinctive structural features. Our analysis identified 61 genes, including 38 protein-coding genes (PCGs) exhibiting distinct codon usage bias (particularly GCU for Alanine, RSCU = 1.65) and 439 predicted RNA editing sites, with nad4 showing the highest editing frequency (37 sites). Notably, we discovered: (1) two large repeat sequences (5,554 bp and 2,076 bp) potentially mediating recombination; (2) 19 chloroplast-derived fragments (12,540 bp) containing 11 functional genes, which provide evidence of intracellular gene transfer (IGT); and (3) a total of 333 dispersed repeats, including 187 palindromic, 145 forward repeats and one reverse repeats, highlighting the structural complexity of this mitogenome. Phylogenetic analysis using 34 angiosperm species revealed A. venetum ’s closest relationship with Trachelospermum jasminoides , supported by conserved synteny blocks. This study provides the first complete mitogenome reference for A. venetum , revealing abundant repeat content and evidence of chloroplast-to-mitochondrion gene transfer. These resources establish a foundation for future comparative genomic investigations within the Apocynaceae and contribute to the growing repertoire of plant mitochondrial genomes in stress-adapted lineages.