Complete mitochondrial sequencing reveals the horizontal transfer and gene rearrangement of Passiflora edulis

Introduction: , an economically important fruit crop, remains poorly characterized, with previous reports suggesting a simple circular structure. Methods: variety 'GH-1'. The assembly was validated by PCR and Sanger sequencing. We further analyzed repeat sequences, transposable elements, mitochondrial plastid DNA (MTPT), codon usage, and performed comparative genomic and phylogenetic analyses. Results: mitogenome comprises two circular chromosomes (mtChr1: 380,183 bp; mtChr2: 334,822 bp), a novel double-circular conformation. It encodes 50 functional genes, 21 tRNAs, and harbors 59 SSRs and 56 long forward repeats. A total of 1,596 transposable elements (predominantly LTR retrotransposons) and nine MTPT fragments (totaling 43,909 bp, 6.14% of the mitogenome) were identified. Comparative analysis revealed extensive gene rearrangements between the purple (PES) and yellow (PEF) varieties. Discussion: The double-circular conformation is likely mediated by abundant forward repeats. The high proportion of MTPTs highlights the dynamic nature of inter-organellar gene transfer. This high-quality mitogenome provides critical insights for phylogenetic studies and breeding programs in Passifloraceae.