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

Introduction The mitochondrial genome (mitogenome) of Passiflora edulis , an economically important fruit crop, remains poorly characterized, with previous reports suggesting a simple circular structure. Methods We employed a hybrid sequencing strategy combining PacBio HiFi long reads and Illumina short reads to assemble the complete mitogenome of P. edulis 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 The P. edulis 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.