Extensive mitogenome divergence across the Rafflesiaceae in size and impact of horizontal gene transfer

Horizontal gene transfer (HGT) drives organellar evolution, particularly in parasitic plants where host connections facilitate extensive DNA exchange. However, how these processes intersect with cellular machinery to reshape mitogenomic architecture remains poorly understood. Here, we investigate the mechanisms governing structural plasticity and asymmetric host-DNA integration in the extreme holoparasitic family Rafflesiaceae. By performing a comprehensive comparative analysis across all three extant genera (Sapria, Rhizanthes, and Rafflesia) and their Tetrastigma host lineage, we discovered extraordinary mitogenome size divergence, ranging from the expanded 824-kb genome of Sapria (40 circular chromosomes) to the streamlined 282-kb genome of Rhizanthes (35 circular chromosomes). Strikingly, these closely related genera display a total lack of chromosomal synteny, which we link to the ancestral loss of key recombination surveillance genes (RECX, ODB1). Furthermore, while all three genera strictly conserve an identical core of 30 protein-coding genes, host-derived HGT is highly asymmetric, ranging from minimal in Rhizanthes to 60% in Sapria. In Sapria, foreign tracts are sequestered into 15 predominantly non-coding circular chromosomes, a structural arrangement that aligns with the circle-mediated HGT model validated in other holoparasites. Collectively, these parallel patterns across phylogenetically distant lineages demonstrate that sorting and maintaining foreign DNA in autonomous circular blocks is a convergent architectural outcome of massive host-to-parasite genetic transfers. SIGNIFICANCE STATEMENTHorizontal gene transfer is widespread in the nuclear genome of the parasitic plant family Rafflesiaceae, but its contribution to mitochondrial genome evolution has been assessed through the analyses of a limited number of genes. By comparing complete mitochondrial genomes of the parasites and their hosts, we found that closely related species evolved dramatically different genome architectures through distinct mechanisms: one lineage accumulated large amounts of host-derived DNA, whereas another expanded through the proliferation of repetitive sequences with limited contribution from foreign DNA. These findings show that different evolutionary processes can generate profoundly divergent mitochondrial genomes even among closely related parasitic plants.