Short repeats drive mitochondrial genome expansion and record hybridization in Camellia

Plant mitochondrial genomes are paradoxical: structurally dynamic yet functionally conserved. In hybrid-prone lineages like Camellia (Theaceae), the forces shaping mitogenome evolution remain unclear. Here, we assemble mitogenomes of eight Camellia species and an outgroup. We show that short repeats (<100 bp) drive genome expansion (PGLS: R{superscript 2} = 0.97, P = 6.3 x 10-), overturning the long-repeat paradigm. Multichromosomal architectures and extensive horizontal transfer (up to 25.5% plastid DNA) characterize hybrid lineages. Stark phylogenomic conflicts among mitochondrial, chloroplast and nuclear genomes expose genome-wide hybridization signatures. Mitochondria thus act as recorders of historical gene flow, capturing repeat explosions triggered by introgression. This work redefines plant mitogenome evolution and provides a framework to resolve taxonomic complexities in rapidly radiating angiosperms.