Variation of the mitochondrial genome in the autotetraploid carp lineage derived from hybridization of Cyprinus carpio (♀) and Megalobrama amblycephala (♂)

Mitochondrial DNA (mtDNA) is strictly maternally inherited in most organisms, yet paternal leakage occurs in some species, particularly hybrids. Analysis of mitochondrial genome variation in the autotetraploid carp (4nNC, derived from female common carp × male blunt snout bream) lineage and its maternal parent allotetraploid fish (4nCB) revealed paternal leakage in multiple mitochondrial regions in 4nCB. The resulting chimeric fragments and associated de novo mutations were stably inherited in the 4nNC lineage, and most mutation sites matched the corresponding bases in diploid wild crucian carp (2nCC). Notably, from the first to the second hybrid generation, mitochondrial polymorphic sites in offspring decreased markedly, and genome structure stabilized, suggesting that persistent distant hybridization imposes strong selective pressure that triggers mitochondrial purifying selection to eliminate incompatible variants and rapidly achieve a new equilibrium. Moreover, complete mitochondrial genome analyses (nucleotide/amino acid sequences and phylogeny) revealed that the 4nNC lineage is more closely related to 2nCC than to its original parents, likely due to paternal leakage within its mitochondrial genome structure. These results demonstrate that following two rounds of distant hybridization, the mitochondrial genome structure of the newly established polyploid hybrid F 1 generation was more stable than that of its hybrid parental F 1 , and subsequent continuous self-crossing markedly reduced variation in each lineage, ultimately yielding genetically stable hybrid lineages. This study provides the first evidence that paternal mtDNA in distant hybridization-derived polyploids is stably transmitted to hybrid and self-crossed offspring, offering new insights into mitochondrial inheritance mechanisms and paternal mtDNA persistence in polyploid hybrids.