Diploid natural gynogenetic goldfish (2nGRCG), triploid hybrids (3nRB) and tetraploid hybrids
(4nRB) are generated by distant hybridization of red common goldfish (RCG, Carassius auratus red var.) and
blunt snout bream (BSB, Megalobrama amblycephala). In the present study, we obtained the complete
mitochondrial DNA (mtDNA) sequences of the hybrid offspring and compared them with the homologous
sequences of RCG and BSB. All mtDNA sequences of these hybrids were 16,580bp in length, and the genes
number, size, and order were quite similar to that of RCG. Genetic analysis revealed that the mtDNA
sequences of these hybrids had high similarity (>99%) and low divergence (<2%) to their maternal RCG, yet
lower similarities (84%) and higher divergences (16%) to their paternal BSB. The phylogenetic analysis also
showed that the sequences of 2nGRCG, 3nRB and 4nRB were clustered with RCG rather than with BSB.
These results indicate that the mitochondrial genomes of 2nGRCG, 3nRB and 4nRB remain maternally
inherited after hybridization and polyploidization. Moreover, clade separation of hybrid offspring from their
paternal BSB in the phylogenetic tree implies that phylogenetic analysis of mtDNA is incomplete for elucidating
the true relationships between different species, particularly when they have undergone hybridization or
allopolyploidization. Our study provides significant information for both evolution and genetic studies of mtDNA
for hybrid species and allopolyploidization species.