The entire sequences of the mitochondrial (mt)DNA control region (CR) and portions of its flanking genes in the red crucian carp (RC) and blunt snout bream (BSB) as well as their polyploid hybrids (3nRB, 4nRB and 5nRB) were determined and subjected to a comparative analysis. The mtDNA-CRs of these five fish species ranged from 923 to 937 bp in length, they had the same flanking gene arrangement as other vertebrates and the pattern of nucleotide substitution bias was also similar to that in other vertebrates. Our data are consistent with the viewpoint of three domains [extended terminal associated sequence (ETAS domain), central conserved sequence block domain and conserved sequence block (CSB) domain] within the mtDNA-CR of mammals. On the basis our comparative analysis of the mtDNA-CRs of these five fish species, we were able to identify the consensus sequences of functional conserved units, including the ETAS, CSB-F, CSB-D, CSB-E, CSB1, CSB2 and CSB3 and putative promoter. The percentage of variable nucleotide positions (41.98%) in the central domain was lower than those in the ETAS and conserved domain (71.70 and 47.12%, respectively), suggesting that the central domain was the most conserved part of the mtDNA-CR. These results provide useful and important information for the further study of mtDNA-CR structure in fish. The sequence similarities of mtDNA-CR among the 3nRB, 4nRB, 5nRB hybrids and their respective female parents were higher than those among the 3nRB, 4nRB, 5nRB hybrids and their respective male parents, providing the direct evidence of stringent maternal inheritance of mtDNA-CR in the 3nRB, 4nRB and 5nRB hybrids.
