Complete mitochondrial genomes of five introduced strains of common carp (Cyprinus carpio) in Japan with 29 diagnostic SNPs distinguishable by restriction enzyme analysis

Complete mitochondrial genome sequences were determined for three common carp individuals captured at Lake Kasumigaura, Japan. They represent three of the five introduced strains of common carp in Japan, having the mtDNA D-loop haplotypes c1, d2 and e1. The three obtained mitogenome sequences were compared with two previously published mitogenomes that are identical in the D-loop region to haplotypes b1 and f1, representing the remaining two of the five introduced strains in Japan. Alignment (16 585 base pairs) of these five mitogenomes revealed 29 SNPs that are diagnostic for the five strains, detected through positive digestion by “rare-cutter” restriction enzymes.