Complete mitochondrial DNA sequence of the Lake Biwa wild strain of common carp (Cyprinus carpio L.): further evidence for an ancient origin

The complete mitochondrial DNA (mtDNA) sequence of Lake Biwa wild common carp (LBW) was determined using a PCR-based method, and the phylogenetic status of the LBW strain within common carp was re-examined using a number of already-published mtDNA sequences of multiple gene regions from various strains, which enabled a geographically more comprehensive analysis including additional strains from South-East Asia (Vietnam and Indonesia). The following three datasets, dataset A [partial D-loop region sequences (ca. 760 bp) from 44 strains], B [ATPase6 and 8 gene sequences (826 bp) from 39 strains] and C (COII gene sequences (690 bp) from 9 strains), were constructed from different studies, and phylogenetic analyses conducted using a goldfish (Carassius auratus auratus) as an outgroup. In all the analyses, a principal phylogenetic dichotomy between the LBW and “Eurasian” strains, which was recently revealed based on cyt b gene and D-loop region sequences, was recovered. Phylogenetic relationships among “Eurasian” (including Japanese ornamental koi) strains were, however, not reconstructed reliably. Low level nucleotide divergence throughout the mitochondrial genome, which was revealed by the whole mtDNA comparison between the LBW and a putative Taiwanese strain, indicated that no single coding/non-coding region could provide sufficient information for resolving phylogeny among the closely-related “Eurasian” strains of the species.