Complete mitochondrial DNA sequence of Aulopus japonicus (Teleostei : Aulopiformes), a basal Eurypterygii: longer DNA sequences and higher-level relationships

For the first step toward resolution of the higher-level relationships of t he order Aulopiformes (Teleostei: Eurypterygii) using longer DNA sequences, we determined the complete mitochondrial DNA sequence for Aulopus japonicu s (Aulopodidae). The entire genome was purified by gene amplification using a long PCR technique, and the products were subsequently used as templates for PCR with 63 fish-versatile and 3 species-specific primers that amplify contiguous, overlapping segments of the entire genome. Direct sequencing o f the PCR products demonstrated that the genome (16 653 base pairs [bp]) co ntained the same 37 mitochondrial genes (2 ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes) as found in other vertebrates, with the gene o rder identical to that in typical vertebrates. Maximum-parsimony analysis u sing nucleotide sequences from the concatenated 12 protein-coding genes (no third codon positions and excluding the ND6 gene) plus 22 tRNA genes (stem regions only) from eight teleosts placed A. japonicus in a reasonable phyl ogenetic position; those from individual protein-coding genes and the conca tenated 22 tRNA genes alone, however, did not reproduce the expected phylog eny with few exceptions, probably owing to insufficient phylogenetic inform ation in these smaller data sets. This result suggests that further taxonom ic sampling and sequencing efforts may clarify limits and intra- and interr elationships of this morphologically and ecologically diverse group of fish es using mitochondrial genomic (mitogenomic) data.