Organization of the mitochondrial genome of a deep-sea fish, Gonostoma gracile (Teleostei : Stomiiformes): First example of transfer RNA gene rearrangements in bony fishes

We determined the complete nucleotide sequence of the mitochondrial genome (except for a portion of the putative control region) for a deep-sea fish. Gonostoma gracile. The entire mitochondrial genome was purified by gene amp lification using long polymerase chain reaction (long PCR), and the product s were subsequently used as templates for PCR with 30 sets of newly designe d, fish-universal primers that amplify contiguous, overlapping segments of the entire genome. Direct sequencing of the PCR products showed that the ge nome contained the same 37 mitochondrial structural genes as found in other vertebrates (two ribosomal RNA, 22 transfer RNA, and 13 protein-coding gen es), with the order of all rRNA and protein-coding genes, and 19 tRNA genes being identical to that in typical vertebrates. The gene order of the thre e tRNAs (tRNA(Glu), tRNA(Thr), and tRNA(Pro)) relative to cytochrome b, how ever, differed from that determined in other vertebrates. Two steps of tand em duplication of gene regions, each followed by deletions of genes, can be invoked as mechanisms generating such rearrangements of tRNAs. This is the first example of tRNA gene rearrangements in a bony fish mitochondrial gen ome.