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Background  Few mitochondrial gene rearrangements are found in vertebrates and large-scale changes in these genomes occur even less frequently. It is difficult, therefore, to propose a mechanism to account for observed changes in mitogenome structure. Mitochondrial gene rearrangements are usually explained by the recombination model or tandem duplication and random loss model.    Results  In this study, the complete mitochondrial genomes of four flatfishes,  Crossorhombus azureus  (blue flounder),  Grammatobothus krempfi, Pleuronichthys cornutus , and  Platichthys stellatus  were determined. A striking finding is that eight genes in the  C. azureus  mitogenome are located in a novel position, differing from that of available vertebrate mitogenomes. Specifically, the  ND6  and seven tRNA genes (the  Q, A, C, Y, S   1   , E, P  genes) encoded by the L-strand have been translocated to a position between  tRNA-T  and  tRNA-F  though the original order of the genes is maintained.    Conclusions  These special features are used to suggest a mechanism for  C. azureus  mitogenome rearrangement. First, a dimeric molecule was formed by two monomers linked head-to-tail, then one of the two sets of promoters lost function and the genes controlled by the disabled promoters became pseudogenes, non-coding sequences, and even were lost from the genome. This study provides a new gene-rearrangement model that accounts for the events of gene-rearrangement in a vertebrate mitogenome.

Complete mitogenome sequences of four flatfishes (Pleuronectiformes) reveal a novel gene arrangement of L-strand coding genes