Complete mitochondrial genome sequences of three rhombosoleid fishes and comparative analyses with other flatfishes (Pleuronectiformes)

Background: Peltorhamphus novaezeelandiae, Colistium nudipinnis, and Pelotretis flavilatus belong to the family Rhombosoleidae of Pleuronectiformes. Their high phenotypic similarity has provoked great differences in the number and nomenclature of the taxa that depend primarily on morphological features. These facts have made it necessary to develop molecular markers for taxonomy and phylogenetic studies. In this study, the complete mitogenomes (mtDNA) of the three rhombosoleid fishes were determined for the comparative studies and potential development of molecular markers in the future. Results: The lengths of the complete mitogenome of the three flatfishes are 16,889, 16,588, and 16,937 bp in the order mentioned above. The difference of lengths mainly results from the presence of tandem repeats at the 3'-end with variations of motif length and copy number in the control regions (CR). The gene content and arrangement is identical to that of the typical teleostean mtDNA. Two large intergenic spacers of 28 and 18 bp were found in P. flavilatus mtDNA. The genes are highly conserved except for the sizes of ND1 (which is 28 bp shorter than the two others), ND5 (13 bp longer), and tRNA(Glu) (5 bp longer) in P. flavilatus mtDNA. The symbolic structures of the CRs are observed as in other fishes, including ETAS, CSB-F, E, D, C, B, A, G-BOX, pyrimidine tract, and CSB2, 3. Conclusions: Comparative genomic analysis within rhombosoleids revealed that the mitogenomic feature of P. flavilatus was significantly different from that of the two others. Base composition, gene arrangement, and CR structure were carried on in the 17 mitogenomes. Apart from gene rearrangement in two tongue soles (Cynoglossus semilaevis and Cynoglossus abbreviatus), the gene order in 15 others is identical to that of the typical fish mitogenomes. Of the 16 studied mitogenomes, 15 species (except for Zebrias zebrinus) have tandem repeats at the 3'-, 5'-, or both 3'- and 5'-ends of the CRs. Moreover, the motif length and copy number intraspecies or interspecies are also variable. These phenomena fully indicate the diversity of repeats in flatfish mtDNA and would provide useful data for studies on the structure of mitogenomes in fishes.