Complete mitochondrial genome of the Pleuronichthys lighti (Pleuronectiformes, Pleuronectidae) with phylogenetic consideration
2017
Yaoxuan Song, Ocean University of China, Qingdao, China | Na Song, Ocean University of China, Qingdao, China | Yongdong Zhou, Marine Fisheries Research Institute of Zhejiang, Zhoushan, China | Pengfei Li, Marine Fisheries Research Institute of Zhejiang, Zhoushan, China | Shujiang Zhao, Zhejiang Ocean University, Zhoushan, China | Tianxiang Gao, Marine Fisheries Research Institute of Zhejiang, Zhoushan, China
Mitochondrial genome has been used to shed light on many fields of both basic and applied research, including the study of molecular evolution. The complete mitochondrial genome sequence of 17368 bp nucleotides from the Pleuronichthys lighti was determined. It was a circular double-stranded DNA molecule with identical set of 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes as well as a non-coding control region. Stand asymmetry in the nucleotide composition was reflected in the codon usage of genes oriented in opposite directions. In the control region, we identified the extended termination associated sequence domain, the central conserved sequence block domain and the conserved sequence block domain, and two complete repeat region. They were "TTACAATA" and "TGTTGTAA", respectively. All known 12 mitochondrial genomes of Pleuronectinae fishes were downloaded and analyzed; there were 5570 variable sites in the consensus sequences of 15241 base pairs, calculation of total sites were 35.5%. The highest sequence divergence was 50% (ATP8) and the Kimura-2-parameter genetic distance was 0.235 (ND6), whereas the COIII had the lowest sequence divergence (28.8%) and genetic distance (0.128); the protein coding genes were mainly acted by purifying selection which was detected by selection tests. Analysis of confidence and the information content for per nucleotide revealed ND5, ATP6, COI and ND4 genes were suitable molecular markers for phylogenetic study of Pleuronectinae fishes. Phylogenetic analysis using Bayesian computational algorithms based on COI genes provided support for the taxonomic status of P. lighti, which was consistent with the traditional taxonomy.
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