Structure of mitochondrial DNA control region and molecular phylogenetic relationship among three flounders of genus Pleuronectes Yan Zhang a, b,1 , Hui Zhang c,1 , Tianxiang Gao c, * , Zhenqing Miao a a Fishery College, Zhejiang Ocean University, Zhoushan 316004, China b Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China c Fisheries College, Ocean University of China, Qingdao 266003, China article info Article history: Received 26 February 2011 Accepted 15 May 2011 Available online 12 June 2011 Keywords: Control region Structure Pleuronectes Phylogenetic relationship Mitochondrial abstract Structure of mitochondrial DNA control region about three flounders – Pleuronectes yokohama, Pleuronectes schrenki and Pleuronectes herzensteini – were reported. The TAS, cTAS, CSB-A to CSB-F and CSB-1 to CSB-3 were detected in these three flounders. The results indicated that the structures of these parts were different from most fishes. All the mtDNA control region sequences of the three founders have tandem repeat sequences in the downstream of CSB-3, which is different from most vertebrates. According to the structure of the mtDNA control region, P. yokohama was more similar with P. schrenki and P. herzensteini was much different from the other two species. In addition, three segments such as control region, Cytb and COI are used to analyze the phylogenic relationships of the three species. The genetic distances and phylogenetic tree results support the classification by traditional morphology. It is not clear if P. yokohama and P. schrenki belong to the same species, and this should be accepted with caution. Ó 2011 Elsevier Ltd. All rights reserved. 1. Introduction As members of the genus of Pleuronectes, the flounders Pleuronectes yokohama, Pleuronectes schrenki and Pleuronectes herzensteini belong to the order of Pleuronectiformes (Nakabo, 2000). They are the important commercial fishery resources in Northwestern Pacific Ocean, especially in Japan (Nakabo, 2000). Up to present, there have been some studies on these three species, but most of them have focused on their life history and the aspect of ecology. There are few genetic studies on P. yokohama, P. herzensteini and P. schrenki (Abe, 2006; Zhang et al., 2008a, 2008b). Due to its compact size (16–17 kb), high rate of mutation and exclusive maternal mode of inheritance (Brown et al., 1979; Harrison, 1989), the mitochondrial genome has been widely used as a marker in molecular genetic studies. As a closed circular molecule, the piscine mtDNA contains a set of 37 genes specifying 13 proteins, two rRNAs, and 22 tRNAs encoded in both the heavy (H) and light (L) DNA strand (Meyer, 1993). The control region (D-loop) is the only non-coding segment in the vertebrate mitochondrial genome (Shui et al., 2008). Numerous studies have documented variation of DNA sequence in this region. Despite the presence of several highly conserved sequences (Saccone et al., 1987), this region is known to exhibit some of the highest rates of evolution on the mitochondrial DNA. Most of this variation consists of nucleotide substitutions and small insertions and deletions. However, considerable variation of length has been observed in an ever-growing list of species (Lunt et al., 1998), which is caused by variation in the number of tandemly repeated sequences. These repeats can be observed * Corresponding author. Tel.: þ86 532 8203 2063; fax: þ86 532 8203 2076. E-mail address: gaozhang@ouc.edu.cn (T. Gao). 1 These authors contribute equally to this paper. Contents lists available at ScienceDirect Biochemical Systematics and Ecology journal homepage: www.elsevier.com/locate/biochemsyseco 0305-1978/$ – see front matter Ó 2011 Elsevier Ltd. All rights reserved. doi:10.1016/j.bse.2011.05.008 Biochemical Systematics and Ecology 39 (2011) 627–634