Abstract
We determined the complete nucleotide sequence of the mitochondrial genome for the summer flounder, Paralichthys dentatus (Pleuronectiformes, Paralichthyidae). This mitochondrial genome, consisting of 17,033 base pairs (bp), encoded genes for 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a putative D-loop region like those found in other vertebrates, with the gene order identical to that of typical vertebrates. Phylogenetic analysis showed that P. dentatus clustered into one clade with its Paralichthyidae counterparts, Paralichtchys lethostigma and Paralichtchys olivaceus, which showed the close relationship among these species.
Keywords: Paralichthys dentatus, mitochondrial genome, genome organization, phylogenetic analysis
Summer flounder, Paralichthys dentatus, is an important commercially and recreationally caught flatfish occurring in continental shelf waters from Maine to Florida in the United States (Morse 1981). In 2002, summer flounder was introduced into China for its relative rapid growth rate and high-temperature tolerance in comparison with native flounder species, P. olivaceus (Wang et al. 2004). Recently, hybridization between P. dentatus and P. olivaceus has been achieved (Tian et al. 2006; Liu et al. 2015). As an alien species, it is essential to investigate the genetic relationship between P. dentatus and native species and evaluate gene flow and possible genetic invasion risk. Mitochondrial DNA is a useful marker for analyses of gene flow, hybridization, and introgression for its compactness, maternal inheritance, fast evolutionary rate, and the resulting short coalescence time (Miya et al. 2003; Oh et al. 2007). However, the mitochondrial genome of P. dentatus remains unclear.
Ten individuals of P. dentatus were sampled from the Great Bay Aquaculture LLC. located at Portsmouth, NH, USA (43˚05′ N, 70˚ 47′ W), the samples were transferred to and stored at our lab located at Yellow Sea Fisheries Research Institute, Qingdao, China. The whole genomic DNA was extracted from muscle tissues and the mitogenome was amplified with universal metazoan primer pairs and completely sequenced with a 3730 × l DNA Analyzer. The complete mitochondrial genome of P. dentatus was 17,033 base pairs (bp) in length (GenBank accession no.: KU053334.1), it contained 13 protein-coding genes (PCGs), 2 ribosomal (r)RNA genes (12S rRNA, 16S rRNA), 22 transfer (t) RNA genes, and a putative control region (D-loop) as do most other fish mitogenomes (Boore 1999; Miya et al. 2003). Overall base compositions of the P. dentatus mitochondrial genome were as follows: A, 28.15% (4795/17,033); C, 27.96% (4763/17,033); G, 16.90% (2878/17,033); and T, 26.99% (4597/17,033). 12 PGCs of P. dentatus had the typical mitochondrial start codon ATG, while the COI had a GTG start codon. Six PCGs (ND1, COI, ATPase 8, ND4L, ND5, and ND6) ended with complete termination codons (TAA), while the other seven used the incomplete stop codon TA– (ND2, ATPase 6, and COIII) or T–– (COII, ND3, ND4, and CytB). Three reading-frame overlaps occurred on the same strand including ATPase subunit (ATPase) 8 and 6 overlapped by 10 nucleotides, ND4L and ND4 overlapped by seven nucleotides, and ND5 and ND6 overlapped by four nucleotides. The tRNA genes ranged from 65 to 74 bp and were distributed among the genome. The 12S rRNA and 16S rRNA genes were 948 and 1712 nucleotides long, respectively, and were located between tRNAPhe and tRNALeu(UAA), separated by tRNAVal. The control D-loop region in P. dentatus was located between tRNAPhe and tRNAPro, which was 1338 bp in length, this control region was AT-rich, with an AT content of 61.84%. The phylogenetic tree between P. dentatus mitochondrial genome and other 13 Pleuronectiformes fishes showed that Paralichthyidae fishes clustered into one branch with Pleuronectidae fishes, and the Paralichthyidae species including P. dentatus, P. lethostigma, and P. olivaceus clustered into one sub-branch with a bootstrap value of 100% (Figure 1).
Figure 1.
Phylogenetic tree of NJ analyses based on complete mitochondrial amino acid sequences of P. dentatus. The species studied in this work is underlined.
Disclosure statement
All the authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
Funding
This study was supported by the China Agriculture Research System [CARS-50] and the National Natural Science Foundation of China [31502145].
References
- Boore JL. 1999. Animal mitochondrial genomes. Nucleic Acids Res. 27:1767–1780. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Liu QH, Ma DY, Xu SH, Xiao ZZ, Xiao YS, Song ZC, Li J.. 2015. Summer flounder (Paralichthys dentatus) sperm cryopreservation and application in interspecific hybridization with olive flounder (P. olivaceus). Theriogenology. 83:703–710. [DOI] [PubMed] [Google Scholar]
- Miya M, Takeshima H, Endo H, Ishiguro NB, Inoue JG, Mukai T, Satoh TP, Yamaguchi M, Kawaguchi A, Mabuchi K, et al. 2003. Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol Phylogenet Evol. 26:121–138. [DOI] [PubMed] [Google Scholar]
- Morse WW. 1981. Reproduction of the summer flounder, Paralichthys dentatus (L.). J Fish Biol. 19:189–203. [Google Scholar]
- Oh DJ, Kim JY, Lee JA, Yoon WJ, Park SY, Jung YH.. 2007. Complete mitochondrial genome of the rock bream Oplegnathus fasciatus (Perciformes, Oplegnathidae) with phylogenetic considerations. Gene. 392:174–180. [DOI] [PubMed] [Google Scholar]
- Tian YS, Chen SL, Liu BW, Wang B.. 2006. Embryonic and postembryonic development of hybrid produced with frozen sperms of Paralichthys dentatus and eggs of Paralichthys olivaceus. J Fish China. 30:433–443. [Google Scholar]
- Wang B, Zhang CH, Zhang J, Jing S, Li JQ, Sun QX, Mao XH.. 2004. Advance of study on reproduction biology and breeding technology of the Summer flounder, Paralichthys dentatus Linnaeus. Marine Fish Res. 25:90–96. [Google Scholar]