Abstract
The complete mitochondrial genome of Rhopilema esculentum collected from Jiaozhou Bay, China, was determined by next-generation sequencing. The mitogenome is a circular molecule 15,855 bp in length, including 13 protein-coding genes (Cox 1, Cox2, Atp 8, Atp 6, Cox 3, ND2, ND5, ND 6, ND3, ND4L, ND1,ND4, Cytb), 5 tRNAs (tRNA-Trp, tRNA-Met, tRNA-Leu, tRNA-Ser, tRNA-Gln), 2 rRNA genes (small subunit RNA and large subunit RNA) and 1 putative control region. The phylogenetic tree in the related species showed that R. esculentum is close to Nemopilema nomurai.
Rhopilema esculentum Kishinouye 1891 (Cnidaria: Scyphozoa: Rhizostomeae: Rhizostomatidae) inhabits a wide range of the northwestern Pacific region including seas around Japan, Korea, and China. In China, R. esculentum is widely distributed in the Bohai Sea, the Yellow Sea, the East China Sea, and the northern South China Sea (Dai et al. Citation2004; Jiang et al. Citation2007). The edible jellyfish R. esculentum has been exploited in Chinese waters for more than 1700 years and is one of the most abundant fishery species in China (Omori & Nakano Citation2001).
To date, a few reports are available on complete mitochondrial genomes as in Aurelia aurita (Shao et al. Citation2006), Aurelia sp. nov. (Hwang et al. Citation2014), Craspedacusta sowerbyi (Zou et al. Citation2012), and Chrysaora quinquecirrha (Hwang Citation2014). It would be therefore important to analyze the complete mitochondrial genome to better understand the molecular phylogenetic relationship between Cnidaria species. In the present paper, we first report the complete mitochondrial DNA from N. nomurai in order to obtain basic genetic information within the genus Rhizostomatidae. It is expected that the information obtained from complete mitochondrial genome sequence of R. esculentum would provide a useful genetic resource to be utilized in the future investigation on population genetics and phylogenomics of Scyphozoa. DNA from about 1 g bell tissue of a single specimen of R. esculentum weighing ∼5 kg collected from Jiaozhou Bay, China, (36.10N, 120.30E) was extracted by the standard phenol-chloroform extraction method (Sambrook & Russell Citation2001) and part of the rest of the sample was preserved in −20 °C at KLMEES Institute of Oceanology with the voucher no. Rmit001.
The complete mitogenome of R. esculentum is 15,855 bp in length and the GenBank accession No. is KY454768. It consists of 13 protein-coding genes (including Cox1, Cox2, Atp8, Atp6, Cox3, ND2, ND5, ND 6, ND3, ND4L, ND1, ND4, Cytb), 5 tRNAs (tRNA-Trp, tRNA-Met, tRNA-Leu, tRNA-Ser, tRNA-Gln), 2 rRNA genes(small subunit RNA and large subunit RNA), and 1 putative control region. All the genes showed complete stop codons using TAA and TAG. There is also slight anti-G bias (13.70% and 13.24%) on the 2nd and 3rd position of all the genes. The start codon of ND3 and ND6 are different from other species, such as A. aurita (Shao et al. Citation2006).
The mitochondrial genome base composition for 13 genes was 28.12% for A, 37.01% for T, 17.40% for G and 17.37% for C. The A + T base composition (65.13%) was higher than G + C(34.77%) based on the sequences of 13 genes, suggesting that the R. esculentum has low G + C ratio in the mitochondrial genome. Phylogenetic relationship revealed NJ tree among 5 related species based on the complete mitochondrial genome downloaded from NCBI (). The NJ phylogenetic tree showed that the R. esculentum is close to Nemopilema nomurai (GenBank No. KY454767) clustered in a separate branch, and was far related to other species.
Figure 1. Phylogenetic relationship revealed by NJ tree.
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The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
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References
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