Sequencing and characterization of mitochondrial DNA genome for Brama japonica (Perciformes: Bramidae) with phylogenetic consideration
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Abstract
In the present study, we isolated and characterized the complete mitochondrial genome sequence of Brama japonica by polymerase chain reaction (PCR) amplification and primer-walking sequencing. The complete DNA was 17,009 bp in length and contained a typical set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a long putative control region. The gene organization and nucleotide composition of complete mitogenome were identical to those of other Bramidae fishes. In contrast, the 12S rRNA gene contained a big poly C structure which was larger than those from other Bramidae species. Of 37 genes, twenty-eight were encoded by heavy strand, while nine were encoded by light strand. Among the 13 protein-coding genes, twelve employed ATG as start codon, while only COI utilized GTG as start codon. In the control region, the terminal associated sequence (TAS), the central and conserved sequence block (CSB-E and CSB-D) and a variable domain (CSB-1, CSB-2 and CSB-3) were identified, while the typical central conserved CSB-F could not be detected in B. japonica. The putative OL region can fold into a conserved secondary structure and the conserved motif (5’-GCCGG-3’) was found at the base of the stem in tRNACys. The overall nucleotide composition of this genome was 26.43% for A, 16.71% for G, 31.35% for C, and 25.50% for T, with a high A+T content of 51.93%. From the NJ phylogenetic tree, we can find that B. japonica was together with other five Bramidae species formed a monophyletic group among 24 species. This work provided a set of useful data for studying on population genetic diversity and molecular evolution in Bramidae and related fish species.
Cite this as
2016. Sequencing and characterization of mitochondrial DNA genome for Brama japonica (Perciformes: Bramidae) with phylogenetic consideration. PeerJ PrePrints 4:e1667v1 https://doi.org/10.7287/peerj.preprints.1667v1Author comment
This is a submission to PeerJ for review.
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Supplemental Information
The complete mitochondrial genome of Brama japonica
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Fenfang Chen performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables.
Hongyu Ma conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Chunyan Ma performed the experiments, analyzed the data.
Heng Zhang contributed reagents/materials/analysis tools.
Mengdi Zhao performed the experiments.
Yongyong Meng performed the experiments.
Hongqing Wei performed the experiments.
Lingbo Ma conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper.
Animal Ethics
The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):
Our project was approved by East China Sea Fisheries Research Institute.
DNA Deposition
The following information was supplied regarding the deposition of DNA sequences:
GenBank (KT908039)
Data Deposition
The following information was supplied regarding data availability:
GenBank (KT908039)
Funding
This work was supported by the National Science & Technology Support Plan (2013BAD13B04), the National Basic Research Special Foundation of China (2013FY110700), the Special Scientific Research Funds for Central Non-Profit Institutes (2015M07), and the National Infrastructure of Fishery Germplasm Resources. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.