Abstract
Thunnu obesus is important in commercial fisheries around the world. Due to human overfishing, climate change and ocean acidification, it was listed as Vulnerable (VU) under the International Union for the Conservation of Nature. In the present study, the complete mitogenome of T. obesus was determined. It is 16,524 bp in length and contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes, one origin of replication on the light-strand (OL) and a control region (CR). The overall base composition is 28.5, 25.4, 29.4 and 16.7% for A, T, C and G, respectively. The 13 PCGs encode 3797 amino acids in total, most of which use the initiation codon ATG except COI use GTG, and TAA or TAG as the stop codon, except COII, ND4 and Cyt b use an incomplete stop codon T. Additionally, a phylogenetic tree was constructed to explore the taxonomic status of T. obesus, which expects for phylogenetic relationship within Thunnu and further conservation strategies for this species.
References
Bartlett SE, Davidson WS (1991) Identification of Thunnus tuna species by the polymerase chain reaction and direct sequence analysis of their mitochondrial cytochrome b genes. Can J Fish Aquat Sci 48:309–317
Brill RW, Bigelow KA, Musyl MK, Fritsches KA, Warrant EJ (2005) Bigeye tuna (Thunnus obesus) behavior and physiology and their relevance to stock assessments and fishery biology. Col Vol Sci Pap ICCAT 57:142–161
Chow S, Kishino H (1995) Phylogenetic relationships between tuna species of the genus Thunnus (Scombridae: Teleostei): inconsistent implications from morphology, nuclear and mitochondrial genomes. J Mol Evol 41:741–748
Chow S, Nakagawa T, Suzuki N, Takeyama H, Matsunaga T (2006) Phylogenetic relationships among Thunnus species inferred from rDNA ITS1 sequence. J Fish Biol 68:24–35
Collette BB, Reeb C, Block BA (2001) Systematics of the tunas and mackerels (Scombridae) Fish. Physiology 19:1–33
Gibbs RH Jr, Collette BB (1967) Comparative anatomy and systematics of the tunas, genus Thunnus U S Fish and Wildlife Service. Fish Bull 66:65–130
Gong L, Shi W, Wang Z, Miao X, Kong X (2013) Control region translocation and a tRNA gene inversion in the mitogenome of Paraplagusia japonica (Pleuronectiformes: Cynoglossidae). Mitochondr DNA 24:671–673. doi:10.3109/19401736.2013.773984
Gong L, Shi W, Si LZ, Wang ZM, Kong XY (2015) The complete mitochondrial genome of peacock sole Pardachirus pavoninus (Pleuronectiformes: Soleidae) and comparative analysis of the control region among 13 soles. Mol Biol + 49:408–417 doi:10.1134/S0026893315030061
Liu TX, Jin XX, Wang RX, Xu TJ (2013) Complete sequence of the mitochondrial genome of Odontamblyopus rubicundus (Perciformes: Gobiidae): genome characterization and phylogenetic analysis. J Genet 92:423–432
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:0955–0964
Miya M 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
Sbisà E, Tanzariello F, Reyes A, Pesole G, Saccone C (1997) Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications. Gene 205:125–140
Stothard P, Wishart DS (2005) Circular genome visualization and exploration using CGView. Bioinformatics 21:537–539
Takeyama H, Chow S, Tsuzuki H, Matunaga T (2001) Mitochondrial DNA sequence variation within and between tuna Thunnus species and its application to species identification. J Fish Biol 58:1646–1657
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739
Wang S-Y, Shi W, Miao X-G, Kong X-Y (2014) Complete mitochondrial genome sequences of three rhombosoleid fishes and comparative analyses with other flatfishes (Pleuronectiformes). Zool Stud 53:80
Wei M, Liu Y, Guo H, Zhao F, Chen S (2016) Characterization of the complete mitochondrial genome of Cynoglossus gracilis and a comparative analysis with other Cynoglossinae fishes. Gene. doi:10.1016/j.gene.2016.06.023
Wong TW, Clayton DA (1985) In vitro replication of human mitochondrial DNA: accurate initiation at the origin of light-strand synthesis. Cell 42:951–958. doi:10.1016/0092-8674(85)90291-0
Wu G, Wu C, Wang Q, Luo J (2016) The complete mitochondrial genome of the Terapon jarbua (Perciformes: Terapontidae). Mitochondr DNA Part A 27:3430–3431. doi:10.3109/19401736.2015.1022734
Zhang B, Sun Y, Shi G (2014) The complete mitochondrial genome of the fourfinger threadfin Eleutheronema tetradactylum (Perciforms: Polynemidae) and comparison of light strand replication origin within Percoidei. Mitochondr DNA 25:411–413. doi:10.3109/19401736.2013.809433
Zhang H, Zhang Y, Qin G, Lin Q (2015) The complete mitochondrial genome sequence of the network pipefish (Corythoichthys flavofasciatus) and the analyses of phylogenetic relationships within the Syngnathidae species. Mar Genom 19:59–64 doi:10.1016/j.margen.2014.11.005
Acknowledgements
This work was supported by the National Key Technology Research and Development Program Foundation of China (2011BAD13B08) and National Natural Science Foundation of China (NSFC) (No. 41406138).
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Gong, L., Liu, LQ., Guo, BY. et al. The complete mitochondrial genome characterization of Thunnus obesus (Scombriformes: Scombridae) and phylogenetic analyses of Thunnus . Conservation Genet Resour 9, 379–383 (2017). https://doi.org/10.1007/s12686-017-0688-2
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DOI: https://doi.org/10.1007/s12686-017-0688-2