The Complete Mitochondrial Genome and Molecular Phylogeny of the Flathead Platycephalus cultellatus Richardson, 1846 from Vietnam (Teleostei; Scorpaeniformes)
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Tran, Biet Thanh
(Department of Fisheries Biology, Pukyong National University)
Nguyen, Tu Van (Institute of Tropical Biology, Vietnam Academy of Science and Technology) Choi, Youn Hee (Department of Fisheries Biology, Pukyong National University) Kim, Keun-Yong (AquaGenTech Co., Ltd.) Heo, Jung Soo (AquaGenTech Co., Ltd.) Kim, Keun-Sik (Research Center for Endangered Species, National Institute of Ecology) Ryu, Jung-Hwa (Ryujunghwa Marine Research Institute) Kim, Kyeong Mi (National Marine Biodiversity Institute of Korea) Yoon, Moongeun (National Marine Biodiversity Institute of Korea) |
1 | Metzker, M.L. 2009. Sequencing technologies - the next generation. Nat. Rev. Genet., 11: 31-46. https://doi.org/10.1038/nrg2626. DOI |
2 | Meyer, A. 1993. Evolution of mitochondrial DNA in fishes. In: Hochachka, P.W. and T.P. Mommsen (eds.), Molecular Biology Frontiers: Biochemistry and Molecular Biology of Fishes. Elsevier Science, Amsterdam, Netherlands, pp. 1-38. |
3 | Page, R.D.M. 1996. Tree View: An application to display phylogenetic trees on personal computers. Bioinformatics, 12: 357-358. https://doi.org/10.1093/bioinformatics/12.4.357. DOI |
4 | Puckridge, M., P.R. Last, D.C. Gledhill and N. Andreakis. 2019. From the tropics to the pole and back again: Radiation in the flathead fishes (Platycephalidae) across Australia and the Indo-West Pacific. J. Biogeogr., 46: 680-693. https://doi.org/10.1111/jbi.13484. DOI |
5 | Qin, Y., N. Song, J. Zou, Z. Zhang, G. Cheng, T. Gao and X. Zhang. 2013. A new record of a flathead fish (Teleostei: Platycephalidae) from China based on morphological characters and DNA barcoding. Chin. J. Oceanol. Limnol., 31: 617-624. https://doi.org/10.1007/s00343-013-2186-z. DOI |
6 | Richardson, J. 1846. Report on the ichthyology of the seas of China and Japan. Rep. Brit. Assoc. Adv. Sci., 1845: 187-320. |
7 | Ronquist, F. and J.P. Huelsenbeck. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19: 1572-1574. https://doi.org/10.1093/bioinformatics/btg180. DOI |
8 | Tavare, S. 1986. Some probabilistic and statistical problems in the analysis of DNA sequences. In: Miura, R.M. (ed.), Some Mathematical Questions in Biology - DNA Sequence Analysis. Am. Math. Soc., Providence, R.I., U.S.A., pp. 57-86. |
9 | Satoh, T.P., M. Miya, K. Mabuchi and M. Nishida. 2016. Structure and variation of the mitochondrial genome of fishes. BMC Genom., 17: 719. https://doi.org/10.1186/s12864-016-3054-y. DOI |
10 | Cheng, J., Z. Wang, N. Song, T. Yanagimoto and T. Gao. 2019. Phylogeographic analysis of the genus Platycephalus along the coastline of the northwestern Pacific inferred by mitochondrial DNA. BMC Evol. Biol., 19: 159. https://doi.org/10.1186/s12862-019-1477-1. DOI |
11 | Cui, L., Y.L. Dong, F.H. Liu, X.C. Gao, H. Zhang, L. Li, J.Y. Cen and S.H. Lu. 2017. The first two complete mitochondrial genomes for the family Triglidae and implications for the higher phylogeny of Scorpaeniformes. Sci. Rep., 7: 1553. https://doi.org/10.1038/s41598-017-01654-y. DOI |
12 | Cui, L., R.B. Cao, Y.L. Dong, X.C. Gao, J.G. Cen and S.H. Lu. 2019. The first complete mitochondrial genome of the flathead Cociella crocodilus (Scorpaeniformes: Platycephalidae) and the phylogenetic relationships within Scorpaeniformes based on whole mitogenomes. Genes, 10: 533. https://doi.org/10.3390/genes10070533. DOI |
13 | Darriba, D., G.L. Taboada, R. Doallo and D. Posada. 2012. jModel Test2: more model, new heuristics and parallel computing. Nat. Methods, 9: 722. https://doi.org/10.1038/nmeth.2109. DOI |
14 | Imamura, H. 1996. Phylogeny of the family Platycephalidae and related taxa (Pisces: Scorpaeniformes). Species Divers., 1: 123-233. https://doi.org/10.12782/specdiv.1.123. DOI |
15 | Imamura, H., M. Komada and T. Yoshino. 2006. Record of the flathead fishes (Perciformes: Platycephalidae) collected from Nha Trang, Vietnam. Coastal Mar. Sci., 30: 293-300. https://doi.org/10.11646/zootaxa.3904.2.1. DOI |
16 | Jorgensen, T.E., I. Bakke, A. Ursvik, M. Andreassen, T. Moum and S.D. Johansen. 2014. An evolutionary preserved intergenic spacer in gadiform mitogenomes generates a long noncoding RNA. BMC Evol. Biol., 14: 182. https://doi.org/10.1186/s12862-014-0182-3. DOI |
17 | Wataru, I., F. Tsukasa, I. Ryota, Y. Koichiro, M. Yasunobu, P.S. Takashi, S. Tetsuya, M. Kohji, T. Hirohiko, M. Masaki and N. Mutsumi. 2013. MitoFish and MitoAnnotator: A mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Mol. Biol. Evol., 30: 2531-2540. https://doi.org/10.1093/molbev/mst141. DOI |
18 | Martin, M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J., 17: 10-12. https://doi.org/10.14806/ej.17.1.200. DOI |
19 | Xu, Z., Y. Ye, H. Yang, M. Xu and B. Guo. 2019. The complete mitochondrial genome of Minous monodactylus (Minoinae: Synanceiidae: Scorpaeniformes) and phylogenetic studies of Scorpaeniformes. Mitochondrial DNA B Resour., 4: 1670-1671. https://doi.org/10.1080/23802359.2019.1606684. DOI |
20 | Zhang, H., K. Shen, S. Feng, C. Wang and S. Xu. 2021. The complete mitochondrial genome of Platycephalus sp. 1 (Teleostei, Platycephalidae) obtained by whole genome sequencing. Mitochondrial DNA B Resour., 6: 1941-1943. https://doi.org/10.1080/23802359.2021.1937361. DOI |
21 | Duchene, S., F.I. Archer, J. Vilstrup, S. Caballero and P.A. Morin. 2011. Mitogenome phylogenetics: the impact of using single regions and partitioning schemes on topology, substitution rate and divergence time estimation. PLoS ONE, 6: e27138. https://doi.org/10.1371/journal.pone.0027138. DOI |
22 | Chen, Z., N. Song, J. Zou, Y. Qin, L. Ma and T. Gao. 2020. Identification of species in genus Platycephalus from seas of China. J. Ocean Univ. China, 19: 417-427. https://doi.org/10.1007/s11802-020-4158-1. DOI |
23 | Hall, T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser., 41: 95-98. |
24 | Luo, X., Q. Li, Z. Wang, J. Xiao, T. Yang, T. Gao and X. Wang. 2019. Complete mitochondrial genome sequence of flathead fish Platycephalus sp. 1 (Scorpaeniformes: Platycephalidae). Mitochondrial DNA B Resour., 4: 1570-1571. https://doi.org/10.1080/23802359.2019.1602007. DOI |
25 | Chen, Z., N. Song, J. Zou and T. Gao. 2018. Rediscovery and elaborate description of Platycephalus cultellatus Richardson, 1846 collected from the coastal waters of South China Sea. Aquat. Living Resour., 31: 32. https://doi.org/10.1051/alr/2018015. DOI |
26 | Alexandros, S. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22: 2688-2690. https://doi.org/10.1093/bioinformatics/btl446. DOI |
27 | Asahida, T., T. Kobayashi, K. Saitoh and I. Nakayama. 1996. Tissue preservation and total DNA extraction from fish stored at ambient temperature using buffers containing high concentration of urea. Fish. Sci., 62: 727-730. https://doi.org/10.2331/fishsci.62.727. DOI |
28 | Boore, J.L. 1999. Animal mitochondrial genomes. Nucleic Acids Res., 27: 1767-1780. https://doi.org/10.1093/nar/27.8.1767. DOI |
29 | Bray, D.J. 2020. Platycephalus in Fishes of Australia. Available at: https://fishesofaustralia.net.au/home/family/48#moreinfo (accessed 18 June 2021). |
30 | Briscoe, A.G., K.P. Hopkins and A. Waeschenbach. 2016. High-throughput sequencing of complete mitochondrial genomes. In: Bourlat, S.J. (ed.), Marine Genomics Methods and Protocols: Methods in Molecular Biology. Humana Press, New York, U.S.A., pp. 45-64. https://doi.org/10.1007/978-1-4939-3774-5_3. DOI |
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