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http://dx.doi.org/10.5352/JLS.2014.24.6.626

Genetic Structure and Phylogenetic Relationship of Red Spotted Grouper (Epinephelus akaara) Based on the Haplotypes and Polymorphisms of Mitochondrial COI Gene Sequences  

Han, Sang-Hyun (Educational Science Research Institute, Jeju National University)
Lee, Young-Don (Marine Science Institute, Jeju National University)
Baek, Hae-Ja (Department of Marine Biology, Pukyong National University)
Oh, Hong-Shik (Educational Science Research Institute, Jeju National University)
Noh, Choong Hwan (East Sea Research Institute, Korea Institute of Ocean Science and Technology)
Publication Information
Journal of Life Science / v.24, no.6, 2014 , pp. 626-632 More about this Journal
Abstract
The genetic structure and phylogenetic relationship were investigated in Korean red spotted grouper populations using the nucleotide sequence polymorphisms of the mitochondrial DNA (mtDNA) cytochrome c oxidase subunit I (COI) gene. The COI gene was sequenced showed 99.1-99.8% identity with the EF607565 sequence previously reported. A total of twenty haplotypes were found, and the Korean population showed nineteen haplotypes. Among those, Hap_03 and Hap_08 showed Jeju-do and China-specific COI sequences, respectively. However, Hap_07 had twelve COI sequences from South Korea and records from Hong Kong and Taiwan. Neighbor-joining (NJ) trees constructed from the phylogenetic analyses based on the polymorphisms of the COI haplotypes showed a monophyletic branching pattern within the genus Epinephelus. This indicated that the red spotted grouper populations had evolved from common maternal ancestors. In addition, the Hap_08, which had the COI sequence recorded only from China Sea, was found in the middle of the NJ tree nearby Hap_07 and showed a close relationship with Hap_07. This indicates that Chinese red spotted grouper is also maternally related to other populations in East Asia. Consequently, East Asian red spotted grouper populations are maternally related, as well as sharing the same evolutionary history, and are still affected by the East Asian ocean current (Kuroshio). These findings help to explain the genetic structure and phylogenetic relationship of red spotted grouper and also contribute to research on artificial breeding and industrialization.
Keywords
Cytochrome c oxidase subunit I (COI); haplotype; phylogenetic relationship; polymorphism; red spotted grouper;
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1 Park, Y. C. Jung, Y. H., Kim, M. R., Shin, J. H., Kim, K. H., Lee, J. H., Cho, T. Y., Lee, H. J. and Han, S. B. 2013. Development of detection method for Niphon spinosus, Epinephelus bruneus, and Epinephelus septemfasciatus using 16S rRNA gene. Korean J Food Sci Technol 45, 1-7.   과학기술학회마을   DOI   ScienceOn
2 Masuda, H., Amaoka, K., Araga, C., Ueno, T. and Yoshno, T. 1984. The Fishes of the Japanese Archipelago, p. 437, Tokia University Press, Tokyo, Japan.
3 Oh, B. S., Oh, D. J., Jung, M. M. and Jung, Y. H. 2012. Complete mitochondrial genome of the longtooth grouper Epinephelus bruneus (Perciformes, Serranidae). Mitochondrial DNA 23, 137-138.   DOI   ScienceOn
4 Qu, M., Zhang, X. and Ding, S. X. 2012. Complete mitochondrial genome of yellow grouper Epinephelus awoara (Perciformes, Epinephelidae). Mitochondrial DNA 23, 432-434.   DOI   ScienceOn
5 Ribeiro, A. O., Caires, R. A., Mariguela, T. C., Pereira, L. H., Hanner, R. and Oliveira, C. 2012. DNA barcodes identify marine fishes of São Paulo State, Brazil. Mol Ecol Resour 12, 1012-1020.   DOI   ScienceOn
6 Sambrook, J., Fritsch, E. F. and Manniatis, T. 1989. Molecular cloning: a laboratory mannual, 2nd ed., Cold Spring Harbor Laboratory; New York, USA.
7 Steinke, D., Zemlak, T. S. and Hebert, P. D. 2009. Barcoding nemo: DNA-based identifications for the ornamental fish trade. PLoS One 4, e6300.   DOI   ScienceOn
8 Ward, R. D., Hanner, R. and Hebert, P. D. N. 2009. The campaign to DNA barcode all fishes, FISH-BOL. J Fish Biol 74, 329-356.   DOI   ScienceOn
9 Zhuang, X., Ding, S., Wang, J., Wang, Y. and Su, Y. 2009. A set of 16 consensus primer pairs amplifying the complete mitochondrial genomes of orange-spotted grouper (Epinephelus coioides) and Hong Kong grouper (Epinephelus akaara). Mol Ecol Resour 9, 1551-1553.   DOI   ScienceOn
10 Li, G. L., Liu, X. C. and Lin, H. R. 2007. Seasonal changes of serum sex steroids concentration and aromatase activity of gonad and brain in red-spotted grouper (Epinephelus akaara). Anim Reprod Sci 99, 156-166.   DOI   ScienceOn
11 Lee, C. K., Hur, S. B., Ko, T. S. and Park, S. 1998. Maturation, sex ratio and sex-reversal of red spotted grouper, Epinephelus akaara. J Aquacult 11, 573-580
12 Lee, T. W. and Lee, C. K. 1996. Age and growth of Epinephelus akaara in the south western sea of Korea. Korean J Ichthyol 8, 16-22.   과학기술학회마을
13 Li, G. L., Liu, X. C. and Lin, H. R. 2006. Effects of aromatizable and nonaromatizable androgens on the sex inversion of red-spotted grouper (Epinephelus akaara). Fish Physiol Biochem 32, 25-33.   DOI   ScienceOn
14 Li, S. W., Long, Z. F., Du, J., Liu, S. G. and Wen, J. J. 2009. Analysis of differential expression and characterization of PIN in the gonads during sex reversal in the red-spotted grouper. Mol Cell Endocrinol 309, 32-38.   DOI   ScienceOn
15 Liu, S. Q., Mayden, R. L., Zhang, J. B., Yu, D., Tang, Q. Y., Deng, X. and Liu H. Z. 2012. Phylogenetic relationships of the Cobitoidea (Teleostei: Cypriniformes) inferred from mitochondrial and nuclear genes with analyses of gene evolution. Gene 508, 60-72.   DOI   ScienceOn
16 Mai, W., Liu, P., Chen, H. and Zhou, Y. 2013. Cloning and immune characterization of the c-type lysozyme gene in red-spotted grouper, Epinephelus akaara. Fish Shellfish Immunol 36, 305-314.
17 Ivanova, N. V., Zemlak, T. S., Hanner, R. and Hebert, P. D. N. 2007. Universal primer cocktails for fish DNA barcoding. Mol Ecol Notes 7, 544-548.   DOI   ScienceOn
18 Mao, M. G., Lei, J. L., Alex, P. M., Hong, W. S. and Wang, K. J. 2012. Characterization of RAG1 and IgM (mu chain) marking development of the immune system in red-spotted grouper (Epinephelus akaara). Fish Shellfish Immunol 33, 725-735.   DOI   ScienceOn
19 Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparable studies of nucleotide sequences. J Mol Evol 16, 111-120.   DOI   ScienceOn
20 Hwang, S., Lee, Y. D., Song, C. B. and Rho, S. 1998. Gonadal development and the effects of 17${\alpha}$-methyltestosterone on sex inversion of the red spotted grouper, Epinephelus akaara. J Aquacult 11, 173-182.
21 Kang, G. Y. and Song, C. B. 2004. Phylogenetic relationships among groupers (genus Epinephelus) based on mitochondrial cytochrome b DNA sequences. J Korean Fish Soc 37, 414-422.   과학기술학회마을   DOI   ScienceOn
22 Kumar, G., Kunal, S. P. and Shyama, S. K. 2013. Evolutionary history and phylogenetic relationship between Auxis thazard and Auxis rochei inferred from COI sequences of mtDNA. Int J Bioinform Res Appl 9, 604-613.   DOI   ScienceOn
23 Lai, T., He, B., Peng, Z., Wang, X. and Pan, L. 2013. Complete mitochondrial genome of the striped grouper Epinephelus latifasciatus (Serranidae, Epinephelinae). Mitochondrial DNA 24, 510-512.   DOI   ScienceOn
24 Dong, Q. F., Liu, C. W., Guo, Y. S., Liu, L. and Wu, Y. 2007. Microsatellite analysis of genetic diversity and phylogenetic relationship of nine species of grouper in genus Epinephelus. Yi Chuan 29, 837-843.   DOI   ScienceOn
25 Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J. and Higgins, D. G. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948.   DOI   ScienceOn
26 Lee, C. B. and Hur, S. B. 1997. Yolk resorption, onset of feeding and survival potential of larvae of red spotted grouper, Epinephelus akaara. J Aquacult 10, 473-483.
27 Lee, C. B. and Hur, S. B. 1998. Effect of live food and water temperature on larval survival of red spotted grouper, Epinephelus akaara. J Aquacult 11, 565-572.
28 Collins, R. A., Armstrong, K. F., Meier, R., Yi, Y., Brown, S. D., Cruickshank, R. H., Keeling, S. and Johnston, C. 2012. Barcoding and border biosecurity: identifying cyprinid fishes in the aquarium trade. PLoS One 7, e28381.   DOI
29 Ding, S., Zhuang, X., Guo, F., Wang, J., Su, Y., Zhang, Q. and Li, Q. 2006. Molecular phylogenetic relationships of China Seas groupers based on cytochrome b gene fragment sequences. Sci China C Life Sci 49, 235-242.   DOI   ScienceOn
30 Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) ver. 3.572, Computer program distributed by the author, Dept. of Genetics, University of Washington, Seattle, USA
31 Han, J., Lv, F. and Cai, H. 2011. Detection of species-specific long VNTRs in mitochondrial control region and their application to identifying sympatric Hong Kong grouper (Epinephelus akaara) and yellow grouper (Epinephelus awoara). Mol Ecol Resour 11, 215-218.   DOI   ScienceOn
32 Antoro, S., Na-Nakorn, U. and Koedprang, W. 2006. Study of genetic diversity of orange-spotted grouper, Epinephelus coioides, from Thailand and Indonesia using microsatellite markers. Mar Biotechnol 8, 17-26.   DOI
33 He, B., Lai, T., Peng, Z., Wang, X. and Pan, L. 2013. Complete mitogenome of the Areolate grouper Epinephelus areolatus (Serranidae, Epinephelinae). Mitochondrial DNA 24, 498-500.   DOI   ScienceOn
34 Hebert, P. D., Cywinska, A., Ball, S. L. and deWaard J. R. 2003. Biological identifications through DNA barcodes. Proc Biol Sci 270, 313-321.   DOI   ScienceOn
35 Heemstra, P. C. and Randall, J. E. 1993. Groupers of the World. FAO Species Catalogue, pp. 106-107, Rome, Italy.
36 Chakraborty, M. and Ghosh, S. K. 2014. An assessment of the DNA barcodes of Indian freshwater fishes. Gene 537, 20-28.   DOI   ScienceOn
37 Di Pinto, A., Di Pinto, P., Terio, V., Bozzo, G., Bonerba, E., Ceci, E. and Tantillo, G. 2013. DNA barcoding for detecting market substitution in salted cod fillets and battered cod chunks. Food Chem 141, 1757-1762.   DOI   ScienceOn
38 Mat Jaafar, T. N., Taylor, M. I., Mohd Nor, S. A., de Bruyn, M., Carvalho, G. R. 2012. DNA barcoding reveals cryptic diversity within commercially exploited Indo-Malay Carangidae (Teleosteii: Perciformes). PLoS One 7, e49623.   DOI
39 Li, J. L., Liu, M. and Wang, Y. Y. 2013. Complete mitochondrial genome of the rock grouper Epinephelus fasciatomaculosus (Pisces: Perciformes). Mitochondrial DNA 24, 625-626.   DOI   ScienceOn