Abstract—
Acanthogobius ommaturus, which belongs to the family Gobiidae, is a euryhaline, demersal fish widely distributed in coastal areas, harbors, and estuaries of China, the Korean Peninsula, and Japan. A genetic analysis based on identification of the structure of mitochondrial DNA control region was carried out in the present study. As a result, the conservative structure, including termination sequence region, central conservative region CSB-E and CSB-D, as well as conservative sequence region CSB-1, CSB-2, and CSB-3, was determined. A total of 32 polymorphic sites were identified and 33 haplotypes were defined, of which only 9 were shared haplotypes. A high level of haplotype diversity (h = 0.923 ± 0.018) and low nucleotide diversity (π = 0.003 ± 0.002) were detected. In general, the genetic differentiation among ten populations was at a medium level. There was a distinct single peak in the nucleotide mismatch distribution, which confirms that A. ommaturus populations have experienced recent expansion. In this study, the control region structure of A. ommaturus was similar to that of most marine fishes; however, the tandem repeat sequence and the CSB-F sequence were not detected. In addition, most of the genetic variation in the control region occurred in the high-variation region.
Similar content being viewed by others
REFERENCES
Beheregaray, L.B. and Sunnucks, P., Fine-scale genetic structure, estuarine colonization and incipient speciation in the marine silverside fish Odontesthes argentinensis,Mol. Ecol., 2001, vol. 10, no. 12, pp. 2849–2866.
Buonnacorsi, V.P., McDowell, J.R., and Graves, J.E., Reconciling patterns of inter-ocean molecular variance from four classes of molecular markers in blue marlin (Makaira nigricans), Mol. Ecol., 2001, vol. 10, pp. 1179–1196.
Cai, S.S., Xu, S.Y., Song, N., Gao, T.X., and Zhang, Z.H., Mitochondrial DNA control region structure and length polymorphism analysis of Setipinna tenuifilis,Acta Hydrobiol. Sin., 2014, vol. 38, pp. 980–986.
Cao, Y., Genetic Diversity of 3 Sparid Species in Coastal Waters of China Based on mtDNA Control Region Sequence, Guangzhou, China: Jinnan Univ., 2016, pp. 22–60 (in Chinese).
Cui, Z., Liu, Y., Li, C.P., You, F., and Chu, K.H., The complete mitochondrial genome of the large yellow croaker, Larimichthys crocea (Perciformes, Sciaenidae): Unusual features of its control region and the phylogenetic position of the Sciaenidae, Gene, 2009, vol. 432, nos. 1–2, pp. 33–43.
Deng, X.Y., Yu, C.G., Shui, Y.Y., Weng, L.C., Ding, J.W., Zhang, P., Xu, L.J., Zheng, J., Xie, X., and Miao, L., Spatial and temporal variation in fish species composition and abundance in Zhoushan coastal waters during spring and autumn, Ecol. Sci., 2018, vol. 37, no. 1, pp. 10–19.
Domingues, V.S., Faria, C., Stefanni, S., Santos, R.S., Brito, A., and Almada, V.C., Genetic divergence in the Atlantic-Mediterranean Montagu’s blenny, Coryphoblennius galerita (Linnaeus 1758) revealed by molecular and morphological characters, Mol. Ecol., 2007, vol. 16, no. 17, pp. 3592–3605.
Dong, X.P., Mu, S.M., Zhou, N., Kang, X.J., Luo, Q., and Bai, J.J., Structure analysis of mtDNA D-loop region and the genetic diversity of Channa argu in different populations, J. Fish. China, 2014, vol. 38, no. 9, pp. 1277–1285.
Engelbrecht, C.C., Freyhof, J., Nolte, A., Rassmann, K., Schliewen, U., and Tautz, D., Phylogeography of the bullhead Cottus gobio (Pisces: Teleostei: Cottidae) suggests a pre-Pleistocene origin of the major central European populations, Mol. Ecol., 2000, vol. 9, no. 6, pp. 709–722.
Excoffier, L. and Lischer, H.E.L., Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows, Mol. Ecol. Resour., 2010, vol. 10, no. 3, pp. 564–567.
Fan, H.Y., Ji, Y.P., Zhang, S.H., Yuan, C.T., and Gao, T.X., Research of fishery biology of the neritic fish Synechogobius ommaturus in the area of the Huanghe Delta, J. Ocean Univ. Qingdao, 2005, vol. 35, pp. 733–736.
Feng, J., Zu, J.Q., Zheng, Z.M., and Chen, Y.C., Study on the individual fecundity of Synechogobius hasta,J. Zhejiang Ocean Univ., 2004, vol. 23, no. 4, pp. 302–314.
Fu, Y.Y., Gu, W.W., Liu, Y.Z., Peng, J.Y., and Chang, H., Genetic analysis of the polymorphism of mtDNA D‑loop and microsatellite loci in Tibet mini-pigs, Acta Lab. Anim. Sci. Sin., 2006, vol. 14, pp. 318–321.
Grant, W.A.S. and Bowen, B.W., Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation, J. Hered., 1998, vol. 89, no. 5, pp. 415–426.
Guo, X.H., Liu, S.J., Liu, Q., and Liu, Y., New progresses on mitochondrial DNA in fish, Acta Genet. Sin., 2004, vol. 31, pp. 983–1000.
Han, Z.Q., Zhuang, Z.M., Gao, T.X., Liu, J.X., Li, Y.H., and Wang, Z.Y., Genetic diversity in Cynoglossus semilaevis by AFLP, RAPD and mtDNA markers, J. Fish. China, 2007, vol. 14, no. 2, pp. 192–200.
He, C.B., Cao, J., Liu, W.D., Zhou, Z.C., Ge, L.L., Gao, X.G., and Wang, X.M., Structure analysis of mtDNA control region of spotted halibut (Verasper variegates) and its related species, Hereditas (Beijing, China), 2007, vol. 29, no. 7, pp. 829–836.
Hewitt, G., The genetic legacy of the Quaternary ice ages, Nature, 2000, vol. 405, pp. 907–913.
Hochachka, P.W. and Mommsen, T., Environmental and ecological biochemistry, Science, 1993, pp. 1–38.
Hwang, J.S. and Wong, C.K., The China Coastal Current as a driving force for transporting Calanus sinicus (Copepoda: Calanoida) from its population centers to waters off Taiwan and Hong Kong during the winter northeast monsoon period, J. Plankton Res., 2005, vol. 27, pp. 205–210.
Jin, X.X., Complete mitochondrial genome and phylogenetic analysis of 16 gobies in East China Sea, Master’s Dissertation, Zhejiang Ocean Univ., 2013.
Kumar, S., Stecher, G., and Tamura, K., MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets, Mol. Biol. Evol., 2016, vol. 33, no. 7, pp. 1870–1874.
Larkin, M.A., Blackshields, G., Brown, N.P., et al., Clustal W and Clustal X version 2.0, Bioinformatics, 2007, vol. 23, no. 21, pp. 2947–2948.
Lee, W.J., Conroy, J., Howell, W.H., and Kocher, T., Structure and evolution of teleost mitochondrial control regions, J. Mol. Evol., 1995, vol. 41, no. 1, pp. 54–66.
Li, S.H., Chen, D.Q., Duan, X.F., Liu, S.P., and Wang, D.Q., Genetic effects of released mature Ctenopharyngodon idellus on natural populations based on the mitochondrial DNA markers in the middle reaches of the Yangtze River, Freshwater Fish., 2014, vol. 44, no. 3, pp. 45–50. https://doi.org/10.13721/j.cnki.dsyy.2014.03.008
Li, Y.L., Liu, X.Z., Dong, J., Yu, X.G., Li, Y.P., Guo, D., and Fu, J., Genetic diversity analysis of silver pomfret (Pampus echinogaster) inhabiting Liaodong Bay based on COI gene sequence, Trans. Oceanol. Limnol., 2015, no. 2, pp. 29–35. https://doi.org/10.13984/j.cnki.cn37-1141.2015.02.005
Liu, H.Z., The structure and evolution of mitochondrial DNA control region of fish: focus on Acheilognathinae fish, Prog. Nat. Sci., 2002, vol. 12, no. 3, pp. 266–270.
Liu, J.X., Gao, T.X., Zhuang, Z.M, Jin, X.S., Yokogawa, K., and Zhang, Y.P., Late Pleistocene divergence and subsequent population expansion of two closely related fish species, Japanese anchovy (Engraulis japonicas) and Australian anchovy (Engraulis australis), Mol. Phylogenet. Evol., 2006, vol. 40, no. 3, pp. 712–723.
Liu, L.G., Yang, P.H., Wang, W.B., Wang, X.Y., Xie, C.H., and Li, M.J., Comparative analysis of the mitochondrial DNA control region in Dongtingking crucian carp and other six strains of Carassius auratus,Acta Hydrobiol. Sin., 2010, vol. 34, pp. 378–387.
Liu, S.F., Wu, R.X., Zhu, L., and Zhuang, Z.M., Complete sequence and gene organization of mitochondrial DNA of the small yellow croaker Larimichthys polyactic,Oceanol. Limnol. Sin., 2010, no. 6, pp. 885–894.
Meng, Z.N., The genetic diversity in Pseudosciaena polyactis, Trichiurus lepturus, Eupleurogrammus muticus and the molecular phylogeny of eight Sciaenoid species in the neritic waters of China, Doctoral Dissertation, Xiamen Univ., 2003.
Ni, H.E. and Lu, J.H., Dynamic analysis on fisheries resources in Zhoushan Fishing Ground, J. Fish. China, 2002, vol. 26, pp. 428–432.
Ovenden, J.R., Salini, J., O’Connor, S., and Street, R., Pronounced genetic population structure in a potentially vagile fish species (Pristipomoides multidens, Teleostei; Perciformes; Lutjanidae) from the East Indies triangle, Mol. Ecol., 2004, vol. 13, no. 7, pp. 1991–1999.
Pan, J.F., Shi, Z.G., Cheng, S.R., Wang, C., and Zhao, C.G., The study of genetic diversity and phylogenetic evolution in indigenous horses (Equus caballus) of Gansu, J. Agric. Biotechnol., 2014, vol. 22, pp. 210–218.
Petri, B., von Haeseler, A., and Pääbo, S., Extreme sequence heteroplasmy in bat mitochondrial DNA, Biol. Chem., 1996, vol. 377, pp. 661–667.
Qin, Q., Xu, Z.Q., Bian, W.J., Wang, M.H., Cai, Y.X., and Ge, J.C., Structure of mitochondrial DNA control region and population genetic diversity analysis of channel catfish (Ictalurus punctatus), Freshwater Fish., 2011, vol. 41, no. 4, pp. 50–54. https://doi.org/10.1111/j.1749-4877.2010.00232.x
Rocha, L.A., Robertson, D.R., Roman, J., and Bowen, B.W., Ecological speciation in tropical reef fishes, Proc. R. Soc. London, Ser. B, 2005, vol. 272, pp. 573–579.
Saccone, C., Pesole, G., and Sbisá, E., The main regulatory region of mammalian mitochondrial DNA: Structure-function model and evolutionary pattern, J. Mol., Evol., 1991, vol. 33, pp. 83–91.
Sambrook, J., Fritsch, E.F., and Maniatis, T., Molecular Cloning: A Laboratory Manual, 2nd ed., New York: Cold Spring Harbor Lab., 1989.
Sha, X.F., Peng, F., Tao, S., Wu, Y., Liu, J.M., Zhang, C., and Li, Q., Development and diversity analysis of mitochondrial and chloroplast microsatellite markers in Salvia miltiorrhiza, Acta Bot. Boreali-Occident.Sin., 2018, vol. 38, pp. 2215–223.
Shi, L.Y., Qi, J.W., Gao, D.D., and Han, J., Species-specific mitochondrial DNA marker, length polymorphism and heteroplasmy in the clam Macridiscus,J. Beijing Norm. Univ., 2018, vol. 54, pp. 203–207.
Song, N., Zhang, X.M., Sun, X.F., Yanagimoto, T., and Gao, T.X., Population genetic structure and larval dispersal potential of spottedtail goby Synechogobius ommaturus in the north-west Pacific, J. Fish Biol., 2010, vol. 77, pp. 388–402.
Song, N., Zhang, X.M., and Gao, T.X., Genetic diversity and population structure of spottedtail goby (Synechogobius ommaturus) based on AFLP analysis, Biochem. Syst. Ecol., 2010, vol. 38, pp. 1089–1095.
Song, N., Song, L., Gao, T.X., and Sun, X.F., Comparative analysis of genetic diversity of Synechogobius ommaturus based on the mitochondrial DNA control region, J. Fish. China, 2011, vol. 35, pp. 321–326.
Su, Y., Conserved and heteroplasmy on mitochondrial DNA control region in animal, Sichuan J. Zool., 2005, vol. 24, pp. 669–671.
Sun, G.Y. and Chen, J.G., Study on the biology of Synechogobius ommaturus,J. Fish. China, 1993, vol. 17, pp. 146–153.
Xie, J.Y., Structure analysis of mtDNA control region in Schizothorax prenanti,Chin. J. Zool., 2011, vol. 46, pp. 97–101.
Walberg, M.W. and Clayton, D.A., Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA, Nucleic Acids Res., 1981, vol. 9, no. 20, pp. 5411–5421.
Wang, D.Y., Length and sequence variation in mitochondrial DNA control region and genetic structure of Bostrichthy sinensis, Master’s Dissertation, Xiamen Univ., 2008.
Wu, H.L., Cheng, Q.T., and Zheng, B.X., Systematic Synopsis of Chinese Fishes, Beijing: Science Press, 1987, pp. 429–436.
Xiao, Z.Y., Xiao, Y.S., Ren, G.J., Gao, T.X., Tu, D.Z., and Han, Z.Q., Comparative analysis on the genetic variation of cultured and wild rock bream Oplegnathus fasciatus population based on mtDNA control region, Oceanol. Limnol. Sin., 2013, vol. 44, no. 1, pp. 249–254.
Yang, Z.T. and Liu, L., Application of mitochondrial molecular marker technology in aquaculture, Guangdong Agric. Sci., 2014, vol. 41, pp. 135–145.
Yin, Y.J., Du, W.L., Wang, L., and Zhang, T., Genetic diversity of Lueyang black-bone chicken based on mitochondrial DNA D-loop region sequence, Anim. Husb. Vet. Med., 2017, vol. 44, no. 1, pp. 173–179.
Zeng, Q.L. and Liu, H.Z., Study on mitochondrial DNA control region of the Ictiobus cyprinellus,J. Hubei Univ., 2001, vol.23, pp. 261–264.
Zhao, S.L. and Wu, H.L., Gobiidae: Acanthogobius, in Fauna Sinica: Ostichthyes, Perciformes (V), Gobioidei, Wu, H.L. and Zhong, J.S., Eds., Beijing: Science Press, 2008, pp. 211–215.
Zhou, W., Wang, J., and Jin, B.S., Genetic variation based on the mitochondrial DNA control region of yellow catfish (Pelteobagrus fulvidraco), J. Fish. China, 2016, vol. 40, pp. 1531–1541.
Zhou, W., Gao, T.X., Wang, J., and Song, N., A comparative study on population genetic diversity of Liza haematocheilus from Dongying based on control region of mitochondrial DNA, Trans. Oceanol. Limnol., 2019, no. 3, pp. 154–166. https://doi.org/10.13984/j.cnki.cn37-1141.2019.03.018
Zhu, M.G., Yang, G., Zhao, T., Zhao, F., Peng, X.Y., Yan, G.S., and Zhuang, P., Feeding habits of Acanthogobius ommaturus in the Yangtze Estuary, J. Fish. Sci. China, 2016, vol. 23, pp. 914–923.
Zhu, S.H., Zheng, W.J., Zhou, J.X., Yang, Y.C., and Shen, X.-Q., Mitochondrial DNA control region structure and molecular phylogenetic relationship of Carangidae, Zool. Res., 2007, vol. 28, no. 6, pp. 606–614.
ACKNOWLEDGMENTS
We thank Drs. Linlin Zhao, Shengyong Xu, and Yuan Li for their assistance in sampling. This study was supported by the National Natural Science Foundation of China (project nos. 41776171 and 41506158).
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Conflict of interests. The authors declare that they have no conflict of interest.
Statement on the welfare of animals. All applicable international, national, and/or institutional guidelines for the care and use of animals were followed. Ethical approval was not required for this study because no endangered animals were involved. All handling of A. ommaturus specimens was conducted in strict accordance with the Animal Care Quality Assurance in China.
Additional information
The text was submitted by the authors in English.
Rights and permissions
About this article
Cite this article
Song, C.Y., Sun, Z.C., Gao, T.X. et al. Structure Analysis of Mitochondrial DNA Control Region Sequences and its Applications for the Study of Population Genetic Diversity of Acanthogobius ommaturus . Russ J Mar Biol 46, 292–301 (2020). https://doi.org/10.1134/S1063074020040082
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S1063074020040082