Skip to main content
Log in

Characterization of the complete mitochondrial genome of the hybrid Epinephelus moara♀ × Epinephelus lanceolatus♂, and phylogenetic analysis in subfamily epinephelinae

  • Published:
Journal of Ocean University of China Aims and scope Submit manuscript

Abstract

This study presents the complete mitochondrial genome of the hybrid Epinephelus moara♀× Epinephelus lanceolatus♂. The genome is 16886 bp in length, and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, a light-strand replication origin and a control region. Additionally, phylogenetic analysis based on the nucleotide sequences of 13 conserved protein-coding genes using the maximum likelihood method indicated that the mitochondrial genome is maternally inherited. This study presents genomic data for studying phylogenetic relationships and breeding of hybrid Epinephelinae.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Boore, J. L., 1999. Animal mitochondrial genomes. Nucleic Acids Research, 27 (8): 1767–1780.

    Article  Google Scholar 

  • Boore, J. L., Macey, J. R., and Medina, M., 2005. Sequencing and comparing whole mitochondrial genomes of animals. Methods in Enzymology, 395: 311–348.

    Article  Google Scholar 

  • Craig, M. T., Pondella, D. J., Franck, J. C., and Hafner, J. C., 2001. On the status of the serranid fish genus Epinephelus: Evidence for paraphyly based upon 16S rDNA sequence. Molecular Phylogenetics and Evolution, 19 (1): 121–130.

    Article  Google Scholar 

  • 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. Science in China Series C, 49 (3): 235–242.

    Article  Google Scholar 

  • Du, F. Y., Ye, L., and Wang, X. H., 2015. Complete mitochondrial genome of the sixbar grouper Epinephelus sexfasciatus (Perciformes: Epinephelidae). Mitochondrial DNA, 26 (3): 461–462.

    Article  Google Scholar 

  • Feliner, G. N., and Aguilar, J. F., 1998. Hybrids and hybrid zones. Trends in Ecology & Evolution, 13 (7): 282.

    Article  Google Scholar 

  • Glamuzina, B., Glavic, N., Skaramuca, B., Skaramuca, B., Kozul, V., and Tutman, P., 2001. Early development of the hybrid Epinephelus costae♂× E.marginatus♀. Aquaculture, 198 (1): 55–61.

    Article  Google Scholar 

  • Hamers, L., 2016. Why do cells’ power plants hang on to their own genomes? Science, 351 (6276): 903–903.

    Article  Google Scholar 

  • 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 (5): 498–500.

    Article  Google Scholar 

  • Heemstra, P. C., and Randall, J. E., 1993. Groupers of the world (family Serranidae, subfamily Epinephelinae): An annotated and illustrated catalogue of the grouper, rockcod, hind, coral grouper, and lyretail species known to date. Food and Agriculture Organization of the United Nations, 16 (125): 1–10.

    Google Scholar 

  • Hsiao, S. T., and Chen, K. S., 2015. Complete mitochondrial genome of the Palemargin grouper Epinephelus bontoides (Pisces: Perciformes). Mitochondrial DNA, DOI: 10.3109/19401736.2015.1115498.

  • Hsiao, S. T., Chen, K. S., Tseng, C. T., and Wu, C. L., 2016. Complete mitochondrial genome of the six blotch hind Cephalopholis sexmaculata (Pisces: Perciformes). Mitochondrial DNA, 27 (2): 1018–1019.

    Article  Google Scholar 

  • James, C. M., Al-Thobaiti, S. A., Rasem, B. M., and Carlos, M. H., 1999. Potential of grouper hybrid (Epinephelus fuscoguttatus ×E. polyphekadion) for Aquaculture. Naga, the ICLARM Quarterly, 22 (1): 19–23.

    Google Scholar 

  • 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 (5): 510–512.

    Article  Google Scholar 

  • Lanfear, R., Calcott, B., Ho, S. Y. W., and Guindon, S., 2012. Partitionfinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution, 29 (6): 1695–1701.

    Article  Google Scholar 

  • Li, J. L., Liu, M., and Wang, Y. Y., 2014. Complete mitochondrial genome of the chocolate hind Cephalopholis boenak (Pisces: Perciformes). Mitochondrial DNA, 25 (3): 167–168.

    Article  Google Scholar 

  • Li, J. L., Liu, M., and Wang, Y. Y., 2013. Complete mitochondrial genome of the rock grouper Epinephelus fasciatomaculosus (Pisces: Perciformes). Mitochondrial DNA, 24 (6): 625–626.

    Article  Google Scholar 

  • Li, Z. F., Fu, Q. Q., and Zhang, Y. S., 2008. An analysis of the nutritive composition and the contents of amino acids in muscle of Epinephelus lanceol. South China Fish Science, 4 (5): 61–64 (in Chinese with English abstract).

    Google Scholar 

  • Liu, M., Li, J. L., Ding, S. X., and Liu, Z. Q., 2013. Epinephelus moara: A valid species of the family Epinephelidae (Pisces: Perciformes). Journal of Fish Biology, 82 (5): 1684–1699.

    Article  Google Scholar 

  • Liu, X. C., Lin, H. R., and Huang, G. G., 2007. Preliminary study on the hybrid red-spotted grouper (Epinephelus akaara) ♂× orange-spotted grouper (Epinephelus coioides)♀. Acta Scientiarum Naturalium Universitatis Sunyatseni, 46 (3): 72–75.

    Google Scholar 

  • Lowe, T. M., and Eddy, S. R., 1997. TRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research, 25: 955–964.

    Article  Google Scholar 

  • McKnight, M. L., and Shafer, H. B., 1997. Large rapidly evolving intergenic spacers in the mitochondrial DNA of the salamander family Ambystomatidae (Amphibia: Caudata). Journal of Molecular Biology and Evolution, 14: 1167–1176.

    Article  Google Scholar 

  • Miya, M., Friedman, M., Satoh, T. P., Takeshima, H., Sado, T., Iwasaki, W., Yamanoue, Y., Nakatani, M., Mabuchi, K., Inoue, J. G., Inoue, J. Y., Poulsen, T. F., Yukuto, S., and Mutsumi, N., 2013. Evolutionary origin of the Scombridae (tunas and mackerels): Members of a paleogene adaptive radiation with 14 other pelagic fish families. PLoS One, 8 (9): E73535.

    Article  Google Scholar 

  • Moritz, C., and Brown, W. M., 1987. Tandem duplications in animal mitochondrial DNA: Variations in incidence and gene content among lizards. The Proceedings of the National Academy of Sciences of the United States of America, 84: 7183–7187.

    Article  Google Scholar 

  • Ojala, D., Montoya, J., and Attardi, G., 1981. tRNA punctuation model of RNA processing in human mitochondria. Nature, 290: 470–474.

    Article  Google Scholar 

  • Okada, T., Yoneshima, H., Mukai, Y., and Sawada, Y., 1996. Tolerance limits of young kelp grouper Epinephelus moara for environmental stresses. Bulletin of the Fisheries Laboratory of Kinki University, 5: 139–146.

    Google Scholar 

  • Peng, Z., Chen, J., Lai, T., Huang, Y., and Wu, L., 2014b. Complete mitochondrial genome of the longfin grouper Epinephelus quoyanus (Serranidae: Epinephelinae). Mitochondrial DNA, 25 (3): 175–176.

    Article  Google Scholar 

  • Peng, Z., Huang, Y., Chen, J., Lai, T., and Wu, L., 2014a. Complete mitochondrial genome of dotted grouper Epinephelus epistictus (Serranidae: Epinephelinae). Mitochondrial DNA, 25 (3): 190–191.

    Article  Google Scholar 

  • Qin, J., Hu, D., Yang, W., and Xiao, J., 2014. Complete mitochondrial genome of the humpback grouper Cromileptes altivelis. Mitochondrial DNA, 25 (3): 200–201.

    Article  Google Scholar 

  • Qu, M., Zhang, X., and Ding, S. X., 2012. Complete mitochondrial genome of yellow grouper Epinephelus awoara (Perciformes, Epinephelidae). Mitochondrial DNA, 23 (6): 432–434.

    Article  Google Scholar 

  • Rand, D. M., 1993. Endotherms, ectotherms, and mitochondrial genome size variation. Journal of Molecular Evolution, 37: 28l–295.

    Article  Google Scholar 

  • Sbisà, E., Tanzariello, F., Reyes, A., Pesole, G., and Saccone, C., 1997. Mammalian mitochon-drial D-loop region structural analysis: Identification of new conserved sequences and their functional and evolutionary implications. Gene, 205 (1–2): 125–140.

    Article  Google Scholar 

  • Shen, M., Shi, X., Qu, M., and Chen, J., 2013. Complete mitochondrial genome of squaretail coral grouper Plectropomus aeolatus (Perciformes, Epinephelidae). Mitochondrial DNA, 24 (4): 365–367.

    Article  Google Scholar 

  • Stamatakis, A., 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analysis with thousands of taxa and mixed models. Bioinformatics, 22 (21): 2688–2690.

    Article  Google Scholar 

  • Sun, Y., Guo, C. Y., Wang, D. D., Li, X. F., Xiao, L., Zhang, X., You, X., Shi, Q., Hu, G. J., Fang, C., Lin, H. R., and Zhang, Y., 2016a. Transcriptome analysis reveals the molecular mechanisms underlying growth superiority in a novel grouper hybrid (Epinephelus fuscogutatus♂× E. lanceolatus♀). BMC Genetics, 17 (1): 24.

    Article  Google Scholar 

  • Sun, Y., Wei, T., Su, X., and Li, T., 2016b. The complete mitochondrial genome of Grammistes sexlineatus (Perciformes, Serranidae). Mitochondrial DNA, 27 (2): 821–823.

    Article  Google Scholar 

  • Tamura, K., Stecher, G., Peterson, D., Filipski, A., and Kumar, S., 2013. MEGA6: Molecular evolutionary genetics analysis version 6.0. Journal of Molecular Biology and Evolution, 30: 2725–2729.

    Article  Google Scholar 

  • Tseng, W. Y., and Poon, C. T., 1983. Hybridization of Epinephelus species. Aquaculture, 34 (1): 177–182.

    Article  Google Scholar 

  • Urbanelli, S., Porretta, D., Mastrantonio, V., Bellini, R., Pieraccini, G., Romoli, R., Crasta, G., and Nascetti, G., 2014. Hybridization, natural selection, and evolution of reproductive isolation: A 25-years survey of an artificial sympatric area between two mosquito sibling species of the Aedes mariae complex. Evolution, 68 (10): 3030–3038.

    Article  Google Scholar 

  • Wang, H., Guo, L., and Ding, S. X., 2015b. The complete mitochondrial genome of Diploprion bifasciatum (Perciformes, Serranidae). Mitochondrial DNA, DOI: 10.3109/19401736. 2015.1007301.

  • Wang, Q., Chen, H., Xu, W., He, J., Xie, Z., Tang, L., Tang, Z., Li, Y., Li, S., Zhang, Y., and Lin, H., 2015a. The complete mitochondrial genome of the hybrid grouper Epinephelus coioides♂× Epinephelus fuscoguttatus♀. Mitochondrial DNA, DOI: 10.3109/19401736.2014.1003902.

  • Wan, Q., Qiao, H. Y., Cheng, Q. Q., and Chen, Y., 2014. Complete mitochondrial genome of Pelteobagrus fulvidraco (Siluriformes: Bagridae): Genome description and related phylogenetic analyses. Mitochondrial DNA, 25 (1): 39–41.

    Article  Google Scholar 

  • Wang, X., Wang, Q., Xie, Z., He, J., Wang, D., Chen, H., Li, S., Zhang, Y., and Lin, H., 2014. The complete mitochondrial genome of the Epinephelus lanceolatus (Perciformes: Serranidae). Mitochondrial DNA, DOI: 10.3109/19401736. 2014.961147.

  • Wolstenholme, D. R., 1992. Animal mitochondrial DNA: Structure and evolution. International Review of Cytology, 141: 173–216.

    Article  Google Scholar 

  • Yang, Y., Xie, Z., Peng, C., Wang, J., Li, S., Zhang, Y., Zhang, H., and Lin, H., 2014. The complete mitochondrial genome of the Epinephelus tukula (Perciformes, Serranidae). Mitochondrial DNA, DOI: 10.3109/19401736.2014.905837.

  • Ye, L., Du, F. Y., Wang, X. H., and Wang, Y., 2014a. Complete mitochondrial genome of the black-dotted grouper Epinephelus stictus. Mitochondrial DNA, 25 (2): 87–88.

    Article  Google Scholar 

  • Ye, L., Wang, X. H., and Du, F. Y., 2014b. Complete mitochondrial genome of the three spot grouper Epinephelus trimaculatus. Mitochondrial DNA, 25 (4): 293–294.

    Article  Google Scholar 

  • Zheng, L., Xie, J., Xie, Z., Xiao, L., Wang, Q., Huang, M., Chen, H., Li, S., Huang, Z., Zhang, Y., and Lin, H., 2014. The complete mitochondrial genome of the Epinephelus corallicola (Perciformes: Serranidae). Mitochondrial DNA, DOI: 10.3109/19401736.2014.989509.

  • Zhu, K., and Yu, D., 2014a. The complete mitochondrial genome of the hybrid of Epinephelus fuscoguttatus♂× Epinephelus fuscoguttatus♀. Mitochondrial DNA, DOI: 10.3109/19401736.2014.971310.

  • Zhu, K., and Yu, D., 2014b. The complete nucleotide sequence of Malabar grouper (Epinephelus malabaricus) mitochondrial genome. Mitochondrial DNA, DOI: 10.3109/19401736.2014. 982569.

  • Zhu, Z. Y., Lo, L. C., and Yue, G. H., 2008. The complete mitochondrial genome of red grouper Plectropomus leopardus and its applications in identification of grouper species. Aquaculture, 276 (1–4): 44–49.

    Article  Google Scholar 

  • 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). Molecular Ecology Resources, 9 (6): 1551–1553.

    Article  Google Scholar 

  • Zhuang, X., Qu, M., Zhang, X., and Ding, S., 2013. A comprehensive description and evolutionary analysis of 22 grouper (Perciformes, Epinephelidae) mitochondrial genomes with emphasis on two novel genome organizations. PLoS One, 8 (8): e73561.

    Article  Google Scholar 

  • Zuker, M., 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research, 31 (13): 3406–3415.

    Article  Google Scholar 

Download references

Acknowledgements

We appreciate Peng Yu (College of Animal Science and Technology, Anhui Agricultural University, Heifei) for his kind support. This research was supported by grants from Dahuanong Aquatic Company, Guangdong, and Taishan Scholar Project, Shandong, China.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Songlin Chen or Guanpin Yang.

Additional information

These authors contribute to this work equally.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Gao, F., Wei, M., Zhu, Y. et al. Characterization of the complete mitochondrial genome of the hybrid Epinephelus moara♀ × Epinephelus lanceolatus♂, and phylogenetic analysis in subfamily epinephelinae. J. Ocean Univ. China 16, 555–563 (2017). https://doi.org/10.1007/s11802-017-3202-2

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11802-017-3202-2

Key words

Navigation