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Phylogeny and Evolution of Multiple Common Carp (Cyprinus carpio L.) Populations Clarified by Phylogenetic Analysis Based on Complete Mitochondrial Genomes

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Abstract

Common carp (Cyprinus carpio L.) is one of the oldest, most widely farmed commercially important freshwater fish in the world. However, many undetermined phylogenetic relationships and origins of common carp lineages remain, which are obstacles to conservation and genetic breeding of this species. Phylogenetic analyses based on molecular tools are helpful to distinguish the origin of species, understand and clarify their evolutionary history, and provide a genetic basis for selective breeding. In this study, we demonstrated a method to extract complete mitochondrial genome sequences from whole-genome resequencing data using the Illumina platform. The complete mitochondrial genome sequences of 26 individuals representing nine strains were obtained and subjected to a phylogenetic analysis. We reconstructed the phylogenetic topologies of the nine strains and analyzed the haplotypes. Results from both analyses suggested that the genome sequences belonged to two distinct subspecies from Europe and East Asia. We also estimated the time of divergence of the nine strains, which was up to 100 KYA. The phylogenetic results clarified the breeding history of Songpu mirror carp and suggest that this species may be hybrid of paternal European mirror carp and maternal Xingguo red carp. The results also support a previous hypothesis that koi may have originated from or have close ancestry with Oujiang color carp in China.

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Acknowledgments

We acknowledge grant support from the National High-Technology Research and Development Program of China (863 Program; 2011AA100401), the National Natural Science Foundation of China (No. 31422057), and the Special Scientific Research Funds for Central Non-profit Institutes of Chinese Academy of Fishery Sciences (2013C011).

Conflict of Interest

The authors declare no competing interests.

Author’s Contributions

PX conceived the study. CD and PX wrote the manuscript. CD, JX, and BW performed the bioinformatics analysis to obtain the complete mitochondrial genome sequences. CD conducted the phylogenetic analysis. JF and ZJ collected samples. XS supervised the genome study. All authors have read and approved the final version of the manuscript.

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Authors and Affiliations

  1. CAFS Key Laboratory of Aquatic Genomics & Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, 100141, Beijing, China

    Chuanju Dong, Jian Xu, Baosen Wang, Xiaowen Sun & Peng Xu

  2. College of Life Science and Technology, Shanghai Ocean University, Shanghai, 201306, China

    Chuanju Dong

  3. Henan Academy of Fishery Sciences, Zhengzhou, 450044, China

    Jianxin Feng

  4. National Agricultural Research and Innovation Centre (NARIC), Research Institute for Fisheries and Aquaculture (HAKI), Szarvas, 5540, Hungary

    Zsigmond Jeney

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  1. Chuanju Dong
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  2. Jian Xu
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  3. Baosen Wang
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  4. Jianxin Feng
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  5. Zsigmond Jeney
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  6. Xiaowen Sun
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  7. Peng Xu
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Correspondence to Xiaowen Sun or Peng Xu.

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Dong, C., Xu, J., Wang, B. et al. Phylogeny and Evolution of Multiple Common Carp (Cyprinus carpio L.) Populations Clarified by Phylogenetic Analysis Based on Complete Mitochondrial Genomes. Mar Biotechnol 17, 565–575 (2015). https://doi.org/10.1007/s10126-015-9639-7

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