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Next-generation sequencing reveals the mitogenomic heteroplasmy in the topmouth culter (Culter alburnus Basilewsky, 1855)

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Abstract

Background

The mitogenomic heteroplasmy is the presence of multiple haplotypes in the mitochondria, which could cause genetic diseases and is also associated with many critical biological functions. The topmouth culter (Culter alburnus Basilewsky, 1855) is one of the most important freshwater fish in the family of Cyprinidae in China. At present, there are no reports on the topmouth culter's mtDNA heteroplasmy and the existence of which is not known.

Methods and results

This study aimed to analyze the mitogenomic heteroplasmy in the topmouth culter by the next-generation sequencing of the fins' total DNA. The results confirmed the existence of the heteroplasmy and indicated the presence of the extensive heteroplasmy in the topmouth culter's mitogenome. There were 38 heteroplasmic variations in the protein-coding genes from the three specimens, with 33 non-synonymous substitutions accounting for 86.84% and five synonymous substitutions accounting for 13.16%. Among them, the ND6 had the most heteroplasmic variations but only one synonymous substitution. After removing the putative nuclear mitochondrial DNA fragments, the ratio of primary haplotype in the three specimens was 43.89%, 74.72%, and 32.76%, respectively. The three specimens contained 21, 7, and 21 haplotypes of the mitogenomes, respectively. Due to the extensive heteroplasmy, we reconstructed the phylogenetic tree of the topmouth culter using the RY-coding method, which improved the performance of the phylogenetic tree to some extent.

Conclusions

This study reported the mitogenomic heteroplasmy in the topmouth culter and enhanced the knowledge regarding the mitogenomic heteroplasmy in phylogenetic studies. As the topmouth culter is a commercial species, the mitogenomic heteroplasmy is crucial for the fisheries management of the topmouth culter.

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Data availability

The genome sequence data supporting this study's findings are openly available in GenBank of NCBI at [https://www.ncbi.nlm.nih.gov] under the accession no. MZ901178, MZ901179, MZ901180, respectively. The associated BioProject number is PRJNA773384.

Code availability

Not applicable.

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Funding

This work was supported by the Hangzhou Agricultural & Social Development Research Program under Grant 20162012A03; Science & Technology Innovation Program of Hangzhou Academy of Agricultural Sciences under Grant 2019HNCT-01.

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Authors and Affiliations

  1. Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang, China

    Kai Liu, Nan Xie & Heng-Jia Ma

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  1. Kai Liu
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Contributions

Kai Liu and Nan Xie conducted the experiments; Kai Liu analyzed the data and wrote the manuscript; Heng-Jia Ma contributed to data analysis and revising the manuscript; All authors read and approved the final manuscript.

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Correspondence to Kai Liu.

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The authors declare that they have no known competing financial interests or personal relationships that could have influenced the work reported in this paper.

Ethical approval

The approval from the Science and Technology Bureau of China and the Department of Wildlife Administration is not required for the experiments conducted in this paper when the fish in question are neither rare nor near extinction (first- or second-class state protection level). According to Measures of Zhejiang Province on Administration of Laboratory Animals, ethical approval was not required because the approval is only necessary when researchers will use mammals.

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Liu, K., Xie, N. & Ma, HJ. Next-generation sequencing reveals the mitogenomic heteroplasmy in the topmouth culter (Culter alburnus Basilewsky, 1855). Mol Biol Rep 49, 943–950 (2022). https://doi.org/10.1007/s11033-021-06913-w

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