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Characterization and phylogenetic analysis of the complete mitogenome of a rare cavefish, Sinocyclocheilus multipunctatus (Cypriniformes: Cyprinidae)

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Abstract

The genus Sinocyclocheilus is a representative group of cave creatures. However, genetic studies on Sinocyclocheilus are rare. The primary objective of this study was to explore the structure and feature of the complete mitochondrial genome of S. multipunctatus, and reconstruct the mitogenomic phylogeny of Sinocyclocheilus. The mitochondrial DNA of S. multipunctatus was amplified by overlapping PCR fragments. The mitogenome was assembled by the SeqMan and annotated using MitoAnnotator. The phylogenetic tree was established using the Bayesian inference and Maximum likelihood methods. The mitogenome of S. multipunctatus is a typical circular molecule of 16,586 bp with base composition A (31.25%), T (25.90%), G (16.35%), and C (26.50%), and consists of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs) genes, two ribosomal RNAs, and a 931 bp control region. Phylogenetic analysis reveals two clades in the Sinocyclocheilus with robust support. S. multipunctatus is close to a newly discovered cavefish, S. ronganensis. We obtained and described the complete mitogenome of S. multipunctatus, and investigated its phylogenetic status, which may provide a valuable resource for future phylogenetic analyses and population genetic studies in Sinocyclocheilus.

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Acknowledgements

This work was supported by the Doctoral Foundation of Guizhou Normal University ([2016]).

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Author notes

  1. Renyi Zhang and Xue Wang have contributed equally to this work.

Authors and Affiliations

  1. School of Life Sciences, Guizhou Normal University, 116 Baoshan Road, Guiyang, 550001, Guizhou, China

    Renyi Zhang

  2. Institute of Fisheries, Guizhou Academy of Agriculture Science, Guiyang, 550006, Guizhou, China

    Xue Wang

Authors
  1. Renyi Zhang
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  2. Xue Wang
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Correspondence to Renyi Zhang.

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Conflict of interest

Renyi Zhang declares that he does not have conflict of interest. Xue Wang declares that she does not have conflict of interest.

Ethical approval

This article does not contain any studies with human subjects by any of the authors. The animal experiment throughout the study was conducted according to the Chinese Ministry of Science and Technology Guiding Directives for Humane Treatment of Laboratory Animals.

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Fig. S1. Putative secondary structures of the 22 tRNA genes identified in the mitochondrial genome of

S. multipunctatus. All tRNA genes are shown in the order of occurrence in the mitochondrial genome starting from tRNA-Phe. The tRNA are labeled with abbreviations of their corresponding amino acid. Dashed lines (-) indicate Watson-Crick base pairings (TIF 3255 KB)

Fig. S2. The OL stem-loop secondary structure in

S. multipunctatus (TIF 72 KB)

Supplementary material 3 (DOCX 13 KB)

Supplementary material 4 (DOCX 16 KB)

Supplementary material 5 (DOCX 13 KB)

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Zhang, R., Wang, X. Characterization and phylogenetic analysis of the complete mitogenome of a rare cavefish, Sinocyclocheilus multipunctatus (Cypriniformes: Cyprinidae). Genes Genom 40, 1033–1040 (2018). https://doi.org/10.1007/s13258-018-0711-3

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  • DOI: https://doi.org/10.1007/s13258-018-0711-3

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