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. 2021 Nov 18;6(12):3438–3439. doi: 10.1080/23802359.2021.1920862

The complete mitochondrial genome and phylogenetic analysis of Sinocyclocheilus angularis (Cypriniformes: Cyprinidae)

Qi Luo 1, Renyi Zhang 1,✉
PMCID: PMC8604459  PMID: 34805522

Abstract

This is the first study to determine the complete mitochondrial genome of Sinocyclocheilus angularis, which is an endemic cavefish native to the Karst region of the Yunnan-Guizhou Plateau. The complete mitochondrial genome size of S. angularis was 16,586 bp, and it consisted of a control region, 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes. The base composition of the mitogenome was 25.14% A, 32.45% T, 27.10% G, and 15.31% C, with an overall GC content of 42.42%. Phylogenetic analysis revealed that all Sinocyclocheilus were clustered into one strong clade and S. angularis was very closely related to S. bicornutus. It will provide an essential genetic tool for the further evolutionary studies and conservation of genus Sinocyclocheilus.

Keywords: Sinocyclocheilus angularis, mitochondrial genome, phylogeny

Sinocyclocheilus angularis, which belongs to order Cyprinoidea, family Cyprinidae, genus Sinocyclocheilus, is an endemic cavefish native to the Karst region of the Yunnan-Guizhou Plateau (Zhao and Zhang 2009). In our study, we analyzed the complete mitochondrial genome sequence and phylogenetic relationship of S. angularis, to provide an essential genetic tool for the further evolutionary studies and conservation of genus Sinocyclocheilus.

In this study, S. angularis sample was collected from Pan county of Guizhou Province, Southwestern China (25°24.50′N, 104°43.29′E). The voucher specimen was stored in 99.5% ethanol and deposited in the fish specimen room, School of Life Science, Guizhou Normal University (Renyi Zhang, e-mail: zhangrenyi@gznu.edu.cn) under the voucher number GZNU202001332. Total genomic DNA was extracted from muscle using DNeasy Blood & Tissue Kit (QIAGEN, Hilden, Germany). The complete mitogenome DNA was sequenced on Illumina HiSeq platform (Illumina, San Diego, CA), and then the short raw sequences were assembled with MitoZ (Meng et al. 2019). The MitoAnnotator on MitoFish homepage was used for mitochondrial genome annotation (Iwasaki et al. 2013) and the web page of tRNAscan-SE was used for the transfer RNA (tRNA) genes identification (Lowe and Eddy 1997). The mitochondrial genome was submitted into GenBank with an accession number MW362289.

The complete mitochondrial genome size of S. angularis was 16,586 bp, which contained of a control region (D-loop), 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and 2 ribosomal RNA (rRNA) genes. The base composition of the mitogenome was 25.14% A, 32.45% T, 27.10% G, 15.31% C, and the overall GC content was 42.42%. The arrangement of these genes is similar to that other species of Sinocyclocheilus (Zhang and Wang 2018; Xu et al. 2019; Luo et al. 2019). All of genes were encoded on heavy strand (H-strand) or light strand (L-strand). Eight tRNAs (tRNA-Gln, tRNA-Ala, tRNA-Asn, tRNA-Cys, tRNA-Tyr, tRNA-Ser, tRNA-Glu, tRNA-Pro) and ND6 gene were encoded on the L-strand and the other genes (tRNA-Phe, 12S rRNA, tRNA-Val, 16S rRNA, tRNA-Leu, ND1, tRNA-Ile, tRNA-Met, ND2, tRNA-Trp, COI, tRNA-Asp, COII, tRNA-Lys, ATPase 8, ATPase 6, COIII, tRNA-Gly, ND3, tRNA-Arg, ND4L, ND4, tRNA-His, tRNA-Ser, tRNA-Leu, ND5, Cyt b, tRNA-Thr) were encoded on the H-strand. All of PCGs began with ATG codon, except COI gene, which started with GTG. Seven PCGs ended with complete stop codon (TAA or TAG), but six genes (ND2, COII, COIII, ND3, ND4, Cyt b) stopped with incomplete (T- or TA-) codon.

To understand the evolutional relationship between S. angularis and other Sinocyclocheilus, we constructed a phylogenetic tree from 16 species of Sinocyclocheilus and 2 outgroup species (Cyprinus carpio and Barbus barbus). The phylogenetic tree based on 13 protein-coding genes of 18 species from Cyprinidae was established by using MrBayes (Ronquist and Huelsenbeck 2003) module in PhyloSuit (Zhang et al. 2020). The result of phylogenetic tree showed that all Sinocyclocheilus were clustered into one strong clade (Figure 1). The S. angularis was very close related to S. bicornutus, and the two species (S. angularis and S. bicornutus) and S. altishoulderus as a sister clade formed a monophyletic group with S. furcodorsalis.

Figure 1.

Figure 1.

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Phylogenetic relationship of S. angularis using Bayesian method by PhyloSuite. Cyprinus carpio and Barbus barbus were served as outgroups. The values at the internode branches represent Bayesian posterior probability.

Acknowledgments

Thanks to Qian Tang and Yunfu Li for their assistance in specimen collection.

Funding Statement

This work was supported by the National Natural Science Foundation of China (31960097) and new seedling plans of Guizhou Normal University ([2019]).

Disclosure statement

The authors declare that they have no conflict of interest. The authors alone are responsible for the content and writing of the paper.

Data availability statement

The data that support the findings of this study are openly available in NCBI at https://www.ncbi.nlm.nih.gov/nuccore/MW362289, reference number MW362289.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

The data that support the findings of this study are openly available in NCBI at https://www.ncbi.nlm.nih.gov/nuccore/MW362289, reference number MW362289.

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