Abstract
The complete mitochondrial genome (mitogenome) sequence of Sinocyclocheilus wumengshanensis from Yunnan Province in China was analysed using next-generation sequencing. The complete mitogenome was 16,585 bp in length and consisted of 13 protein-coding genes, two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and one D-loop region. Nucleotide composition of the whole mitogenome was 30.5% A, 25.2% T, 27.0% C, and 17.2% G. The gene arrangement and nucleotide composition of the mitogenome of S. wumengshanensis were similar to those of other Sinocyclocheilus species. Phylogenetic analyses using mitogenomes of 12 species showed that 10 Sinocyclocheilus species clustered as one monophyletic clade with strong supports and S. wumengshanensis was closely related to S. grahami.
Keywords: Sinocyclocheilus wumengshanensis, mitogenome sequence, next-generation sequencing
Sinocyclocheilus wumengshanensis is a species of freshwater fish in the genus Sinocyclocheilus (Cypriniformes: Cyprinidae) endemic to China. This species distributes in the karst landform regions within Zhanyi, Xuanwei and Xundian counties of Yunnan province, southwestern China (Li et al. 2003). In this study, we first reported the complete mitochondrial genome (mitogenome) of S. wumengshanensis, which could provide useful first-hand data for molecular phylogenetics and population genetics studies on this species and its closely related Sinocyclocheilus species.
The specimen of S. wumengshanensis was collected in Xuanwei County, Yunnan province, China (26.0°N, 104.0°E). The entire specimen was stored in 95% ethanol and registered in the Zoological Specimen Museum of Yunnan University under the voucher number YNUSM20160817008. Genomic DNA was extracted from muscle tissue by DNeasy Blood & Tissue Kit (QiaGen, Hilden, Germany). Shotgun DNA library was constructed and sequenced with Illumina Miseq platform (Illumina, San Diego, CA). The complete mitogenome sequence was assembled with Trinity v2.3.2 (Haas et al. 2013) and SPAdes (Bankevich et al. 2012). The DOGMA (Wyman et al. 2004) and tRNAscan-SE (Lowe and Eddy 1997) were utilized to annotate protein-coding genes (PCGs), ribosomal RNA (rRNA) genes, and transfer RNA (tRNA) genes, via comparing their similarities to those of S. grahami mitogenome sequence (Wu et al. 2010).
The complete mitogenome sequence of S. wumengshanensis had been deposited in GenBank database with an accession number MG021442. The complete mitogenome was 16,585 bp in length and consisted of 13 PCGs, two rRNA genes, 22 tRNA genes, and one D-loop or control region. Nucleotide composition of the whole mitogenome was 30.5% A, 25.2% T, 27.0% C, and 17.2% G. The gene arrangement and nucleotide composition of the mitogenome of S. wumengshanensis were similar to those of other Sinocyclocheilus species (Wu et al. 2010; Li et al. 2017). The locations of 37 genes on H-strand or L-strand and the start codon usage for 13 PCGs were exactly identical to those of S. jii mitogenome sequence (Li et al. 2017). For stop codon usage, nine out of 13 PCGs had complete stop codon (TAA or TAG), while four PCGs (COII, ATP8, ND4, and Cyt b) terminated with incomplete stop codon (T-).
To gain an insight into relative phylogenetic position of S. wumengshanensis, phylogenetic analyses were conducted based on mitogenome sequences of 10 Sinocyclocheilus species and two outgroup species, using Bayesian method by MrBayes3 (Ronquist and Huelsenbeck 2003) and maximum likelihood (ML) method by MEGA6 (Tamura et al. 2013). The two methods generated completely identical tree topologies (Figure 1). The phylogenetic results showed that 10 Sinocyclocheilus species clustered as one monophyletic clade with strong supports and that S. wumengshanensis was closely related to S. grahami.
Figure 1.
Phylogenetic relationships of 12 Cyprinidae fishes by Bayesian and maximum likelihood (ML) methods based on complete mitochondrial genome sequences. The accession numbers for each species are indicated in brackets. Numbers in the nodes represent support values.
Disclosure statement
The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
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