Abstract
In this study, we first determined the complete mitochondrial genome sequence of Sinocyclocheilus jii, which is an endemic species to Southwestern China. The complete mitochondrial genome is 16,577 bp in length, consisting of 37 genes coding for 13 proteins, two rRNAs, 22 tRNAs, and one control region. Its gene arrangement pattern was identical to that of most vertebrates. Phylogenetic analysis using mitochondrial genomes of 11 species showed that nine Sinocyclocheilus species clustered as one monophyletic clade and S. jii was the most basal species on the phylogenetic tree of the Sinocyclocheilus fishes.
Keywords: Mitochondrial genome sequence, Sinocyclocheilus jii, Cyprinidae
Sinocyclocheilus jii belonging to the genus Sinocyclucheilus (Cypriniformes, Cyprinidae) is a freshwater fish that distributes only in the karst landform areas within Fuchuan County and Gongcheng County, Guangxi, China (Zhang and Dai 1992; Zhao and Zhang 2009). In this investigation, we would first report the complete mitochondrial genome (mitogenome) sequence of S. jii, which will provide useful molecular data for conservation biology, genetics and evolutionary studies on this species and its closely related species.
The specimen of S. jii under study was collected in Gongcheng, Guangxi, China (25.2°N, 110.9°E). The whole specimen was preserved in 95% alcohol and registered in the Zoological Specimen Museum of Yunnan University under the voucher number YNUSJ201308060038. All the experiments, including genomic DNA extraction, applied primers, PCR and sequencing, were carried out by following the standard laboratory procedures described by Wu et al. (2010). The protein-coding genes and ribosomal RNA genes were identified using DOGMA (Wyman et al. 2004), through comparing their similarity to previously reported mitochondrial genomes of Sinocyclocheilus grahami (Wu et al. 2010). The 22 tRNA genes of S. jii can fold into a typical cloverleaf secondary structure that was estimated by the program tRNAscan-SE (Lowe and Eddy 1997).
The complete mitogenome sequence of S. jii had been deposited in the GenBank with an accession number MF100765. The mitogenome was 16,577 bp in size, including 13 protein-coding (PCGs), two ribosomal RNA (rRNA), 22 transfer RNA (tRNA) genes, and one control region (D-loop). All mitochondrial genes of S. jii showed the typical gene arrangement conforming to the vertebrate consensus (Boore 1999). All genes were encoded on the H-strand, except for the ND6 gene and eight tRNA genes (tRNA-Gln, tRNA-Ala, tRNA-Asn, tRNA-Cys, tRNA-Tyr, tRNA-Ser (UCN), tRNA-Glu, and tRNA-Pro) which were encoded on the L-strand. Twelve of the PCGs began with ATG, but COI gene started with GTG. Most PCGs used complete (TAA or TAG) stop codon, while COII, ND4, and Cyt b genes ended with incomplete (T-) stop codon. The overall base composition in descending order for S. jii is A (31.77%), C (27.00%), T (25.00%), and G (16.23%) with 43.23% GC content.
In order to acquire some implication about phylogenetic position of S. jii within the Sinocyclocheilus species, mitogenome sequence of S. jii in this study, together with previously reported mitogenome sequences of eight Sinocyclocheilus fishes and two outgroup species from GenBank were used to perform phylogenetic analysis. Phylogenetic tree of 11 Cyprinidae fishes was built with MrBayes (Ronquist and Huelsenbeck 2003) and RAxML (Stamatakis 2006). Both the two methods generated the identical phylogenetic tree topologies (Figure 1). In the results, nine Sinocyclocheilus species clustered as one monophyletic clade with strong supports. The phylogenetic results strongly supported that S. jii was the most basal species among the Sinocyclocheilus species.
Figure 1.
Phylogenetic relationships of 11 Cyprinidae fishes by Bayesian and maximum-likelihood (ML) methods based on complete mitochondrial genome sequences. The accession numbers for each species are indicated after the scientific names. Numbers in the nodes represent the posterior probability for Bayesian analysis and bootstrap value for ML analysis.
Disclosure statement
The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References
- Boore JL. 1999. Animal mitochondrial genomes . Nucleic Acids Res. 27:1767–1780. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lowe TM, Eddy SR.. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955–964. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ronquist F, Huelsenbeck JP.. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 19:1572–1574. [DOI] [PubMed] [Google Scholar]
- Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22:2688–2690. [DOI] [PubMed] [Google Scholar]
- Wu XY, Wang L, Chen SY, Zan RG, Xiao H, Zhang YP.. 2010. The complete mitochondrial genome of two species from Sinocyclocheilus (Cypriniformes: Cyprinidae) and a phylogenetic analysis within Cyprininae. Mol Bio Rep. 37:2163–2171. [DOI] [PubMed] [Google Scholar]
- Wyman SK, Jansen RK, Boore JL.. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics. 20:3252–3255. [DOI] [PubMed] [Google Scholar]
- Zhang CG, Dai DY.. 1992. A new species of Sinocyclocheilus from Guangxi, China (Cypriniforms: Barbinae). Acta Zootaxonomica Sinica. 17:377–380. [Google Scholar]
- Zhao YH, Zhang CG.. 2009. Endemic fishes of Sinocyclocheilus (Cypriniformes: Cyprinidae) in China: species diversity, Cave adaptation, Systematics and Zoogeography. Beijing: Science Press. [Google Scholar]