Abstract
In this study, the complete mitochondrial genome of Sinocyclocheilus qujingensis has been determined by polymerase chain reaction method for the first time. The overall base composition of Sinocyclocheilus qujingensis mitogenome is 31.2% for A, 26.9% for C, 16.6% for G and 25.4% for T. The percentage of G + C content is 43.5%. The mitogenome is a circular DNA molecule of 16,588 bp in length with a D-loop region and contains 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and 13 protein-coding genes. The mitochondrial genome sequencing for Sinocyclocheilus qujingensis in this study provides important molecular data for further evolutionary analysis for Cyprinoidea.
Sinocyclocheilus qujingensis, which belongs to order Cyprinoidea, family Cyprinidae, genus Sinocyclocheilus, is a valuable species of freshwater fish which is only found in karst region of Yunnan-Guizhou Plateau.
In this study, Sinocyclocheilus qujingensis samples were collected from Huize county of Yunnan Province in China (26°44′N; 103°28′E). The specimen is stored in Heilongjiang River Fisheries Research Institute and its accession number is hrfri2018044. The genome DNA was extracted following the traditional phenol–chloroform method (Taggart et al. Citation1992). Twenty-six primers were designed to amplify the PCR products for sequencing. The sequencing results were then assembled using ContigExpress 9.0 software (New York, NY). The transfer RNA (tRNA) genes were identified using the program tRNAscan-SE 1.21 (http://lowelab.ucsc.edu/tRNAscan-SE). The locations of protein-coding genes were determined by comparing with the corresponding known sequences of other Sinocyclocheilus fish species.
The complete mitochondrial genome length of Sinocyclocheilus qujingensis was 16,588 bp in length (GenBank accession number MH937706). It consisted of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and one D-loop region. The overall base composition of the mitogenome is 31.2% for A, 26.9% for C, 16.6% for G and 25.4% for T. The percentage of G + C content is 43.5%. To validate the phylogenetic position of Sinocyclocheilus qujingensis, we perform multiple sequence alignment and MEGA 6.0 (Tamura et al. Citation2013) to construct a neighbor-joining tree containing complete mitochondrial genome DNA of 20 species in Cyprinoidea. As shown in the phylogenetic tree (), our sequence was clustered in genus Sinocyclocheilus, including Sinocyclocheilus anophthalmus, Sinocyclocheilus grahami, Sinocyclocheilus furcodorsalis and Sinocyclocheilus altishoulderus.
Figure 1. A neighbour-joining (NJ) tree of the 20 species from Cyprinoidea was constructed based on complete mitochondrial genome data. The analyzed species and corresponding NCBI accession numbers are as follows: Sinocyclocheilus anophthalmus (NC_023472.1), Sinocyclocheilus graham (GQ148557.1), Sinocyclocheilus qujingensis (MH937706), Sinocyclocheilus furcodorsalis (GU589570.1), Sinocyclocheilus altishoulderus (FJ984568.1), Acrossocheilus fasciatus (KF781289.1), Acrossocheilus monticola (NC_022145.1), Spinibarbus caldwelli (NC_022149.1), Spinibarbus denticulatus (AP013335.1), Gymnocypris przewalskii (NC_019604.1), Garra orientalis (AP011202.1), Garra rufa (NC_022941.1), Cirrhinus reba (NC_029445.1), Cirrhinus molitorella (AP011390.1), Crossocheilus burmanicus (NC_029446.1), Crossocheilus langei (NC_029443.1), Crossocheilus siamensis (NC_031827.1), Crossocheilus atrilimes (NC_029447.1), Myxocyprinus asiaticus (AY526869.1), Rhodeus ocellatus kurumeus (AB070205.1).
Disclosure statement
The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
Additional information
Funding
References
- Taggart JB, Hynes RA, Prodouhl PA, Ferguson A. 1992. A simplified protocol for routine total DNA isolation from salmonid fishes. J Fish Biol. 40:963–965.
- Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 30:2725–2729.