Molecular identification and phylogenetic analysis of mitogenome of the Xenocypris davidi from Cao’e River

Abstract

In this study, the complete mitochondrial genome sequence of a Xenocypris davidi from Cao’e River was sequenced. The complete mitogenome of X. davidi was 16,630 bp in length, it contains the structure of 22 transfer RNA genes, 13 protein coding genes, 2 ribosomal RNA genes, and 1 non-coding region. The gene arrangement and organization in the mitogenome of X. davidi were in accordance with other Cyprinidae fishes. The results of phylogenetic analysis revealed that the mitochondrial genome sequence could provide useful information for the conservation genetics and evolution study of X. davidi.

Keywords:

• Xenocypris davidi
• mitochondrial genome
• identification
• phylogenetic analysis

Xenocypris davidi Bleeker, a medium-sized fish mainly distributed in the Changjiang River, Qiantang River, and Minjiang River of China (Xiao et al. 2001; Li et al. 2009; Xu et al. 2011; Tang et al. 2013). It feeds on epiphytic algae, underwater humus, and debris from higher aquatic plants, and therefore, it was cultured and used as an important water control fish in recent years (Xu et al. 2011; Zhang et al. 2016). The Cao’e River is one of the largest tributaries of the Qiantang River in Zhejiang province of east China. However, the wild population of X. davidi in Cao’e River decreases rapidly because of artificial irrigation works, environment pollution, and increasing capture pressure.

The mitochondrial genome sequence could be useful data in conservation genetics and evolution study for various aquatic species (Liu and Cui 2009; Chen et al. 2013; Yang et al. 2014; Wang et al. 2016) .

In this study, an individual of X. davidi was sampled from the Cao’e River (29°57′52.7′′N 120°52′32.4′′E), its complete mitogenome was sequenced and identified (designated XD-1). The previously published mitogenome of X. davidi (GenBank accession no. KF039718, designated XD-2) was used to design PCR amplification primers (Liu 2014). The XD-1 specimen and its DNA are kept in the Shaoxing Aquatic Service Platform now.

The complete mitochondrial genome of X. davidi is 16,630 bp in length (GenBank accession no. MN264265), it contains 22 tRNA genes, 13 protein-coding genes (PCDs), 2 rRNA genes, and one non-coding region. These genes showed a conserved arrangement with other Cyprinidae fishes (Yang et al. 2014; Jia et al. 2016).

The total length of the PCD sequences is 11,425 bp. The total length of all tRNA genes was 1566 bp, varying from 68 bp (tRNA^Cys) to 76 bp (tRNA^Leu and tRNA^Lys). The 12S rRNA gene (961 bp) and 16S rRNA (1693 bp) gene of X. davidi are located between the tRNA^Phe and tRNA^Leu(UUR)gene, and are separated by the tRNA^Val gene. The D-loop region is 935 bp in length, which is located between the tRNA^Pro and tRNA^Phe gene. All of the PCD genes except COX I (started with a GTG) are initiate with an ATG. Five PCD genes terminate with TAA (ND1, COXI, ATP6, ND4L, and ND6), three PCDs (COX II, ND3, and Cyt b) ended with T–, two PCDs (COX III and ND4) ended with TA-, whereas three PCDs (ND2, ND5, and ATP8) ended with TAG (data not shown). The overall nucleotide composition of X. davidi mitogenome is A: 31.24%, G: 16.19%, T: 25.38%, and C: 27.18%, respectively. Which showed an similar A + T rich feature (56.62%) with other vertebrate mitogenomes (Tzeng et al. 1992; Jondeung et al. 2007; He et al. 2014).

The generated phylogenetic tree indicated that X. davidi is clustered in genus Xenocypris as expected (Figure 1), but it showed distant kinship with other Cyprinidae fishes. This results indicated that the mitogenome sequence could be useful information in the field of conservation genetics and evolution for aquatic species.

Figure 1. The phylogenetic analysis of X. davidi and other Cyprinidae fishes based on the mitogenome sequences.

Disclosure statement

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article.

Additional information

Funding

This work was supported by the Young & Middle-aged Academic Backbone Project of Shaoxing University [2014]; the Public Welfare Project of Science Technology Department of Zhejiang Province [2011C22084]; and the National Mollusk Industry Technology System [KL2015-3].