Complete mitochondrial genome and phylogenetic implications of the rainbow bitterling Acheilognathus tonkinensis (Cypriniformes: Cyprinidae)

Abstract

Acheilognathus tonkinensis is a magnificent bitterling fish of genus Acheilognathus belonging to the sub-family Acheilognathinae of the family Cyprinidae. In this study, we first determined and described the 16,767 bp mitochondrial DNA sequence of A. tonkinensis. The mitogenome encoded 13 protein-coding genes (PCGs), 22 tRNA genes, 12S, and 16S rRNA genes, and a D-loop region. The overall nucleotide composition was 29.4% A, 27.1% T, 17.0% G, and 26.5% C, with a slight AT bias (56.5%). Phylogenetic analysis suggested that A. tonkinensis had the closest evolutionary relationship with A. macropterus. The availability of mitogenome sequence of A. tonkinensis would facilitate species identification of the Acheilognathinae, as well as genetic evaluations for resource conservation and management of this species.

Keywords:

• Acheilognathus tonkinensis
• mitochondrial genome
• phylogeny

The rainbow bitterling, Acheilognathus tonkinensis (Cypriniformes: Cyprinidae), has a wide range in south-east Asia and is mainly distributed in freshwater rivers of central and southern China (Chen et al. 1998). Its unique spawning behavior and brilliant color has made it widely popular and which brought extremely high ornamental and economical value to it. Thus it is likely to be impacted by overfishing, water pollution, and damming. Nowadays, research on this species is largely focused on karyotype, reproductive strategy, and heavy metal accumulation (Arai et al. 1992; Liu et al. 2006; Wang et al. 2017), but little information is available on the mitochondrial sequences. The present study reported the complete mitogenome of A. tonkinensis and validated its taxonomic status, which would be conducive to further molecular genetic studies and conservation of this species.

The specimen of A. tonkinensis was collected in July 2016 from Wuxuan County, Guangxi, China (23°35′35.29″N, 109°39′45.27″E) and was deposited in Guangxi Colleges and Universities Key Laboratory of Aquatic Healthy Breeding and Nutrition Regulation, Guangxi University. Genomic DNA was isolated from the dorsal muscle by Animal Tissues Genomic DNA Extraction Kit (Solarbio, Beijing, China). The sequence was amplified through conventional and long PCR with fourteen primer pairs, and then sequenced in Sangon Biotech (Shanghai, China). Mitochondrial genome was assembled and annotated by Geneious 10.1.2 (Biomatters Ltd., Auckland, New Zealand) using the A. macropterus reference mitogenome (GenBank Accession No. KJ499466.1) (Zhu et al. 2016).

The mitochondrial genome of A. tonkinensis was 16,767 bp in length (GenBank Accession No. MH261370) and was A + T-biased (56.5%) with a base composition of 29.4% A, 27.1% T, 17.0% G, and 26.5% C, respectively. It retained the canonical set of 37 genes observed in bony fish mitogenomes, presenting 13 PCGs, 22 tRNA genes, 2 rRNA genes, a putative origin of light-strand replication, and an AT-rich control region (D-Loop). Besides, 12 PCGs were initiated by ATG except COI gene used GTG as a start codon. The stop codon TAA was identified in 6 PCGs (ND1, COI, ATP8, ND4L, ND5 and ND6), while the aberrant single-nucleotide termination codon (T) was found in the rest of the coding genes. Two rRNAs (958 bp 12S and 1678 bp 16S) were composed of 54.0% AT, and the D-loop was 1119 bp long with the AT content of 66.6%.

To confirm the phylogenetic place of A. tonkinensis in the Acheilognathinae, a maximum likelihood dendrogram was constructed by MEGA 7.0 software based on all PCGs of 17 Acheilognathinae fishes (Kumar et al. 2016). Two species of Barbinae were employed as an outgroup taxa. Evolutionary model was selected by the program PhyML 3.0 (Guindon et al. 2010), where the GTR + G + I substitution model was recognized as the best fit to the data. The distance dendrogram revealed the closest evolutionary relationship of A. tonkinensis to the chinese bitterling A. macropterus (Figure 1), and the arrangement of taxa within the Acheilognathinae was in accordance with the previously reported results (Chang et al. 2014).

Figure 1. Maximum-likelihood tree (GTR + G + I model) of Acheilognathus tonkinensis and 16 related Acheilognathinae species based on 13 concatenated PCGs. Bootstrap values (1000 replicates) are indicated at each node. Two species of Barbinae were utilized as outgroup taxa. The mitogenomic information of A. tonkinensis is marked with pentagram.

Disclosure statement

The authors report no conflicts of interest, and are solely responsible for this paper.

Additional information

Funding

This work was supported by the Science and Technology Major Project of Guangxi Zhuang Autonomous Region (AA17204088-3), the Natural Science Foundation of Guangxi Zhuang Autonomous Region (2015GXNSFBA139066, 2017GXNSFAA198044) and the project to enhance the basic ability of young teachers of Guangxi Zhuang Autonomous Region (KY2016YB021).