The complete mitogenome of Glyptothorax deqinensis (Siluriformes: Sisoridae)

Abstract

Glyptothorax deqinensis is a small endangered Sisoridae fish mainly distributed in the southwest of China. In the present study, the complete mitochondrial genome of G. deqinensis was firstly sequenced. The total length of the G. deqinensis mitogenome is 16,542 bp, including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region. Among these genes, 28 are encoded by the H-strand and 9 by the L-strand. The information mitogenome obtained herein will provide useful tools for future studies on population genetic and phylogenetic analyses of this fish.

Glyptothorax deqinensis is a small benthic Sisoridae fish which naturally distributed in the southwest of China (Chu and Chen 1990). Because of influences of human activities, such as overfishing, water pollution, habitat destruction, and water conservancy project construction (Shao et al. 2016), natural resources of G. deqinensis has sharply declined in recent years, and it has been listed as endangered fish species in China (Jiang et al. 2016). However, studies on this fish are quite limited, and no available genetic information has been reported presently. In this study, the complete mitochondrial genome (mtgenome) of G. deqinensis was sequenced and characterized for the first time.

Sample of G. deqinensis was collected from the Deqin (Yunnan province, China) section of the Lancang River (N 28°32′27.15″, E 98°47′52.53″). Fin clips of samples were taken and stored in anhydrous ethanol at 4 °C. After sampling, the specimen was stored in 95% ethanol and kept in the herbarium of Yangtze River Fisheries Research Institute (accession number LC20180411002). Total DNA was extracted following the standard phenol/chloroform method (Sambrook and Russell 2001), and DNA quality was measured by a Nanodrop2000 spectrophotometer (Thermo Scientific, USA). Using the mitogenome of Glyptothorax trilineatus (NC_021608.1) as a reference sequence, 18 pairs of primers were designed to amplify mitochondrial DNA segments of G. deqinensis. Genome annotation was performed using MITOS2 webserver (Bernt et al. 2013), and compositions of the four nucleotides were calculated using MEGA4 (Tamura et al. 2007).

After sequencing and assembly of mtDNA segments amplified by the 18 primer pairs, a circular mtgenome with a length of 16,542 bp was finally obtained (GenBank accession no. MN082046), which was similar to that of other fishes from the genus Glyptothorax (Li 2016; Huang et al. 2017). The overall nucleotide composition for A, T, G, and C is 31.2, 25.2, 15.5, and 27.1%, respectively, with a G + C content of 42.6%. After annotations of the G. deqinensis mitogenome, 37 genes, including 13 protein-coding genes, two ribosomal RNA genes (12S rRNA and 16S rRNA) and 22 transfer RNA genes, were identified and a putative control region was also found. Among the 37 genes, 28 genes are encoded by the heavy (H) strand, whereas the other 9 genes, including a protein-coding gene (ND6) and 8 tRNA genes (tRNA^Gln, tRNA^Ala, tRNA^Asn, tRNA^Cys, tRNA^Tyr, tRNA^Ser, tRNA^Glu, and tRNA^Pro) are located on the light (L) strand. The mtgenomic structure of G. deqinensis was the same as that of other fishes from Glyptothorax (Li 2016; Huang et al. 2017).

Among the 13 protein-coding genes, 12 genes used typical metazoan start codon ATG, while the start codon was GTG for COXI. Termination codon for 6 of the 13 protein-coding genes were normal, with TAA for ND1, COI, ATPase8, ND4L, and ND5, and TAG for ND6, while the remaining 7 genes ended with incomplete stop codon of T- (ND2, COXII, COXIII, ND3, ND4, and Cytb) and TA- (ATPase 6).

Moreover, mtDNA sequences of 10 Sisoridae fishes were downloaded from GenBank for phylogenetic analysis. The 10 sequences were from Glyptothorax cavia (KY230517.1), Glyptothorax fokiensis (JQ917224.1), Glyptothorax sinensis (KJ739617.1), Glyptothorax zanaensis (KU212205.1), Glyptothorax trilineatus (JQ026262.1), Glyptothorax laosensis (KP271438.1), Gagata dolichonema (JQ026250.1), Pseudecheneis sulcata (JQ026259.1), Glaridoglanis andersonii (JQ026254.1), and Glyptosternon maculatum (JQ026251.1). The neighbor-joining (N-J) method in MEGA 4.0 (Tamura et al. 2007) was used to perform phylogenetic analyses. The N-J tree showed that G. deqinensis was clustered together with Glyptothorax fishes under strong bootstrap value support (Figure 1), which confirmed the phylogenetic status of G. deqinensis, and provided useful information for further phylogenetic and evolutionary studies on the genus Glyptothorax, as well as the family Sisoridae.

Figure 1.

The neighbor-joining phylogenetic tree of Glyptothorax deqinensis with other Sisoridae species based on mitochondrial genome sequences. Numbers along with branches are Bayesian posterior probability and bootstrap values for the phylogenetic tree.

Disclosure statement

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