The molecular characterization of complete mitochondrial genome of spotted snakehead fish, Channa punctata (Bloch 1793)

Abstract

The complete mitochondrial genome of spotted snakehead fish, Channa punctata (Bloch 1793) was determined by MiSeq platform. The genome was 16,409 bp in length, in which canonical 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region (D-Loop) were encoded. Relatively higher overall A + T contents (53.70%) was identified compared with G + C contents (46.30%). Among 13 protein-coding genes, only one unusual start condon (GTG) was identified in COX1, whereas six genes including COXII, COXIII, NAD2, NAD3, NAD4, and Cytb were ended with the incomplete stop codons (TA-/T–). Based on the currently identified mitogenomes of Channa fish species, C. punctata was most closely related to Channa gachua with 82% sequence identity.

Keywords:

• Next generation sequencing
• Channa punctata
• mitochondrial genome
• phylogeny
• snakehead fish

The Spotted snakehead, Channa punctata (Bloch 1793) is a common air-breathing fish found in swamps, ditches, beels, and ponds (Jayaram 1981; Pethiyagoda 1991). This species widely distributed in the freshwaters and brackish water of Bangladesh, India, Pakistan, Afghanistan, Sri Lanka, Nepal, Myanmar, and China (Talwar and Jhingran 1991; Riede 2004; Mukhopadhyay and Ghosh 2007). Since C. punctata shares the habitat with its relatives such as Channa gachua, and Channa striata (Talwar and Jhingran 1991; Molur and Walker 1998; Froese and Pauly 2011), conservation and management of their resources based on the genetic information is strongly required.

C. punctata was collected from the river in Khulna, Bangladesh (22°50′44.3″ N, 89°32′27.7″E) in March 2017. The specimen was identified by its morphological characteristics and its COX1 sequence to the NCBI database (GenBank number: KT762386). The specimen is stored in the Department of Fisheries and Marine Science laboratory, Noakhali Science and Technology University, Noakhali, Bangladesh. The full mitochondrial DNA sequence of C. punctata was determined by next-generation sequencing (NGS) platform. Mitochondrial DNA was extracted by the mitochondrial DNA isolation kit (Abcam, UK) and the purified mitochondrial DNA was further fragmented into smaller sizes (∼350 bp) by Covaris M220 Focused-Ultrasonicator (Covaris Inc., Woburn, MA, USA). A library was constructed by TruSeq^® RNA library preparation kit V2 (Illumina), and its quality and the quantity were analyzed by 2100 Bioanalyzer (Agilent Technologies). The high-throughput sequencing was performed by MiSeq platform with 600-cycle kit (Illumina). Geneious software (v.11.0.2) was applied for the mitogenome assembly (Kearse et al. 2012).

The complete mitochondrial genome of C. punctata (GenBank Number: MK007075) was 16,409 bp in length, which consisted of 13 protein-coding genes, 22 tRNAs, 2 ribosomal RNAs (12S and 16S), and a control region (D-Loop). Nine genes were encoded on the L strand while the other 28 genes were located on the H strand. Relatively higher overall A + T contents (53.70%) were identified compared with G + C contents (46.30%). Among 13 protein-coding genes, only one unusual start condon (GTG) was identified in COX1, whereas six genes including COXII, COXIII, NAD2, NAD3, NAD4, and Cytb were ended with the incomplete stop codons (TA-/T–).

The phylogenetic tree was constructed to understand the evolutional relationship of C. punctata with other seven currently reported mitogenomes of Channa species using MEGA7.0 program with minimum evolutionary (ME) algorithm (Kumar et al. 2016). Based on the mitogenome sequences, C. punctata showed the highest similarity to C. gachua (GenBank number: NC036948) with 82% nucleotide sequence identity (Figure 1). Based on the COX1 gene sequence, C. punctata was most closely related to C. gachua (MH156949) and C. striata (KX389278) with 84% sequence identity. Those result supported the previous result about the evolution of Asian snakehead fishes (Adamson et al. 2010) and more mitogenome sequences would help us to establish the clear evolutional relationship of snakehead fishes.

Figure 1. Phylogenetic tree of Channa punctata within Channidae family. Phylogenetic tree of Channa punctata complete genome was constructed by MEGA7 software with Minimum Evolution (ME) algorithm with 1000 bootstrap replications. GenBank Accession numbers were shown followed by each species scientific name. Anabas testudineus was used as an outgroup species.

Disclosure statement

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

Additional information

Funding

This work was supported by the Pukyong National University Research Fund in 2018