Complete mitochondrial genome of Odontobutis potamophila (Teleostei, Perciformes, Odontobutidae) from the newly found population of the Upper Yangtze River

Abstract

The Odontobutis potamophila is endemic commercial fishery species to China and distributed mainly in middle and lower Yangtze River of China. Here, we describe a complete mitochondrial genome from the newly found population of O. potamophila in the Three Gorges Reservoir where located in the upper Yangtze River. It was 16,939 bp in size and encodes for two rRNAs, 22 tRNAs, 13 protein-coding genes, and a D-loop control region. Phylogenetic analysis confirmed the evolutionary relationship of the O. potamophila in the upper Yangtze to other five species of the genus Odontobutis. The mitochondrial genome would help to elucidate the origin of the new population of O. potamophila.

Keywords:

• Odontobutis potamophila
• Three Gorges Reservoir
• mitochondrial genome
• phylogenetic analysis
• Upper Yangtze River

Odontobutis potamophila (Günther, 1861), belongs to the genus Odontobutis with high economic value in China, mainly distributes in the middle and lower reaches of the Yangtze River and its tributaries (Wu et al. 1993). The all reports regarding genetic characteristics of O. potamophila based on samples collected in the middle and lower reaches of the Yangtze River basin (Ma et al. 2015; Xu et al. 2015; Li and Liu 2016). Three Gorges Reservoir (TGR) was completely formed in 2006 after the Three Gorges Dam cut the upper Yangtze River. The original river flow pattern was changed in TGR, which caused alteration of the population structure, species composition, and spatial and temporal distributions of fishes (Xie et al. 2018). According to historical documents, there is no record about the distribution of O. potamophila in the upper Yangtze River basin (Ding 1994). However, we collected 20 specimens of O. potamophila in the TGR of the upper Yangtze River, Chongqing of China in 2018. To our knowledge, this is a newly found population of O. potamophila in the upper Yangtze River. The specimens were stored in 90% ethanol and kept in the fishes and animal specimens room (CAST 30-0119) of Museum of Southwest University.

In this study, we determined the complete mtDNA sequence of an O. potamophila (100.5 mm standard length, 13.50 g mass, No. 20180100011), which was collected from Jiulongpo (29.527382 N, 106.53606 E) in TGR of Chongqing during October 2018. Total genomic DNA extracted from dorsal muscle tissues by the standard procedure (Sambrook and Russell 2001). Twenty-seven pairs of PCR primers were designed to amplify the segments using PCR and then products were sequenced and assembled. The mitochondrial genome of O. potamophila (GenBank accession No. MK408452) was a circular molecule of 16,939 bp with 13 protein-coding genes, two rRNA, 22 tRNA genes, and D-Loop region of 859 bp. All genes show the typical gene arrangement conforming to the vertebrate consensus (Noack et al. 1996). Except for the eight tRNA genes and ND6 gene, all the other mitochondrial genes were encoded on the heavy strand, which was similar to other fishes (Hu et al. 2015). There were two overlapping sequences between genes. Among the 13 protein-coding genes, except COX2 and CYTB use an incomplete stop codon ‘T,’ the rest are encoded by the typical TAA or TAG stop codons and except COX1 with GTG as start codon, the remaining 11 protein-coding genes start with an ATG codon.

The sequences of complete mitochondrial genome of O. potamophila and other 7 species including 5 species from the genus Odontobutis and 2 species as outgroup were used for phylogenetic analysis (Figure 1). The results confirmed that O. potamophila is closely related to the O. interrupta than other 4 species in the genus Odontobutis, within a monophyletic clade (Ma et al. 2015). The mitogenome would help to elucidate the origin of the new upstream population of O. potamophila.

Figure 1. Phylogenetic tree of six species of the genus Odontobutis based on the sequences of complete mitochondrial genome by Bayesian inference and maximum likelihood methods. Siniperca chuatsi from Family Serranidae, Channa argus from Family Channidae as outgroup. Phylogenetic analysis confirms that O. potamophila (indicated as boxed) belongs to the clade of the genus Odontobutis and more closely related to the O. interrupta. Bootstrap values (1000 replicates) are shown for each node, and GenBank accession numbers are provided in parentheses accompanying each taxon.

Disclosure statement

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

Additional information

Funding

This work was supported by the Ecological Fishery Technological System of Chongqing Agriculture and Rural Commission under Grant [No. 4321700088]; Key R&D Project [cstc2017shms-zdyfX0040] from Chongqing Science and Technology Commission.