Complete mitochondrial genome of the Yangtze grenadier anchovy, Coilia Brachygnathus (Clupeiformes: Engraulidae) from the upper Yangtze River

Abstract

The Yangtze grenadier anchovy, Coilia brachygnathus, is a commercial fishery species in the middle and lower Yangtze River of China. Here, we describe a complete mitochondrial genome from the newly found population of C. brachygnahus in the upper Yangtze River. It was 16,857 bp in size and encodes for 2 rRNAs, 22 tRNAs, 13 protein-coding genes as well as a D-loop control region. Phylogenetic analysis confirmed the evolutionary relationship of the C. brachygnathus in the upper Yangtze to other five species of the genus Coillia. The mitochondrial genome would help to elucidate the origin of the new population of C. brachygnathus.

Keywords:

• Coilia brachygnathus
• Three Gorges Reservoir
• mitochondrial genome
• phylogenetic analysis
• upper Yangtze River

Coilia brachygnathu Kreyenberg et Pappenheim (1908), also called Yangtze grenadier anchovy, belongs to the genus Collia with high-economic value and mainly distributed in the Indo-Pacific region. There are 13 species in the genus Coilia worldwide, four of which are found in China. Coilia nasus, C. mystus, C. grayii, and C. brachygnathus are mainly distributed in the coastal areas and the middle and lower reaches of the Yangtze River and its adjoining lakes (Yuan et al. 1980). The genus Coilia generally consists of migratory fish between the river and the sea. However, C. brachygnathus is an exception which is a freshwater resident species mainly found in the tributaries and adjoining lakes of the middle and lower Yangtze River previously (Liu 1995; Jiang et al. 2014; Chen et al. 2016). According to historical documents, there is no record about any one species of the genus Coilia distribution in the upper Yangtze River (Ding 1994). However, we collected 24 specimens of C. brachygnathus in the Three Gorges Reservoir of the upper Yangtze River, Chongqing of China from 2014 to 2018. To our knowledge, this is a newly found population of C. brachygnathus in the upper Yangtze River. The specimens were stored in the Fishes Specimens Room of Southwest University Museum.

In this study, we determined the complete mtDNA sequence of a C. brachygnathu (225.6 mm standard length, 55.58 g mass), which was collected from Wushan（31.07736 N, 109.88955 E）in TGR of Chongqing during May 2017. DNA was extracted from the muscle tissues by the phenol-chloroform extraction procedure (Sambrook and Russell 2001). Twenty-two primer sets were designed to amplify the segments by PCR and the products were sequenced and assembled. The complete mitogenome of the C. brachygnathus was 16,857 bp (GenBank accession No. MK050975) with 13 protein-coding genes, 2 rRNA, 22 tRNA genes and D-Loop region of 1213 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 (Xu et al. 2016). There were seven overlapping sequences between genes. Except for CO I with GTG as a start codon, the remaining 12 protein-coding genes starts with an ATG codon, which is typical in all bony fishes (Boore 1999).

The sequences of four genes, 12S rRNA, 16S rRNA, Cytb and COI of C. brachygnathus and other 7 species including five species from the genus Coilia, including C. nasus, C. mystus, C. grayii, C. lindmani, and C. reynaldi and two species as outgroup, Clupea pallasii and Cyprinus carpio were used for phylogenetic analysis (Figure 1). The results confirmed their phylogenetic relationship. C. brachygnathus is closely related to the C. nasus than other four species in the genus Coilia, within a monophyletic clade. The mitogenome would help to elucidate the origin of the new upstream population of C. brachygnathus.

Figure 1. Phylogenetic tree of six species of the genus Coilia based on the sequences of four mitochondrial genes (12S rRNA, 16S rRNA, Cyt b, and CO I) by Bayesian inference and maximum likelihood methods. Pacific herring, Clupea pallasii from Order Clupeiformes and common carp, Cyprinus carpio from Order Cyprinifomes as outgroup. Phylogenetic analysis confirms that C. brachygnathus (indicated as boxed) belongs to the clade of the genus Coilia and more closely related to the C. nasus. 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. 40810017]; Key R&D Project [cstc2017shms-zdyfX0040] and Basic Research Project [cstc 2015jcyjA80027] from Chongqing Science and Technology Commission.