The complete mitochondrial genome of Acrossocheilus yunnanensis (Teleostei: Cypriniformes: Cyprinidae) and its phylogenetic position.

The complete mitochondrial genome of Acrossocheilus yunnanensis was determined in this study. It contained 13 protein-coding genes (PCGs), 22 tRNA, 2 rRNAs, and a control region with the base composition 31.47% A, 27.83% C, 24.65% T, and 16.05% G. Here we compared this newly determined mitogenome with another one from the same species reported before. The variable sites and the genetic distances between the two mitogenomes were 134 bp and 0.8%. Sixty-five variable sites occurred in the PCGs. The results from the phylogenetic analysis showed that the genus Acrossocheilus is not a monophyletic group and Acrossocheilus yunnanensis demonstrates a close relationship with Acrossocheilus monticola.

Acrossocheilus yunnanensis (Cypriniformes: Cyprinidae: Barbinae) is mainly distributed in the Pearl River and Yangtze River drainages in East Asia (Froese and Pauly 2019). It is an important food source in this region. Here the complete mitochondrial genome sequence of A. yunnanensis was determined (GenBank accession No. MN395748) and was compared with another A. yunnanensis mitogenome data reported before (Wu et al. 2016). The specimens (Voucher No. 20190528005) were collected from Chishui City (28.35 N, 105.42 E), Guizhou Province, China, and were stored in the museum of the Freshwater Fish Research Laboratory (Zunyi Normal College, Guizhou, China). Primers used in this study and methods for collecting DNA sequences followed the procedures outlined in Wang et al. (2011).

The complete mitochondrial genome of A. yunnanensis was a circular molecule with 16,590 bp in length. It contained 13 PCGs, 22 tRNA genes, 2 rRNA genes, and a control region. Most of the genes were encoded on H-strand, while ND6 and 8 tRNA genes were encoded on L-strand. The overall nucleotide composition was 31.11% A, 24.81% T, 27.80% C, and 16.27% G, with a slight AT bias. All the mitochondrial PCGs in the A. yunnanensis use the standard ATG start codon, except for ND3, which utilizes GTG. One PCGs contain TAA stop codon, four contain TAG stop codon and four contain TGA stop codon, while four contain the incomplete stop codon T–.

Comparing with another mitogenome of A. yunnanensis, the length of it was 16,596 bp (accession No. KR062067; Wu et al. 2016). The genetic distance between the two mitogenomes was 0.8%. 11 indels and 134 variable sites exist in between the two mitogenomes. Among these variable sites, 77 transitions (57%) and 57 transversions (43%) were found. There were 65 variable sites appeared in the PCGs and 7 sites in control region. The other 62 variable sites occurred in 12S rRNA, 16S rRNA, and tRNAs.

To confirm the phylogenetic position of A. yunnanensis among the genus Acrossocheilus, phylogenetic analysis based on the complete mitogenome using maximum-likelihood (ML) and Bayesian methods (BI) were conducted using IQ-TREE (Nguyen et al. 2015; Hoang et al. 2018) and MrBayes 3.2.6 (Ronquist et al. 2012), respectively. The ModelTest was used to calculate the optimal nucleotide substitution model (Posada and Crandall 1998). Phylogenetic relationships inferred by the BI and ML methods were congruent, the ML tree is given in Figure. 1. The results from the analyses show that the genus Acrossocheilus is not a monophyletic group and A. yunnanensis demonstrates a close relationship with Acrossocheilus monticola.

Figure 1.

Phylogenetic tree of Acrossocheilus yunnanensis and the other 21 cyprinid species based on maximum-likelihood (ML) method. The ML bootstrap values are shown at the nodes.