Abstract
The long polymerase chain reaction and primer walking method were applied for the sequencing of the complete mitochondrial genome sequence of a cyprinid species (Metzia longinasus) collected from the Hongshuihe River of the Pearl River drainage, Guangxi Province in China. It is 16,614 bp in length, containing 2 rRNA, 22 tRNA, 13 protein-coding genes and 1 control region generally found in most vertebrates. Most of the mitochondrial genes are encoded on the heavy strand except for eight tRNA and ND6 genes. The base composition of this genome was 31.9% A, 26.2%C, 26.2%T and 15.7%G, showing a lower level of G (15.7%) and a slighter AT bias (58.1%). This is the 2nd completely sequenced mitogenome from genus Metzia. The mtDNA sequence of M. longinasus shared 93% sequence similarity with that of M. formosae and it could contribute to a better solution of its phylogenetic position within cyprinid fishes based on the complete mitogenomic data.
Metzia longinasus (Teleostei, Cypriniformes) is a newly discovered species from Hongshuihe River of the Pearl River drainage at Du’an County, Guangxi Province in China (Gan et al., Citation2009). Here, we obtained its complete mitochondrial genome based on the long PCR technique (Miya & Nishida, Citation1999) with the universal primers used in previous study (Wang et al., Citation2011). We annotated the genome sequence using DOGMA (Wyman et al., Citation2004; Austin, TX) and the GenBank accession number for the species is KF955011.
The length of the complete mitochondrial genome of M. longinasus is 16,614 bp and the gene order and structure are fairly similar to most other fishes (Huang et al., Citation2012; Peng et al., Citation2006). It is a circular molecule that consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region (). The coding strands of these genes are also identical to other fishes: ND6 gene and eight tRNA genes (tRNA-Gln, Ala, Asn, Cys, Tyr, Ser, Glu and Pro) by L-strand and the others by H-strand.
Table 1. Characteristics of the mitochondrial genome of Metzia longinasus.
Currently, there is only one complete mitogenome sequence data from the genus Metiza available for comparison (M. formosae; Lin et al., Citation2013). The total length of the mitogenome for the two species was identical. The initiation codon and stop codon of the 13 protein-coding genes in the two mitogenomes were also identical except for the incomplete stop codon of COIII which was “T” for M. formosae, while for M. longinasus it was “TA”. As for the other genes, five protein-coding genes (ND2, COII, ND3, ND4 and cytb) were terminated with incomplete stop codon “T” or “TA” and the typical stop codon “TAA” was used for ND1, COI, ATP6, ND4L, ND5, and ND6, while the ATP8 was terminated by “TAG”. Six genes/segments (12S rRNA, 16S rRNA, tRNA-Ala, tRNA-Asp, tRNA-Pro and D-loop) are variant at length, while the remaining genes of the two species had the same sequence length. Meanwhile, MEGA5 (Tamura et al., Citation2011; Tempe, AZ) was used to analyze the variable sites between the two sequences. There were 1140 substitution sites between them with approximately 6.9% sequence divergence.
Based on the previous studies (Dai & Yang, Citation2003; Gaubert et al., Citation2009; Yue & Luo, Citation1996), the phylogenetic position of the genus Metiza was not well resolved. Furthermore, the monophyly of Meztia was also questioned by Shibukawa et al. (Citation2012). Thus we expected that the complete mitochondrial genome sequence of M. longinasus could make some contributions towards the phylogeny reconstruction of Metiza.
Declaration of interest
The authors declare no conflict of interest. The authors alone are responsible for the content and writing of the paper.
Acknowledgements
The authors thank Mr. Jiahu Lan for the sample collections. The authors also thank Ms. Jinfeng Zhao and Yanping Li (Southwest University School of Life Sciences) for the assistance with the laboratory work.
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