Complete mitochondrial genome of a dwarf blue sheep (Pseudois schaeferi) and its phylogenetic analysis

Abstract

The dwarf blue sheep (Pseudois schaeferi) belongs to the subfamily Caprinae within the Cetartiodactyla. Here, we report on the complete mitochondrial genome of a dwarf blue sheep from Nangqian of Qinghai, China. The genome (MK087727) has a length of 16,709 bp and exhibits the typical structure of mammalian mitochondrial genomes. Phylogenetically, the new dwarf blue sheep formed a strongly supported sister lineage to the previously reported P. schaeferi (JQ040802). These results support for dwarf blue sheep as a subspecies of Pseudois nayaur and provide more molecular data for conservation of the endemic species.

Keywords:

• Dwarf blue sheep
• mitochondrial DNA
• phylogenetic analysis
• Pseudois schaeferi

The dwarf blue sheep (Pseudois schaeferi) belongs to the subfamily Caprinae within the Cetartiodactyla and is endemic species in China. It is distributed in Sichuan, Tibet, Yunnan, and Qinghai in China (Wu et al. 1990; Wang and Wang 2003). Due to over-hunting and habitat degradation, dwarf blue sheep is in a very low density, thus classified as Endangered (EN) in the Red List by the International Union for Conservation of Nature (Wang et al. 2000; Huffman and Harris 2014). It has been recognized as a full species (Wang and Hoffman 1987; Wang et al. 2000; Liu et al. 2007), recent molecular evidence suggests that the most appropriate categorization is as a subspecies of Pseudois nayaur (Zeng et al. 2008; Tan et al. 2012). Only one complete mitochondrial genome of dwarf blue sheep was reported (Liu et al. 2016), thus more molecular data need to be provided for the taxonomic classification and conservation of the rare species.

We report on the sequencing of a mitochondrial genome of a dwarf blue sheep generated from what was collected from Nangqian of Qinghai (N31°32′, E95°21′) and the fecal sample was kept in the laboratory of zoology, Sichuan agricultural university, China. Total genomic DNA was extracted with the QIAamp DNA Stool Mini Kit (Comwin Biotech, Beijing, CHN) following the standard protocol. We designed 17 pairs of primer and amplified dwarf blue sheep mitogenome successfully.

The mitogenome of dwarf blue sheep has a circular genome of 16,709 bp (GenBank accession number MK087727). The overall base composition of the mitogenome was biased toward A + T content at 59.76% (A: 33.40%, T: 26.39%, C: 26.90%, and G: 13.30%). It includes 13 protein-coding genes (PCGs), 22 transfer RNAs, 2 ribosomal RNAs, and the control region in the order typically found in mammals (Anderson et al. 1981). All the PCGs were distributed on the H-strand, except for the ND6 gene and 8 tRNA genes which were encoded on the L-strand. The lengths of 12S rRNA and 16S rRNA were 957 bp and 1574 bp and separated by the tRNA^Val gene. The control region (D-Loop) locates between tRNA^Pro and tRNA^Phe, the length is 1062 bp from 15435 to 16496bp.

To further explore the taxonomic status of dwarf blue sheep, a maximum likelihood (ML) phylogenetic tree (Figure 1) was reconstructed in MEGA7.0 (Kumar et al. 2016). The phylogenetic analysis included the complete mitochondrial genomes of one dwarf blue sheep, four blue sheep (P. nayaur), and other six Caprinae species, using the water buffalo (Bubalus bubalis) as an outgroup. The newly generated mitochondrial genome formed a strongly supported sister lineage to the previously reported P. schaeferi (JQ040802). Compared with the P. n. szechuanensis (KP998469), the newly generated mitochondrial genome is 98% similar and 328 variable sites in total. The genus Pseudois group was clustered together, indicating that P. schaeferi may be a subspecies of Pseudois nayaur. The evolutionary relationships of these analyzed species are consistent with previously reported results (Zeng et al. 2008; Tan et al. 2012). The complete mitochondrial genome sequence provides more molecular data for the taxonomic classification and conservation of the endemic species.

Figure 1. Maximunm likelihood (ML) phylogenetic tree of the complete mitochondrial genomes. One dwarf blue sheep, four blue sheep (Pseudois nayaur), and other six Caprinae species, using the water buffalo (Bubalus bubalis) as an outgroup. Number at each node indicates the ML bootstrap support values. The solid circle represents the sequence in this study. GenBank accession numbers are given after the species name.

Acknowledgements

We thank Qian Su, Xue Liu, Pu Zhao, and Yuhan Wu for their assistance in the laboratory.

Disclosure statement

The author reports no conflicts of interest. The author alone is responsible for the content and writing of the paper.

Additional information

Funding

This work was supported by the National Natural Science Foundation of China [31370407].