Complete mitochondrial genome and phylogenetic analysis of Alpine musk deer (Moschus chrysogaster)

Abstract

In this study, we described the complete mitochondrial genome of Alpine musk deer (Moschus chrysogaster) from China. It has a circular genome of 16,352 bp (GeneBank number: MK697349) with a higher A + T content of 62.06%, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes (12S rRNA and 16S rRNA), and 1 control region (D-loop), which was similar to typical vertebrate mitochondrial DNA. The phylogenetic analysis indicated that our sequence clustered with two Alpine musk deer subspecies from Sichuan, China. The results could provide more molecular information to support the conservation and genetic resources of Alpine musk deer.

Keywords:

• Alpine musk deer
• mitochondrial genome
• phylogenetic analysis

The Alpine musk deer (Moschus chrysogaster) belongs to Moschidae, Artiodactyla, Mammalia, which is distributed in western China, including Tibet, Qinghai, Sichuan, and Gansu (Groves and Grubb 1989; Sheng 1992; Smith et al. 2009). Apline musk deer are generally solitary animals whose habitat is in coniferous forest, alpine shrubs at an altitude of 3000–5000 m (Meng et al. 2003). Due to the large amount of musk collection and habitat destruction, now, there are no more than 1000 wild individuals (Sheng 1998; Meng et al. 2003; Yang et al. 2003). It is now listed as a threatened species in the Red List by the International Union for the Conservation of Nature and Natural Resources (IUCN), and classified as national first class protected animal in China. The taxonomy of musk deer remains debatable (Flerov et al. 1952; Groves et al. 1995; Yang et al. 2013). However, Grove and Feng (1986) believed that Tawny Musk Deer (Moschus fuscus) and Himalayan Musk Deer (Moschus chrysogaster) (Harris 2016) were subspecies of Apline Musk Deer.

Mitochondrial DNA is a powerful molecular tool for phylogenetic analysis and genetic diversity assessment of animals, there are currently only four complete mitochondrial genome (mitogenome) sequences reported about Alpine Musk Deer in GeneBank (Zhu et al. 2013). Here, we obtained a muscle sample of Apline Musk Deer from the forest public security of Baoxing county (N30°22′14.87″, E102°48′46.56″), which is located in the Hengduan Mountains between the Qinghai-Tibet Plateau and the Sichuan Basin. The sample was stored at zoology laboratory, Sichuan Agricultural University (Accession: sicau-lz-A596). Total genomic DNA was extracted by standard phenol–chloroform extraction (Sambrook and Russell 2001). We designed 11 primer pairs to amplify the complete Alpine Musk Deer mitochondrial genome.

The complete Alpine Musk Deer mitochondrial genome (GenBank number: MK697349) was 16,352 bp with an enriched A + T (62.06%). It is similar to most vertebrates, and the overall base composition was: A, 33.96%；T, 28.10%; G, 12.92%; and C, 25.02%. The complete sequence contained 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes (12S rRNA, and 16S rRNA), and one control region (D-loop). ND6 and eight tRNA genes were encoded on the light strand, other PCGs were distributed on the heavy strand. Most PCGs used the initiation codon ATG and ATT except ND3, which used ATA; 12 of the PCGs used complete (TAA) or incomplete (T– –) as stop codon; and the cytochrome b (Cytb) gene ended with AGA.

To further explore the taxonomic status of Alpine musk deer, a maximum likelihood (ML) phylogenetic tree was reconstructed in MEGA7.0, using an alignment comprising 19 complete mitogenome sequences from Artiodactyla, including two reported complete mitochondrial genome (mitogenome) sequences about Alpine Musk Deer and a Lesser Kudu (Tragelaphus imberbis) (LN873135) as an outgroup (Figure 1). According to the ML tree, genus Moschidae and genus Cervidae clustered into two different branches. Our sequence was more closely related to the Anhui Musk Deer (Moschus anhuiensis) species. The result could provide more molecular information which can be used for the taxonomic classification and conservation.

Figure 1. Maximum likelihood (ML) phylogenetic tree of Alpine musk deer (Moschus chrysogaster) and the other 18 sequences from the order Artiodactyla with a sequence of Lesser Kudu (Tragelaphus imberbis) (LN873135) as an outgroup. Number at each node indicates the bootstrap support values. GenBank accession numbers are given in the brackets after the species name. The sequence characterized in this study is annotated with a black circle symbol.

Acknowledgements

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

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

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