Complete mitochondrial genome of Capreolus pygargus (Cervidae: Capreolinae), a protected and threatened species in China.

We sequenced the complete mitochondrial genome (mitogenome) of Siberian Roe Deer, Capreolus pygargus, in China by the shotgun genome-skimming methods. The mitogenome of C. pygargus is totally 16,353 bp in length and contains 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. The sequence has a higher A + T content of 63.4% than G + C 36.6% and with a base composition of 33.4% A, 23.2% C, 13.4% G, and 30.0% T. All of the 13 PCGs initiate a typical ATN codon except Nd4L with GTG. Six PCGs terminate with a TAA codon, while Cyt b, Atp8, and Nd1 terminate with AGA, TAG, and TA-, respectively. Whereas, Cox3, Nd2, Nd3, and Nd4 terminate with a single T-. The phylogenetic trees of the subfamily Capreolinae with 13 PCGs indicated that Capreolus species were well-supported as a monophyletic group, which is sister to the clade of Hydropotes with well-support.

Siberian Roe Deer Capreolus pygargus is classified to the tribe Capreolini (Artiodactyla: Cervidae: Capreolinae), and was widely distributed in northeastern Asia, Siberia, Kyrgyzstan, Kazakhstan, and southern Ural Mountains (Bannikov 1954; Dulamtseren et al. 1989). As a widespread and common deer in its range, C. pygargus was listed in IUCN Red List of Threatened Species ver. 3.1 regarded as ‘Least Concern’ (Lovari et al. 2016). Matosiuk et al. (2014) reported the complete mitochondrial genome (mitogenome) of four C. pygargus individuals and analyzed the evolutionary neutrality of the genus Capreolus in Eurasia. So far, there was no study reported on the complete mitogenome of C. pygargus in China. Here, we sequenced the complete mitogenome of C. pygargus (GenBank Accession No. MK795818) in Shanxi, China, and constructed the phylogenetic relationship of C. pygargus and other Capreolinae species combined with the data from GenBank.

The muscle material was obtained from a dead adult individual of Capreolus pygargus that was killed by other animals and found by the forest ranger. The specimen was stored at the Manghe National Nature Reserve, Shanxi, China (Voucher No. Z14). We obtained the mitogenomic sequence of C. pygargus by the shotgun genome-skimming method on an Illumina HiSeq 4000 platform (Zimmer and Wen 2015). We performed the de novo assembly using SPAdes v. 3.7.1 (Bankevich et al. 2012) and annotated the complete mitogenome of C. pygargus within Geneious 11.0.3 using the complete mitogenomes of Capreolus species available from GenBank as references.

The complete mitogenome of Capreolus pygargus is a circular double-stranded DNA with 16,353 bp in length and contains 13 protein-coding genes (PCGs) (Cox1-Cox3, Nd1-Nd6, Nd4L, Atp6, Atp8, and Cyt b), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes (12S and 16S rRNA), and one control region (D-loop). The A + T content of 63.5% (33.5% A; 30.0% T) is much higher than that of G + C (36.5%) (23.2% C; 13.3% G). All the 37 genes are encoded on the H-strand except for eight tRNAs (tRNA-Pro, Cys, tRNA-Ala, tRNA-Tyr, tRNA-Glu, tRNA-Ser, tRNA-Gln, and tRNA-Asn), and one PCG (Nd6). The 13 PCGs initiate with ATN (ATA for Nd2, Nd3 and Nd5, and ATG for Cox1-Cox3, Atp6, Atp8, Nd1, Nd4, Nd6, and Cyt b) except for Nd4L starting with GTG. Six of the 13 PCGs terminate with TAA (Cox1, Cox2, Atp6, Nd4L, Nd5, and Nd6), whereas Cyt b and Atp8 terminate with AGA and TAG, respectively. Moreover, Cox3 and Nd1-Nd4 each terminated with a single T-. The genomic characters are similar to the other Capreolus spsecies (Matosiuk et al. 2014).

Based on the 13 PCGs, we constructed the phylogenetic tree using RAxML program under GTRGAMMA model and with 1000 bootstrap replicates (Stamatakis 2014). The phylogenetic relationship (Figure 1) supported the monophyly of the genus Capreolus, which is sister to the clade comprised by the genus Hydropotes within the same tribe Capreolini. However, two individuals from the species C. capreolus are grouped closely to these of the species C. pygargus, which we should further examine to confirm their classification by more samples and/or more data.

Figure 1.

Phylogenetic tree of Capreolus pygargus and other Capreolinae species inferred from 13 protein-coding genes using maximum-likehood method with Muntiacus crinifrons and Elaphodus cephalophus as outgroups. Numbers associated with branches are ML-BS >70% and “*” represents nodes with 100% BS.