Skip to main content
NCBI home page
Mitochondrial DNA. Part B, Resources logoLink to Mitochondrial DNA. Part B, Resources
. 2020 Feb 7;5(1):1081–1083. doi: 10.1080/23802359.2020.1723447

Complete mitochondrial genome of Mustela sibirica (Carnivora: Mustelidae), a protected and endangered species in China

Wei Gao a, Zhihao Lu b, Yukang Liang a, Zhu-Mei Ren a,✉
PMCID: PMC7748545  PMID: 33366884

Abstract

We sequenced the complete mitochondrial genome (mitogenome) of Mustela sibirica in China by the shotgun genome skimming methods. The mitogenome of M. sibirica is 16,558bp in length with the base composition of 32.9% A, 27.3% T, 26.0% C, and 13.9% G, and consists of 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and one non-coding control region. The 13 PCGs use ATG as initiation codons except ND3, ND5 and ND2 which initiate with codons ATA and ATT, respectively. Four (COX3, ND1, ND2 and ND4) of the 13 PCGs terminate with a single T– –, and the remainder with a TAA termination codon except ND3 and CYT B using TA– and AGA as termination codon. The phylogenetic tree based on 13 protein-coding genes indicated that M. sibirica is sister to the clade grouped with three species M. nigripes, M. eversmannii, and M. putorius, and Mustelinae species formed a monophyletic group, which is close to the Lutrinae clade within Mustelidae.

Keywords: Mustela sibirica, Mustelidae, mitochondrial genome, phylogeny

The mammal species Mustela sibirica (Carnivora, Mustelidae, Mustelinae) is a medium-sized weasel native to Asia, where it is widely distributed and inhabits various forest habitats and open areas. The distribution range of M. sibirica extends to northern Myanmar, North Korea, Pakistan, Nepal, India, Bhutan, Russia, Taiwan, and northern Thailand (Wilson and Reeder 2005). The species is listed as Least Concern on the IUCN Red List (Abramov et al. 2016). The previous studies on M. sibirica mainly focused on its biological characteristics, ecology, and genetic diversity (Suzuki et al. 2013; Son et al. 2017; Zhao et al. 2019). However, not many studies have examined the complete mitogenome of M. sibirica in Northern China. Here, we sequenced its complete mitogenome to provide more information on the mitochondrial structure, function, and phylogenetic relationship with other members of Mustelidae.

The muscle material was obtained from a dead adult individual of M. sibirica, that was killed by poachers and captured by the forest police in Yangcheng county (112°25′10″E, 35°15′53″N). The specimen (Voucher No. MB-2018M01) and its DNA were stored at the animal herbarium of Manghe National Nature Reserve, Shanxi, China. The genome DNA was sequenced by the shotgun genome-skimming method on an Illumina HiSeq 4000 platform (Zimmer and Wen 2015). The mitogenomic sequence was assembled and annotated within Geneious v11.0.3 using the complete mitogenomes of M. sibirica from GenBank as the references. We also performed de novo assembly using SPAdes v. 3.7.1 (Bankevich et al. 2012).

The complete mitogenome of M. sibirica is a typical circular double-stranded DNA with 16,558bp in length (Accession No. MN206976). The base composition is 32.9% A, 27.3% T, 26.0% C and 13.9% G with the A + T content higher than that of G + C, which is basically consistent with those of other Mustelidae species (Yu et al. 2016). The complete mitogenome of M. sibirica totally included 13 protein-coding genes (PCGs, ND1-ND6, ND4L; COX1-3; ATP6 and ATP8; CYT B), 22 tRNAs, two rRNAs (12S and 16S rRNA) and one non-coding control region (D-loop), among which ND6 and six tRNAs are encoded in the reverse-strand, while the remainder in the forward-strand. The 13 PCGs use ATG as initiation codons except for ND3, ND5 and ND2 initiating with ATA and ATT, respectively. Four PCGs (COX3, ND1, ND2 and ND4) terminate with a single T– –, and the remainingr with a TAA termination codon except for ND3 and CYT B using TA– and AGA as termination codon, respectively.

We downloaded the complete mitogenomic sequences of Mustelidae species from GenBank with Otariidae species Arctocephalus townsendi and A. pusillus as outgroups to construct the phylogenetic relationship using RAxML program under the GTR-GAMMA model with 1000 bootstrap replicates (Stamatakis 2014). The results indicated that M. sibirica is sister to the clade comprised by the three species M. oputorius, M. eversmannii, and M. nigripes, and Mustela species formed a highly supported monophyletic group close to Lutrinae (Figure 1). The mitochondrial genetic information is very crucial not only to contribute with essential data, but to thoroughly understand the evolutionary history and rare genetic resource conservation of Mustelidae.

Figure 1.

Figure 1.

Open in a new tab

Strict consensus tree of Mustela sibirica and other Mustelidae species based on 13 protein-coding genes using RAxML program with Arctocephalus townsendi and A. pusillus as outgroups. Numbers associated with branches are ML-BS > 70 values, and ‘*’ represents nodes with 100% BS.

Funding Statement

This study was partially supported by the National Natural Science Foundation of China [31870366, 31170359], Shanxi International Science and Technology Cooperation Project (2018).

Disclosure statement

No potential conflict of interest was reported by the author(s).

References

  1. Abramov AV, Duckworth JW, Choudhury A, Chutipong W, Timmins RJ, Ghimirey Y, Chan B, Dinets V. 2016. Mustela sibirica. The IUCN Red List of Threatened Species. e.T41659A45214744. 10.2305/IUCN.UK.2016-1.RLTS.T41659A45214744.en. [DOI] [Google Scholar]
  2. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 19(5):455–477. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Son SH, Hwang HS, Lee JK, Eom TK, Park CR, Lee EJ, Kang JH, Rhim SJ. 2017. Influence of tree thinning on the abundance of mammals in a Japanese larch Larix kaempferi plantation. Anim Cells Syst (Seoul). 21(1):70–75. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 30(9):1312–1313. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Suzuki S, Peng JJ, Chang SW, Chen YJ, Wu Y, Lin LK, Kimura J. 2013. Insular variation of the craniodental morphology in the Siberian weasel Mustela sibirica. J Vet Med Sci. 75(5):575–581. [DOI] [PubMed] [Google Scholar]
  6. Wilson DE, Reeder DM. 2005. Mammal Species of the World – A Taxonomic and Geographic Reference. 3rd ed. Baltimore (MD): Johns Hopkins University Press. [Google Scholar]
  7. Yu L, Peng D, Liu J, Luan PT, Liang L, Lee H, Lee M, Ryder OA, Zhang YP. 2016. On the phylogeny of Eurasian badgers (Mustelidae: Melinae): analysis of seventeen nuclear non-coding loci and mitochondrial complete genomes. BMC Evol Biol. 11:29. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Zhao B, Xue S, Zhu W, Lv T, Wei Q, Shang S, Zhang H. 2019. Development of microsatellite markers for the Siberian weasel Mustela sibirica. Genes Genet Syst. 93(6):255–258. [DOI] [PubMed] [Google Scholar]
  9. Zimmer EA, Wen J. 2015. Using nuclear gene data for plant phylogenetics: progress and prospects II. Next-gen approaches. J Syt Evol. 53(5):371–379. [Google Scholar]

Articles from Mitochondrial DNA. Part B, Resources are provided here courtesy of Taylor & Francis

RESOURCES