Sequencing and analysis of the complete mitochondrial genome of the large mole (Mogera robusta) from China

Abstract

The complete mitogenome sequence of the large mole (Mogera robusta) was determined using long PCR. The genome was 16,890 bp in length and contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, one origin of L strand replication, and one control region. The overall base composition of the heavy strand is A (35.2%), C (22.8%), T (29.1%), and G (12.9%). The base compositions present clearly the A–T skew, which is most obviously in the control region and protein-coding genes. Mitochondrial genome analyses based on MP, ML, NJ, and Bayesian analyses yielded identical phylogenetic trees. The two Mogera species formed a monophyletic group with the high bootstrap value (100%) in all examinations.

Keywords:

• Control region
• mitogenome
• phylogenetic trees
• the large mole

In this paper, the complete mitochondrial genome of the large mole (Mogera robusta) was sequenced for the first time on ABI 3730XL using a primer walking strategy and the long and accurate PCR, with five pairs of long PCR primers and with 14 pairs of sub-PCR primers. A muscle sample was obtained from a female the large mole captured from Hengdaohezi regions of Changbaishan Mountains in Heilongjiang Province, China (44°48′44″ N, 129°02′04″ E). The muscle tissue was preserved in 95% ethanol and stored at −75 °C before use. The specimen and its DNA is stored in Animal and Plant Herbarium of Mudanjiang Normal University. The voucher number is Q201702.

The mitochondrial genome is a circular double-stranded DNA sequence that is 16,890 bp long including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, one origin of L strand replication, and one control region. The accurate annotated mitochondrial genome sequence was submitted to GenBank with accession number MK431828. The arrangement of the multiple genes is in line with other Talpidae species (Mouchaty et al. 2000; Nikaido et al. 2003; Cabria et al. 2006; Hou et al. 2016; Xu et al. 2016; Gutiérrez et al. 2018; Jia et al. 2018) and most mammals (Nikaido et al. 2001; Fontanillas et al. 2005; Meganathan et al. 2012; Yoon et al. 2013; Xu et al. 2012, 2013; Kim et al. 2013, 2017; Huang et al. 2014, 2016; Xu et al. 2016; Liu et al. 2016; Liu, Tian, Jin, Jin, et al. 2017; Liu, Tian, Jin, Dong, et al. 2017; Liu, Wang, et al. 2017; Liu, et al. 2018; Liu, Dang, et al. 2019; Liu, Qin, et al. 2019; Jin et al. 2017).

The control region of the large mole mitochondrial genome was located between the tRNA-Pro and tRNA-Phe genes, and contains only promoters and regulatory sequences for replication and transcription, but no structural genes. Three domains were defined in the large mole mitochondrial genome control region (Zhang et al. 2009): the extended termination-associated sequence (ETAS) domain, the central conserved domain (CD) and the conserved sequence block (CSB) domain.

The total length of the protein-coding gene sequences was 11,409 bp. Most protein-coding genes initiate with ATG except for ND2, ND3 and ND5, which began with ATA or ATT. Seven protein-coding genes terminated with TAA whereas the Cyt b gene terminated with AGA. The incomplete stop codons (T– – or TA–) were used in ND1, COX3, ND3 and ND4. A strong bias against A at the third codon position was observed in the protein-coding genes. The frequencies of CTA (Leu), ATT (Ile), TTA (Leu), and ATA (Met) were higher than those of other codons. The length of tRNA genes varied from 62 to 73 bp.

Most the large mole mitochondrial genes were encoded on the H strand, except for the ND6 gene and eight tRNA genes, which were encoded on the L strand. Some reading frame intervals and overlaps were found. One of the most typical was between ATP8 and ATP6. The L-strand replication origin (OL) was located within the WANCY region containing five tRNA genes (tRNATrp, tRNA-Ala, tRNA-Asn, tRNA-Cys, tRNA-Tyr). This region was 38 bp long and had the potential to fold into a stable stem-loop secondary structure. The total base composition of the large mole mitochondrial genome was A (35.2%), C (22.8%), T (29.1%), and G (12.9%). The base compositions clearly present the A-T skew, which was most obviously in the control region and proteincoding genes.

In order to explore the evolution of Insectivora shrews which include Soricidae and Talpidae, especially the evolution of genus Mogera from China, here, we investigate the molecular phylogenetics of Chinese the large mole using complete mitochondrial genome sequence of 34 species. All sequences generated in this study have been deposited in the GenBank (Figure 1)

Figure 1. Phylogenetic tree generated using the Maximum Parsimony method based on complete mitochondrial genomes. Crocidura lasiura (KR007669), Crocidura shantungensis (JX968507), Crocidura attenuata (KP120863), Crocidura russula (AY769264), Episoriculus macrurus (KU246040), Episoriculus caudatus (KM503097), Neomys fodiens (KM092492), Nectogale elegans (KC503902), Anourosorex squamipes (KJ545899), Blarinella quadraticauda (KJ131179), Suncus murinus (KJ920198), Soriculus fumidus (AF348081), Sorex araneus (KT210896), Sorex cylindricauda (KF696672), Sorex unguiculatus (AB061527), Sorex tundrensis (KM067275), Sorex caecutiens (MF374796), Sorex roboratus (KY930906), Sorex isodon (MG983792), Sorex gracillimus (MF426913), Sorex mirabilis (MF438265), Sorex daphaenodon (MK110676), Sorex minutissimus (MH823669), Talpa europaea (Y19192), Urotrichus talpoides (AB099483), Uropsilus soricipes (JQ658979), Uropsilus gracilis (KM379136), Mogera wogura (AB099482), Mogera robusta (MK431828), Condylura cristata (KU144678), Galemys pyrenaicus (AY833419), Scapanulus oweni (KM506754), Talpa occidentalis (MF958963), Uropsilus andersoni (MF280389), and Erinaceus europaeus (NC002080).

Mitochondrial genome analyses based on MP, ML, NJ, and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of shrews. The phylogram obtained from Maximum Parsimony method is shown in Figure 1. It shows that two major phyletic lineages were present in Insectivora: Soricidae and Talpidae. Soricidae comprised Crocidura lasiura, Crocidura shantungensis, Crocidura attenuata, Crocidura russula, Episoriculus macrurus, Episoriculus caudatus, Neomys fodiens, Nectogale elegans, Anourosorex squamipes, Blarinella quadraticauda, Soriculus fumidus, Suncus murinus, Sorex araneus, Sorex tundrensis, Sorex caecutiens, Sorex roboratus, Sorex isodon, Sorex gracillimus, Sorex mirabilis, Sorex cylindricauda, Sorex unguiculatus, Sorex daphaenodon and Sorex minutissimus was supported by bootstrap values of 100%. Talpidae comprised Talpa europaea, Urotrichus talpoides, Mogera wogura, Condylura cristata, Uropsilus soricipes, Mogera robusta, Galemys pyrenaicus, Uropsilus gracilis, Talpa occidentalis, Uropsilus andersoni and Scapanulus oweni was supported by bootstrap values of 100%. The 10 Mogera species formed a monophyletic group with the high bootstrap value (100%) in all examinations.

Disclosure statement

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.

Additional information

Funding

This research was supported by the Mudanjiang Normal University Project [PT2018007], Heilongjiang Provincial Natural Funds [C2017065], and the Doctoral Scientific Research Foundation Project of Mudanjiang Normal University [MNUB201404].