The complete mitochondrial genome sequence of Chimarrogale leander (Insectivora: Soricidae)

Introduction

The Asiatic water shrew, Chimarrogale leander, belongs to the family Soricidae and is mainly distributed in southern China (Thomas 1902). They have large bodies, long noses, small eyes, well-developed ears, and hairy fingers, feet, and toes. They inhabit by mountain streams, swimming or diving in water (Wang 1986). In order to further understand its mitochondrial genome characteristics, phylogeny and evolutionary characteristics, this paper carried out its genomic analysis and characterized it.

Methods

This experiment complies with Anhui University GB/T35892-2018 Guidelines for Ethical Review of Laboratory Animal Welfare. The approval committee name is Experimental Animal Ethics and Management Committee of Anhui University the approval number is IACUC (AHU)-2022-044, and approval date is April 13, 2022. The ethical approval included permission for us to take and sacrifice the animal.

A specimen of C. leander was collected from Yaoluoping Nature Reserve (N: 30°57′57.06″, E: 116°04′04.96″) in the Dabie Mountains, Anhui, China and stored in Anhui University Museum (contact person and email: Baowei Zhang, zhangbw@ahu.edu.cn) under the voucher number AHU2010YLP01. We compared the morphological characteristics of the specimens and found that they were similar to C. leander (Wang 1986). Then DNA was extracted and PCR reaction was carried out. Blast comparison was carried out to ensure that this species belongs to C. leander. The genomic DNA extraction, library preparation and Illumina sequencing were done by Novogene Bioinformatics Technology Co., Ltd. (Tianjin, China).

We sequenced the data using the Illumina HiSeq™ 2000 platform, pruned the sequencing results using Trimmomatic software (RRID:SCR_011848) (Bolger et al., 2014), and assembled them using the MITObim program (RRID:SCR_015056) (Hahn et al., 2013). The annotation was performed using MITOS WebServer (Bernt et al., 2013) for the entire mitogenome of C. leander, and manually adjusted it according to the published mitogenomes of the Soricidae family and submitted the complete sequence of mitochondrial gene to GenBank (Accession number ON646617).

To better understand the phylogenetic position of C. leander within Soricidae, we constructed a phylogenetic tree by using maximum likelihood (ML) method implemented in IQ-TREE v2.1.2 (RRID:SCR_017254) (Minh et al., 2020), which was based on 13 complete mitochondrial genome sequences of Soricidae. There was another species (Mogera wogura) included as the outgroup (GenBank accession numbers are shown in Figure 1).

Figure 1. The Phylogenetic tree of C. leander with ML based on the complete mitochondrial sequence.

ML analysis shows startup support values sequentially on nodes. ML, maximum likelihood.

Results

The complete mitochondrial DNA (mtDNA) sequence of C. leander is a circular molecule, 17,357 bp in length and included 13 protein-coding genes, two rRNAs genes, 22 tRNAs genes and a D-loop region. The overall nucleotide composition is A: 33.1%, T: 31.5%, C: 22.5% and G: 12.9%, with a total A + T content of 64.6%. The mitogenome of C. leander shows the typical gene order observed in Soricidae mitogenomes (Li et al., 2016; Qing et al., 2019; Wang et al., 2016). Within 37 mitochondrial genes, the ND6 gene and eight tRNA genes (tRNA^Gln, tRNA^Ala, tRNA^Asn, tRNA^Cys, tRNA^Tyr, tRNA^Ser, tRNA^Glu and tRNA^Pro) were encoded on the light strand and all other genes were encoded by the H-strand. Most mitochondrial protein-coding genes, have ATG as its start codon, whereas ND2 (1,042 bp), ND3 (348 bp) and ND5 (1,820 bp) begin with ATA. Eight genes use TAA as stop codons, whereas the ND1 (955 bp) and ND2 end with TAG, and Cyt b (1,140 bp) ends with AGA. COX3 (785 bp) uses TA, and ND4 (1378 bp) uses T as an incomplete stop codon, which are presumably completed as TAA by posttranscriptional polyadenylation (Ojala et al., 1981). In all 13 protein-coding genes, the shortest gene is ATP8 (204 bp) and the longest gene is control region (D-loop) (1,864 bp). The two rRNA genes were 968 bp (rrnS) and 1,564 bp (rrnL) in length, respectively.

The phylogenetic results show that C. leander is closely related to Nectogale elegans and these are sister to two species of Chodsigoa (Huang et al., 2014; Pu et al., 2019; Qing et al., 2019). Overall, the relationships inferred agree with those of Dubey et al. (2007). Mitochondrial DNA is a powerful tool for studying the evolution of the genome, which can help us speculate about evolution in ancient times (Boore 1999). This study provides useful data for further study of population evolution and phylogenetic relationships.

Data availability