Complete mitochondrial genome of the Korean crevice salamander (Karsenia koreana) (Amphibia, Urodela: Plethodontidae)

Abstract

The Korean crevice salamander, Karsenia koreana, is the only known plethodontid salamander in Asia. In this study, we provide the first report of this salamander’s complete mitochondrial genome. The mitogenome had a length of 16,780 bp and consisted of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 2 noncoding regions. The presented sequence may be highly useful for future phylogenetic and evolutionary studies of Plethodontidae.

Keywords:

• Karsenia koreana
• Korean crevice salamander
• mitogenome
• Plethodontidae

The Korean crevice salamander (Karsenia koreana) is the only known Asian plethodontid salamander and is mainly distributed in central South Korea (Min et al. 2005; Lee and Park 2016). Despite multiple recent phylogenetic studies (Vieites et al. 2011; Shen et al. 2016; Wake 2017), this salamander’s phylogenetic location within Plethodontidae and how the current biogeographic distribution of this species was established have not been thoroughly elucidated to date. In 2011, Vieites et al. reported a partial mitochondrial genome sequence of K. koreana; this sequence did not include some cytochrome b sequences, the complete sequences of two tRNAs (tRNA-Pro and -Thr), and a displacement loop region (Vieites et al. 2011). In this study, we provide the first report of the complete mitochondrial genome of K. koreana, which may be useful for future phylogenetic and evolutionary studies of Plethodontidae.

We obtained the complete mitogenome from a specimen of K. koreana collected on Woraksan Mountain in Danyang, Chungbuk, South Korea (36.90°N and 128.28°E). The specimen was preserved in 70% ethanol and stored at the herpetology laboratory of Kangwon National University (Voucher No. G391KK). We extracted whole genomic DNA from the tail tissue of the specimen using Qiagen’s DNeasy Blood & Tissue kit (Qiagen Korea Ltd., Seoul, South Korea) following the manufacturer’s instructions. The whole mitochondrial DNA sequence was sequenced using the HiSeq 2000 platform (Illumina, San Diego, USA). To assemble and annotate the full mitochondrial DNA sequence, we used Geneious 9.0.4 (Biomatters Ltd., Auckland, New Zealand), tRNA Scan-SE1.21 software (http://lowelab.ucsc.edu/tRNA Scan-SE/) (Lowe and Eddy 1997), and Dual Organellar GenoMe Annotator (Wyman et al. 2004). The phylogenetic tree of K. koreana and related plethodontid salamanders was constructed with PAUP* v4.0b10 (Swofford 2003) using the complete mitogenome sequence obtained in this study and complete mitogenome sequences from GenBank (Figure 1). We applied Bayesian inference and maximum likelihood methods to construct the tree using 1000 bootstrap replicates.

Figure 1. Maximum likelihood tree based on the complete mitochondrial genomes of Karsenia koreana and 12 other plethodontid salamanders. We used two species from each of Salamandridae and Proteidae as outgroup taxa. The accession number of each mitogenome is presented after the scientific name of the species. On each branch, the Bayesian posterior probability (above) and bootstrap value (below) are presented.

The mitogenome length of K. koreana was 16,780 bp (GenBank Accession No. MK512368). The base composition of the mitogenome was 33.3% A, 30.6% T, 13.3% G, 22.8% C, revealing an A-T rich (63.9%) structure. The mitogenome contained 13 protein-coding genes, 2 rRNA genes (12S and 16S rRNA), 22 tRNA genes, and 2 noncoding regions of an L-strand replication origin and a displacement loop region. The arrangement pattern and transcription directions of the mitogenome were identical to those of other plethodontid salamanders (Hydromantes brunus and Desmognathus wrighti) reported previously (Mueller et al. 2004).

The phylogenetic tree of K. koreana and related plethodontid salamanders was consistent with the finding of Shen et al. (2016) that K. koreana and the genus Hydromantes in Plethodontinae are not sister taxa. In contrast, Vieites et al. (2011) identified K. koreana and Hydromantes as sister taxa, possibly due in part to their inclusion of only partial tRNA genes and lack of noncoding regions in their analysis. In the present study, the high Bayesian posterior probabilities and bootstrap values of the phylogenetic tree provide strong support for the inclusion of K. koreana in Plethodontinae (Figure 1).

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 study was supported by the research grant of Kangwon National University in 2018.