The complete mitochondrial genome and phylogenetic analysis of Rhabdophis adleri (Squamata: Colubridae)

Abstract

The study has determined the complete mitochondrial genome sequence of the Rhabdophis adleri. The mitogenome was 17,505 bp in size, containing 26.33% T, 27.08% C, 33.38% A, and 13.21% G, 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, as well as 2 Dloop regions. The gene arrangement, nucleotide composition, and the codon usage pattern of the mitochondrial genome of R. adleri were alike in other alethinophidian snakes. The phylogenetic reconstruction analyses yielded similar topologies, having been expressed that R. adleri can strongly be placed within Colubridae.

Key Words:

• Rhabdophis adleri
• mitochondrial genome
• phylogenetic analysis

Rhabdophis adleri is an endemic snake species of Hainan, China (Zhao 1997), has since been considered a terrestrial wild animal with important economic and scientific value since 2000 (Li 2011). The validity of R. adleri was explored by morphological characteristics, distribution (Zhao 1997), hemipenial morphology (Zhu et al. 2013), nuchal and nucho-dorsal glands (Mori et al. 2016), but little is known to the complete mitochondrial DNA of R. adleri. Mitochondrial DNA is widely used molecular marker for estimating phylogenetic relationships in animals (Lin and Danforth 2004; Gissi et al. 2008). In present study, the complete mitogenome of R. adleri was sequenced and annotated, its main features were provided. We further discussed the phylogenetic relationships of the snakes based on the protein-coding sequences.

The specimen of R. adleri (ZGX125, Zhu GX Field tag, stored in the zoological specimens room, College of Life Science, SICAU) was collected from Five Finger Mountain (Mt. Wuzhi, 18°43′41″N, 109°51′48″E), Hainan Province. The total genomic DNA was extracted from the muscle of R. adleri using Genomic DNA Extraction Kit according to the instruction. Sixteen pairs of primers were performed to amplify contiguous, overlapping segments covering the complete mitogenome of R. adleri. The mitogenome sequence and protein-coding genes were assembled and analyzed by MEGA 5.0 (Tamura et al. 2011). Phylogenetic analysis by BI was carried out using MrBayes 3.1.2 (Huelsenbeck and Ronquist 2001) and ML analysis was performed using PAUP4.0b10 (Swofford 2003) (Figure 1).

Figure 1. Molecular phylogenetic tree of 42 snake species. Values on the nodes indicate bootstrap and posterior probability support (BS/PP), ★ indicated Rhabdophis adleri.

Total length of the R. adleri mitochondrial genome was 17,505 bp, and it was a typically circular molecular. Total base composition was 26.33% T, 27.08% C, 33.38% A, and 13.21% G. It contained 37 typical mitochondrial genes (13 PCGs, 22 tRNAs, and 2 rRNAs) and two control regions (Dloop1 and Dloop2). Most mitochondrial genes were encoded on the H-strand, except for the ND6 and nine tRNA genes: tRNA^Gln, tRNA^Ala, tRNA^Asn, tRNA^Cys, tRNA^Tyr, tRNA^Ser (UCN), tRNA^Glu, tRNA^Thr, and tRNA^Pro, which were encoded on the L-strand. The gene order, orientation and nucleotide composition were similar to the previously published Colubrinae mitogenomes (Li et al. 2016; Peng et al. 2016; Weng et al. 2016). The 12S rRNA(928 bp) was located between tRNA^Phe and tRNA^Val, while 16 S rRNA (1447 bp) was between tRNA^Val and ND1. Dloop1 was located between tRNA^Pro and tRNA^Phe, while Dloop2 was between tRNA^Ile and tRNA^Leu (UUR). Like most snakes in the current study, the mitochondrial genome of R. adleri contained a duplicated Dloop region between ND1 and ND2, except some scolecophidian snakes that had only one Dloop region (He et al. 2010).

The phylogenetic position of R. adleri was constructed using the 12 concatenated protein-coding genes. The results indicated that all analyses produced four major groups, the Iguanidae (the out group), Colubridae, Elapidae and Viperidae (Figure 1). Rhabdophis adleri and R. tigrinus formed a single monophyletic group, and belonged to Colubridae (Zhao 1997; Zhao et al. 2016). Our study first revealed complete mitochondrial genome of R. adleri, which can contribute to the conservation of this important economic and scientific wild animal’s genetic resources.

Acknowledgements

We thank Dr. Jichao Wang and Ling Ding for their assistance in sample collection.

Disclosure statement

The authors declare that they have no competing interests. The authors alone are responsible for writing of this paper.

Additional information

Funding

This work was supported by a grant of the National Natural Science Foundation of China (NSFC31401959) and Certificate of China Postdoctoral Foundation Grant to Zhu GX (2016M592688).