http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1038789

MITOGENOME ANNOUNCEMENT

The complete mitochondrial genome of the Amur rat-snake Elaphe schrenckii (Squamata: Colubridae) Peng Liu and Wen-Ge Zhao

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College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, P.R. China

Abstract

Keywords

In this study, the whole mitochondrial genome of Elaphe schrenckii (Squamata: Colubridae) is first sequenced. It is a circular molecule of 17,165 bp in size and consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and 2 control regions (CRI and CRII). Except for eight tRNAs and ND6 gene, all other mitochondrial genes were encoded on the heavy strand (H strand). The gene order and orientation of E. schrenckii mitogenome are basically identical to that of other alethinophidian snakes. Mitochondrial genome analyses based on MP, ML and NJ yielded identical phylogenetic trees, indicating a close phylogenetic affinity of 12 species of Colubridae snakes. This study will facilitate the further research of the population genetics of this species and systematic analyses of the genus Elaphe.

Colubridae, Elaphe schrenckii, mitogenome, phylogenetic analysis

The Amur rat-snake (Elaphe schrenckii) belonging to the genus Elaphe of family Colubridae, is a large and slender rat-snake, which is mainly distributed in Northeastern China and Korea (Zhao, 2006). This snake has been listed as Vulnerable (VU) species in China Species Red List (Wang & Xie, 2004). In this study, we determined the complete mitochondrial genome sequences of the Amur rat-snake from China with a muscle sample for the first time using a primer-walking strategy and the long and accurate PCR. The complete mtDNA is 17,165 bp in length and contains 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and two control regions (CRI and CRII), which is similar to that of other reported Colubridae snakes (Chen et al., 2014; He et al., 2010; Jang & Hwang, 2011; Li et al., 2014a,b; Wan et al., 2014; Yan et al., 2014). The accurate annotated mitochondrial genome sequence was submitted to GenBank with accession number KP888955. The overall base composition of H-strand is as follows: A (35.11%), C (25.11.0%), G (14.69%), T (25.08%), with an obvious AT bias (60.19%), as generally shown in other vertebrates’ mitogenomes (Jang & Hwang, 2011). Except ND2 with ATT, COI and ND4L with GTG, ND6 with ATA, the other nine PCGs begin with ATG as start codon. ATP8, ATP6, ND4L, ND4, and ND5 genes are terminated with TAA as stop codon,

History Received 16 March 2015 Revised 1 April 2015 Accepted 5 April 2015 Published online 28 May 2015

COI ends with AGA, ND6 ends with AGG, and the other six PCGs end with an incomplete stop codon (a single stop nucleotide T). In 13 PCGs, the shortest one is ATP8 gene (156 bp in length), and the longest one is ND5 gene (1767 bp in length). The 22 tRNA genes with the size ranging from 54 to 73 bp are interspersed along the whole genome. The sequence length of the 12S and 16S rRNA is 926 and 1483 bp, respectively. The putative origin of L-strand replication (OL) with length of 35 bp in the WANCY cluster of five tRNA genes has the potential to fold into a stem-loop secondary structure that is similar to most vertebrates (Li et al., 2014b). But some peculiar features such as an incomplete copy of tRNA-Pro exists in the 50 end of CRII is not observed in the mitogenome, which has been found in some snakes of Colubridae (He et al., 2010; Yan et al., 2014). Mitochondrial genome analyses based on MP, ML and NJ yielded identical phylogenetic trees, indicating a close phylogenetic affinity of 12 species snakes of Colubridae and a outgroup of Viperidae. The phylogram obtained from NJ method is shown in Figure1. It appeared E. Bimaculata, E. davidi and E. Schrenckii formed a monophyletic group with the high bootstrap value (100%), but E. poryphyracea is a special species. The present study will facilitate the further research of the population genetics of this species and systematic analyses of the genus Elaphe.

Correspondence: Wen-Ge Zhao, College of Life Science and Technology, Harbin Normal University, Harbin 150025, Heilongjiang, China. Tel: +86 451 88060576. Fax: +86 451 88060635. E-mail: [email protected]

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P. Liu & W.-G. Zhao

Mitochondrial DNA, Early Online: 1–2

Figure 1. Phylogenetic tree generated using the NJ method based on complete mitochondrial genomes. Elaphe bimaculata (KM065513.1), Elaphe davidi (KM401547.1), Elaphe schrenckii (KP888955), Orthriophis taeniurus (KC990021.1), Oocatochus rufodorsatus (NC_022146), Elaphe poryphyracea (GQ181130.1), Euprepiophis perlacea (KF750656.1), Dinodon rufozonatum (KJ179950.1), Dinodon semicarinatus (NC_001945), Oligodon ningshaanensis (KJ719252), Sibynophis chinensis (KF360246.1), Sibynophis collaris (JN211315.1), Gloydius ussuriensis (NC_026553).

Acknowledgements We thank Zhong-Bin Yue for collecting specimen of E. schrenckii.

Declaration of interest This work was supported by grants from the National Natural Science Foundation of China (#31172079). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.

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The complete mitochondrial genome of the Amur rat-snake Elaphe schrenckii (Squamata: Colubridae).

In this study, the whole mitochondrial genome of Elaphe schrenckii (Squamata: Colubridae) is first sequenced. It is a circular molecule of 17,165 bp i...
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