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. 2016 Feb 1;1(1):41–42. doi: 10.1080/23802359.2015.1137813

Sequencing and analysis of mitochondrial genome of Elaphe carinata (Reptilia, Squamata, Colubridae)

Changhong Ding a,*, Bo Zhou a,*, Hui Guo a, Yunbao Duan b, Zhenyue Wang a,✉
PMCID: PMC7800545  PMID: 33473400

Abstract

The complete mitochondrial genome of Elaphe carinata was sequenced and analysed using muscle tissue for the first time. The genome is 17 154 bp in length. The complete mitochondrial genome contains 22 tRNA genes, 13 protein-coding genes (PCGs), two rRNA genes, two control regions (CRI and CRII) and one putative origin of L-strand replication. The gene order and nucleotide composition of E. carinata are very similar with E. davidi, E. schrenckii, E. anomala and E. bimaculata. A phylogenetic tree of mitochondrial genomes analyses of 16 species snakes of Colubridae was made based on the Neighbour-Joining (NJ) method, E. carinata has the most closely relationship with E. davidi, while E. poryphyracea and Euprepiophis perlacea are special species.

Keywords: Elaphe carinata, mitochondrial genome, mitogenome, snake

Elaphe carinata belonging to genus Elaphe of family Colubridae, is a large, ferocious and non-toxic snake, in China is mainly distributed in the south. It can be used for the treatment of epilepsy, pharyngitis, scrofula, scabies and other symptoms. In this study, complete mitochondrial genome of the E. carinata was sequenced and analysed for the first time using muscle tissue obtained from a wild individual (preserved in Traditional Chinese Medicine Resources Laboratory of Heilongjiang University of Chinese Medicine) in Yunnan, China. GenBank accession number KU180459 will be shown after the manuscript is accepted.

Organization of the complete mitochondrial genome sequence of E.carinata is shown in Table 1. Its total length is 17 154 bp. It consists of 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, two control regions (CRI and CRII) and one putative origin of L-strand replication, which is similar to that of other reported snakes (Jang & Hwang 2011; Yan et al. 2014), especially to that of E. davidi (KM401547.1), E. schrenckii (KM888955.1), E. anomala (KM900218.1) and E. bimaculata (KM065513.1). As other vertebrates, most of these genes are coded on the heavy strand except for eight tRNA genes and ND6. The total composition is 25.2% C, 35.8% A, 27.0% T and 12.0% G with an obvious AT bias (62.8%), which is identical to that of other typical vertebrate mitogenomes (Mulcahy & Macey 2009; Jang & Hwang 2011).

Table 1.

Gene organization of the complete mitochondrial genome of E. carinata.

  Position
   Base composition(%)
 Codon
  
Gene Form To Size (bp) T C A G Start Stop Strand
tRNA-Phe 2 62 62 29.0 19.4 35.5 16.1     H
12s rRNA 63 989 927 19.4 25.4 37.8 17.5     H
tRNA-Val 990 1052 63 25.4 22.2 39.7 11.1     H
16s rRNA 1053 2535 1483 22.3 21.3 40.7 14.4     H
ND1 2536 3490 955 27.1 27.3 34.7 10.9 ATG T– H
tRNA-Ile 3491 3556 66 16.7 28.8 27.3 27.3     H
CRII 3557 4598 1042 32.1 27.5 30.0 10.4     –
tRNA-Leu 4599 4671 73 27.0 22.0 39.7 15.1     H
tRNA-Gln 4673 4743 71 28.2 22.5 40.8 8.5     L
tRNA-Met 4745 4806 62 19.4 30.6 29.0 21.0     H
ND2 4807 5838 1032 25.9 26.5 40.1 7.6 ATT TAG H
tRNA-Trp 5837 5901 65 24.6 23.1 36.9 15.4     H
tRNA-Ala 5904 5968 65 26.2 24.6 38.5 10.8     L
tRNA-Asn 5969 6041 73 21.9 27.4 32.9 17.8     L
OL 6042 6076 35 25.7 17.1 31.4 25.7     –
tRNA-Cys 6077 6136 60 25.0 30.0 20.0 25.0     L
tRNA-Tyr 6137 6198 62 32.3 22.6 35.4 9.6     L
COX1 6200 7801 1602 30.0 24.0 30.4 15.6 GTG AGA H
tRNA-Ser 7792 7858 67 32.8 23.9 28.4 14.9     L
tRNA-Asp 7859 7921 63 30.2 22.2 30.2 17.5     H
COX2 7922 8606 685 24.5 25.1 35.4 14.8 ATG T– H
tRNA-Lys 8607 8669 63 33.3 15.9 31.7 19.0     H
ATP8 8671 8826 156 26.3 23.7 45.5 4.5 ATG TAA H
ATP6 8817 9497 681 30.8 23.6 36.7 8.8 ATG TAA H
COX3 9497 10 280 784 26.4 25.6 34.1 13.9 ATG T– H
tRNA-Gly 10 281 10 341 61 26.2 21.3 37.7 14.8     H
ND3 10 342 10 684 343 30.3 23.6 36.2 9.9 ATG T– H
tRNA-Arg 10 685 10 748 64 26.6 21.9 36.0 15.6     H
ND4L 10 749 11 039 291 31.6 20.6 37.1 10.7 ATG TAA H
ND4 11 039 12 376 1338 27.9 27.3 34.8 10.1 ATG TAA H
tRNA-His 12 378 12 440 63 27.0 22.2 36.5 14.3     H
tRNA-Ser 12 441 12 494 54 18.5 35.1 27.8 18.5     H
tRNA-Leu 12 495 12 565 71 26.8 22.5 31.0 19.7     H
ND5 12 566 14 332 1767 27.0 24.5 38.8 9.6 ATG TAA H
ND6 14 328 14 828 501 17.8 26.5 51.3 4.4 ATG AGG L
tRNA-Glu 14 834 14 896 62 27.4 22.6 37.1 12.9     L
Cytb 14 895 16 011 1117 29.0 26.4 34.7 9.8 ATG T– H
tRNA-Thr 16 012 16 076 65 26.2 24.6 29.2 20.0     H
tRNA-Pro 16 077 16 137 61 26.2 29.5 32.8 11.5     L
CRI 16 138 17 154 1017 32.0 27.5 30.2 10.3     –
Total     17 154 27.0 25.2 35.8 12.0      
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As reported in other snakes. Except for ND2 (ATT) and COXI (GTG), the other 11 PCGs use ATG as start codon. When it comes to stop codons, eight PCGs end with the complete stop codon: TAA (ATP8, ATP6, ND4L, ND4 and ND5), TAG (ND2), AGA (COXI), AGG (ND6), while incomplete stop codons T are used in other five PCGs (ND1, ND3, COX2, COX3 and Cytb), which may be completed by posttranscriptional poly-adenylation (Boore 2001).

The mitogenome of E. carinata contains two CRs, surrounded by tRNA-Pro and tRNA-Phe (CRI), and by tRNA-Ile and tRNA-Leu (CRII), respectively. CRI has 1017 bp and CRII has 1042 bp in length, which is identical to that of other typical vertebrate mitogenomes (Li et al. 2014; Liu et al. 2015a, 2015b). The 22 tRNA genes are interspersed along the whole genome. The sequence length of the 12S rRNA and 16S rRNA are 927 and 1483 bp, respectively. The putative origin of L-strand replication (OL) is 35 bp in length, located between tRNA-Asn and tRNA-Cys, which is similar to most vertebrates (Su et al. 2007; Liu et al. 2015a, 2015b).

A phylogenetic tree (Figure 1) of mitochondrial genomes analyses of 16 species snakes of Colubridae was made based on the NJ method, E. carinata has the most closely relationship with E. davidi and formed a monophyletic group with E. davidi, E. schrenckii, E. anomala and E.bimaculata, meanwhile E. poryphyracea and Euprepiophis perlacea are special species.

Figure 1.

Figure 1.

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Phylogenetic tree of mitochondrial genomes analyses of 16 species snakes of Colubridae based on the NJ method.

We hoped that this firstly sequenced and analysis of mitochondrial genome of E. carinata will be conducive to further studies on population genetics, molecular phylogeny and pharmacy of this species.

Acknowledgements

Chang-hong Ding is in postdoctoral mobile station in the Chinese medicine direction of Heilongjiang University Of Chinese Medicine.

Disclosure statement

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

Funding information

This work was supported by the National Natural Science Foundation of China (Grant No.30930700); Science and Technology Research Project of Heilongjiang Province (12531019); Research Foundation of Heilongjiang University Of Chinese Medicine (31158).

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