Abstract
The complete mitochondrial genome sequence of the Ptyas mucosus was sequenced and reported for the first time using muscle tissue. The total length is 17 151 bp and sequence analysis showed its structure is in accordance with other snakes. The complete mitochondrial genome contains 2 rRNA genes, 21 tRNA genes, 13 protein-coding genes (PCGs), 2 control regions and 1 putative origin of L-strand replication. The gene order and nucleotide composition of P. mucosus are very similar with E. bimaculata, E. anomala and E. schrenckii. A phylogenetic tree of mitochondrial genomes indicated P. mucosus had the most closely relationship with E. bimaculata, and formed a monophyletic group with E. bimaculata, E. anomala and E. schrenckii.
Keywords: Mitochondrial genome, phylogenetic tree, Ptyas mucosus, snake
In this study, the complete mitochondrial genome sequence of Ptyas mucosus was sequenced and reported 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 Guangxi, China (E109°08′48.12″, N25°20′38.54″). P. mucosus belongs to the family Colubridae, in China is mainly distributed in the south, with fierce personality and fast attack speed, preying on rodents, toads, frogs, lizards and other snakes. It can be used as medicine with effects of treating rheumatic arthritis and nameless pain. We hope this firstly sequenced P. mucosus mitogenome sequence will be conducive to further studies on molecular phylogeny, conservation biology and pharmacy.
The complete mitochondrial genome sequence of P. mucosus was deposited in GeneBank after accurately annotated with the accession number KT982276. Its total length is 17 151 bp and sequence analysis showed is in accordance with other snakes (Yan et al. 2016; Liu & Zhao 2015a, 2015b) which contains 2 rRNA genes, 21 tRNA genes, 13 protein-coding genes(PCGs), 2 control regions and 1 putative origin of L-strand replication (OL) (Table 1). The total composition is 25.2% C, 35.8% A, 27.1% T and 11.9% G, and a strong A-T bias (54.4%) is found, which is identical to that of the typical vertebrate mitogenome (Mulcahy & Macey 2009; Jang & Hwang 2011).
Table 1.
Characteristics of the complete mitochondrial genome of P. mucosus.
| Position |
Base composition (%) |
Codon |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Gene | Form | To | Size(bp) | T | C | A | G | Start | stop | strand |
| tRNA-Phe | 2 | 62 | 62 | 35.5 | 29.0 | 16.1 | 19.3 | H | ||
| 12s rRNA | 63 | 989 | 927 | 37.8 | 19.4 | 17.5 | 25.3 | H | ||
| tRNA-Val | 990 | 1052 | 63 | 39.1 | 22.0 | 11.0 | 23.4 | H | ||
| 16s rRNA | 1053 | 2535 | 1483 | 40.6 | 22.4 | 15.5 | 21.4 | H | ||
| ND1 | 2536 | 3490 | 955 | 34.7 | 27.1 | 10.9 | 27.3 | ATG | T– | H |
| CRII | 3491 | 4597 | 1107 | 31.2 | 27.5 | 30.2 | 11.2 | – | ||
| tRNA-Leu | 4598 | 4670 | 73 | 39.7 | 23.2 | 15.0 | 21.9 | H | ||
| tRNA-Gln | 4672 | 4742 | 71 | 8.4 | 28.1 | 40.8 | 22.5 | L | ||
| tRNA-Met | 4744 | 4805 | 62 | 19.4 | 30.6 | 29.0 | 20.9 | H | ||
| ND2 | 4806 | 5837 | 1032 | 40.1 | 25.8 | 7.5 | 26.4 | ATT | T– | H |
| tRNA-Trp | 5838 | 5900 | 65 | 36.9 | 24.6 | 15.3 | 23.0 | H | ||
| tRNA-Ala | 5903 | 5966 | 64 | 39.0 | 26.5 | 10.9 | 23.4 | L | ||
| tRNA-Asn | 5968 | 6040 | 73 | 32.8 | 21.9 | 17.8 | 27.3 | L | ||
| OL | 6041 | 6075 | 35 | 25.7 | 17.1 | 31.4 | 25.7 | – | ||
| tRNA-Cys | 6076 | 6135 | 60 | 20.0 | 25.0 | 25.0 | 30.0 | L | ||
| tRNA-Tyr | 6136 | 6197 | 62 | 35.4 | 32.2 | 9.6 | 22.5 | L | ||
| COX1 | 6199 | 7799 | 1602 | 30.2 | 29.8 | 15.5 | 24.0 | GTG | AGA | H |
| tRNA-Ser | 7790 | 7857 | 67 | 26.0 | 30.1 | 13.6 | 23.2 | L | ||
| tRNA-Asp | 7858 | 7920 | 63 | 26.0 | 30.1 | 13.6 | 23.2 | H | ||
| COX2 | 7921 | 8605 | 685 | 35.4 | 24.5 | 14.8 | 25.1 | ATG | T– | H |
| tRNA-Lys | 8606 | 8668 | 63 | 31.7 | 33.3 | 19.0 | 15.8 | H | ||
| ATP8 | 8670 | 8825 | 156 | 45.5 | 26.2 | 4.4 | 23.7 | ATG | TAA | H |
| ATP6 | 8816 | 9496 | 681 | 36.7 | 30.8 | 8.8 | 23.6 | ATG | TAA | H |
| COX3 | 9496 | 10 279 | 784 | 34.0 | 26.4 | 13.9 | 25.6 | ATG | T– | H |
| tRNA-Gly | 10 280 | 10 340 | 61 | 37.7 | 26.2 | 14.7 | 21.3 | H | ||
| ND3 | 10 341 | 10 683 | 343 | 36.1 | 30.3 | 9.9 | 23.6 | ATG | T– | H |
| tRNA-Arg | 10 684 | 10 747 | 64 | 35.9 | 26.5 | 15.6 | 21.8 | H | ||
| ND4L | 10 748 | 11 038 | 291 | 37.1 | 31.6 | 10.6 | 20.6 | ATG | TAA | H |
| ND4 | 11 038 | 12 375 | 1338 | 34.7 | 27.8 | 10.0 | 27.2 | ATG | TAA | H |
| tRNA-His | 12 377 | 12 439 | 63 | 36.5 | 26.9 | 14.2 | 22.2 | H | ||
| tRNA-Ser | 12 440 | 12 493 | 54 | 27.7 | 18.5 | 18.5 | 35.1 | H | ||
| tRNA-Leu | 12 494 | 12 564 | 71 | 30.9 | 26.7 | 19.7 | 22.5 | H | ||
| ND5 | 12 565 | 14 331 | 1767 | 38.8 | 27.0 | 9.5 | 24.5 | ATG | TAA | H |
| ND6 | 14 326 | 14 824 | 498 | 51.4 | 17.6 | 4.4 | 26.35 | ATG | AGG | L |
| tRNA-Glu | 14 834 | 14 895 | 62 | 37.0 | 27.4 | 12.9 | 22.5 | L | ||
| Cytb | 14 894 | 16 010 | 1117 | 34.7 | 29.0 | 9.8 | 26.4 | ATG | T– | H |
| tRNA-Thr | 16 011 | 16 075 | 65 | 29.2 | 26.1 | 20.0 | 24.6 | H | ||
| tRNA-Pro | 16 076 | 16 136 | 61 | 32.7 | 26.2 | 11.4 | 29.5 | L | ||
| CRI | 16 137 | 17 151 | 1015 | 32.0 | 27.5 | 30.1 | 10.3 | – | ||
| Total | 17 151 | 27.1 | 25.2 | 35.8 | 11.9 | |||||
As other vertebrates, most genes are encoded on the heavy strand except for ND6 and eight tRNA genes. ATG is the most commonly used start codon in P. mucosus mitochondrial PCG, while ND2 start with ATT and COX1 start with GTG. When it comes to stop codons, most of PCGs terminate with TAA except COX1 and ND6 gene terminate with AGA and AGG respectively. In addition, incomplete stop codons T are used in ND1, ND2, ND3, COX2, COX3 and Cytb. The length of 12S rRNA gene and 16S rRNA gene are 927 bp and 1483 bp in length, respectively.
The mitochondrial genome sequence of P. mucosus contains two large non-coding regions (CRs; D-loop), which engaged in the processes of replication and transcription of mitochondrial DNA. CRI has 1015 bp, discovered between tRNA-Pro and tRNA-Phe, which is the typical position for CRI in vertebrate genomes. CRII is 1107 bp in length, located between ND1and tRNA-Leu, which is different from some snakes (Li et al. 2014; Liu & Zhao 2015a, 2015b). The putative origin of L-strand replication (OL) with length of 35 bp, which located between tRNA-Asn and tRNA-Cys, is similar to most vertebrates (Su et al. 2007).
A phylogenetic tree (Figure 1) of mitochondrial genomes analyses of 20 species snakes of Colubridae was made based on the NJ method, P. mucosus has the most closely relationship with E. bimaculata, and formed a monophyletic group with E. bimaculata, E. anomala and E. schrenckii.
Figure 1.
Phylogenetic tree of mitochondrial genomes analyses of 20 species snakes of Colubridae based on the NJ method.
Acknowledgements
Chang-hong Ding is in post-doctoral mobile station in Chinese medicine direction of Heilongjiang University of Chinese Medicine.
Declaration of interest
The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. 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). This work was also supported by grants from the Hainan Science and Technology Department of China (CXY20130027).
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