Skip to main content
NCBI home page
Mitochondrial DNA. Part B, Resources logoLink to Mitochondrial DNA. Part B, Resources
. 2019 Jul 23;4(2):2727–2728. doi: 10.1080/23802359.2019.1644979

The complete mitochondrial genome of Sphenomorphus indicus (Reptilia: Scincidae)

Xin-Sheng Tang 1,✉, Dian-Cheng Yang 1, Ya-Juan Lin 1, Liang-Liang Dai 1
PMCID: PMC7706459  PMID: 33365702

Abstract

The complete mitochondrial genome (mitogenome) sequence of Sphenomorphus indicus was sequenced and characterized by next-generation sequencing technology. The total length of mitogenome is 17,027 bp and contains 13 protein-coding genes, 22 tRNA genes, 2 ribosome RNA genes, and 2 non-coding regions (the control region and the putative L-strand replication origin). Most of the genes of S. indicus are encoded on the H-strand, except for the ND6 subunit gene and 8 tRNA genes which is distributed on the L-strand. Phylogenetic reconstruction suggested that S. indicus is the sister group of the S. incognitus within the genus Sphenomorphus. The complete mitochondrial genome sequence presented here will be useful to study the evolutionary relationships and genetic diversity of S. indicus.

Keywords: Sphenomorphus indicus, mitochondrial genome, phylogeny

The genus Sphenomorphus Fitzinger, 1843, is one of the most diverse groups of the family Scincidae with about 140 recognized species (Nguyen et al. 2011; Roy et al. 2013; Uetz et al. 2019). Only one complete mitochondrial genome (Sphenomorphus incognitus) was reported about this genus (Tang et al. 2019). Sphenomorphus indicus is widely distributed in the center and south of China, India, Nepal, Bhutan, Myanmar, Thailand, Laos, Vietnam, Cambodia, and south to west of Malaysia (Zhao et al. 1999; Uetz et al. 2019). In this study, the mitogenome of S. indicus was determined and described, in order to obtain basic genetic information about this species.

The specimen of S. indicus was collected from Yixian County, Huangshan, Anhui, China, and was preserved and deposited in the Museum of Huangshan University (Voucher number: HUM2017088). The complete mitogenome sequence of S. indicus was sequenced by next-generation sequencing technology (Illumina Hiseq 2500) at Shanghai Majorbio Bio-pharm Technology Co., Ltd (Shanghai, China). Genome sequences were assembled by the software SOAPdenovo v2.04 (Luo et al. 2012).

The complete mitogenome of S. indicus (Genbank accession number MK450438) was sequenced to be 17,027 bp which consisted of 13 typical vertebrate protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 1 D-loop. The overall base composition of the genome is as follows: A (30.6%), T (25.5%), C (28.8%), and G (15.1%), of which the percentage of A + T is 56.1%. Most of the S. indicus mitochondrial genes are encoded on the H-strand except for the ND6 gene and 8 tRNA genes, which are encoded on the L-strand. All protein-coding genes use ATG as a start codon, except for the COI gene, which initiates with GTG. Eight of the 13 protein-coding genes (ND1, COI, ATPase 8, ATPase 6, ND4L, ND5, ND6, and Cytb) end with complete stop codons (TAA, AGA, and AGG), and the other five genes end with T as the incomplete stop codons, which were presumably completed as TAA by post-transcriptional polyadenylation (Anderson et al. 1981). The 12S rRNA (938 bp) and 16S rRNA (1526 bp) are located between the tRNA-Phe and tRNA-Lue genes and separated by the tRNA-Val gene. The D-loop of the S. indicus mitogenome in size is 1650 bp and is located between the tRNA-Pro and tRNA-Phe genes.

To validate the newly determined sequence, the whole mitochondrial genome sequence of the S. indicus determined in this study and together with other nine closely related species from GeneBank to perform phylogenetic analysis. A maximum likelihood (ML) tree was constructed based on the dataset by the online tool RAxML (Kozlov et al. 2018). Phylogenetic analysis result suggested that S. indicus is the sister group of the S. incognitus within the genus Sphenomorphus (Figure 1). It indicated that our newly determined mitogenome sequence could meet the demands and explain some evolution issues.

Figure 1.

Figure 1.

Open in a new tab

A maximum likelihood (ML) tree of the Sphenomorphus indicus in this study and other 9 closely related species was constructed based on the dataset of the whole mitochondrial genome by online tool RAxML. The numbers above the branch meant bootstrap value. Bold black branches highlighted the study species and corresponding phylogenetic classification. The analyzed species and corresponding NCBI accession numbers are as follows: Phrynosoma blainvillii (MG387969), Plestiodon egregius (AB016606), P. chinensis (KT279358), P. elegans (KJ643142), Sphenomorphus indicus (MK450438), S. incognitus (MH329292), Scincella huanrenensis (KU507306), S. vandenburghi (KU646826), Gekko chinensis (KP666135), G. gecko (AY282753).

Disclosure statement

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

References

  1. Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, et al. 1981. Sequence and organization of the human mitochondrial genome. Nature. 290:457–465. [DOI] [PubMed] [Google Scholar]
  2. Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A. 2018. RAxML-NG: a fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference. bioRxiv. doi: 10.1101/447110 [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, et al. 2012. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience. 1:18. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Nguyen TQ, Schmitz A, Nguyen TT, Orlov NL, Böhme W, Ziegler T. 2011. A review of the genus Sphenormorphus Fitzinger, 1843 (Squamata: Sauria: Scincidae) in Vietnam, with description of a new species from northern Vietnam and Hainan Island, southern China and the first record of S. mimicus Taylor, 1962 from Vietnam. J Herpetol. 45:145–154. [Google Scholar]
  5. Roy AD, Das I, Bauer AM, Tron RKL, Karanth P. 2013. Lizard wear shades. A spectacled Sphenomorphus (Squamata: Scincidae), from the sacred forests of Mawphlang, Meghalaya, Northeast India. Zootaxa. 3071:257–276. [DOI] [PubMed] [Google Scholar]
  6. Tang XS, Yang DC, Huang S. 2019. The complete mitochondrial genome of Sphenomorphus incognitus (Reptilia: Scincidae). Mitochondr DNA B. 4:307–308. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Uetz P, Freed P, Hošek J. 2019. The reptile database [accessed 2019 Apr 22]. http://reptile–database.org.
  8. Zhao EM, Zhao KT, Zhou KY, et al. 1999. Fauna Sinica. Reptilia. Vol. 2 Beijing: Science Press; p. 340–349. [Google Scholar]

Articles from Mitochondrial DNA. Part B, Resources are provided here courtesy of Taylor & Francis

RESOURCES