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. 2019 Jul 11;4(2):2301–2302. doi: 10.1080/23802359.2019.1627939

The complete mitochondrial genome of Laudakia wui (Iguania; Agamidae)

Hai-Qun Jin a,b, Yong Zhang a,b, Li-Fang Peng a,b, Shuang-Quan Duan a,✉, Song Huang b
PMCID: PMC7687397  PMID: 33365515

Abstract

In this study, the complete mitochondrial genome of Laudakia wui, has been firstly determined by shotgun sequencing. The overall length of mitogenome is 16,455 bp and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 2 control regions. Majority of the genes (13 protein-coding genes, 2 rRNA and 14 tRNA) were distributed on the H-strand, in addition to the two ND6 genes and eight tRNA genes, which were encoded on the L-strand. The phylogenetic tree was built by L. wui and 13 other related species. The DNA data presented here will be useful to study the evolutionary relationships and genetic diversity of L. wui.

Keywords: Mitogenome, Laudakia wui, phylogeny

Laudakia wui is an endemic species in the Tibet Autonomous Region of China (Zhao et al. 1999). It belongs to the genus Laudakia in the family Agamidae and has been identified as the Agama himalayana scra (Hu et al. 1987). During 1995–1996, Zhao Ermi observed and compared the rock lizard specimens and then found all the specimens from Bomi country, Xizang, being a new form, named as the Laudakia wui sp. nov. (Zhao 1998). The survival status of the L. wui on the Red List of China’s Vertebrates is near-threatened (Jiang et al. 2016). We predicted and described its full sequence of mitochondrial DNA to help us obtain its basic genetic information.

We attained the specimen of L. wui from Bomi County, Tibet Autonomous Region, China (Voucher numbers: LZ024). The tissue of the specimen was preserved and deposited in the refrigerator at −80 °C of the Museum of Huangshan university. The complete and circular mitochondria (Genbank accession number: MK411597) of the L. wui was sequenced to be 16,455 bp, which consisted of typical vertebrate 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 2 control regions (D-loop). The base composition was 36.7% for A, 12.5% for G, 27.2% for C, and 23.6% for T. The percentage of A + T (61.3%) reflected a typical sequence feature of the vertebrate mitogenome. Most of the L. wui genes are encoded on the H-strand except for the two ND6 genes and eight tRNA genes, which are encoded on the L-strand. The positions of RNA genes were predicted by the MITOS (Bernt et al. 2013), and the locations of PCGs were identified by comparing with the homologous genes of other closely related species. Among the mitochondrial protein-coding genes, the ATP8 was the shortest, while the ND5 was the longest. The 12s rRNA is 881 bp long and the 16s rRNA is 1496 bp in length. The two rRNA are located between the tRNA-Phe and tRNA-Leu genes and separated by the tRNA-Val gene. The 22 tRNA genes range in size from 57 to 75 bp. The gene order, contents and base composition are identical to those found in typical vertebrates (Boore 1999; Sorenson et al. 1999).

Phylogenetic analysis was performed based on the complete mitogenomes of L. wui and together with other 13 related species from GenBank to further validate the newly determined sequences. These species were as follows: Laudakia tuberculata, Phrynocephalus grumgrzimailoi, Phrynocephalus mystaceus, Phrynocephalus frontalis, Phrynocephalus przewalskii, Phrynocephalus albolineayuts, Xenagama taylori, Hydrosaurus amboinensis, Pogona vitticeps, Pseudotrapelus sinaitus, Chlamydosaurus kingii, Acanthosaura armata, Leiolepis belliana (out group). We aligned these sequences using Clustal X (Thompson et al. 1997). A maximum-likelihood (ML) tree was constructed based on the dataset by the online tool RAxML (Stamatakis et al. 2008). The phylogenetic analysis result was consistent with the previous research with high support. It indicated that our new determined mitogenome sequences could meet the demands and explain some evolution issues.

Figure 1.

Figure 1.

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A maximum likelihood (ML) tree of L. wui in this study and other 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 number as follows: Laudakia tuberculata (MK411595), Phrynocephalus grumgrzimailoi (KM093859), Phrynocephalus mystaceus (KC578685), Phrynocephalus frontalis (MF039064), Phrynocephalus przewalskii (MF039064), Phrynocephalus albolineatus (KP279760), Xenagama taylori (DQ008215), Hydrosaurus amboinensis (AB475096), Pogona vitticeps (AB475096), Pseudotrapelus sinaitus (AB262447), Chlamydosaurus kingii (EF090422), Acanthosaura armata (EF090422), Leiolepis belliana (AB537554).

Disclosure statement

The authors declare that the study was conducted in the absence of any commercial of financial relationships that could be constructed as potential conflicts of interest.

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