Complete mitochondrial genome of Scincella modesta (Squamata: Scincidae).

The first complete mitochondrial genome sequence was determined for an oviparous lizard, Scincella modesta (Scincella, Scincidae). The total length of the complete mitochondrial genome was 17,511 bp, encodes 13 protein-coding genes, 22 tRNAs, 2 rRNA genes, and 2 non-coding regions. The overall base composition of S. modesta is A: 31.9%, T: 27.2%, G: 14.5%, and C: 26.5%. Most of the S. modesta mitochondrial genes are encoded on the H-strand except for the ND6 gene and eight tRNA genes, which are encoded on the L-strand. Mrbayes and ML tree based on 13 protein-coding genes indicated that S. vandenburghi is the sister group of the S. modesta within the genus Scincella. The complete mitogenome sequence of S. modesta provided fundamental data for resolving phylogenetic and genetic problems related to genus Scincella.

The majority of lizard species in the family Scincidae are found in the subfamily Lygosominae. The lygosomine skinks of the genus Scincella contain small skinks comprising 35 species of small-sized ground lizards (Greer and Shea 2003; Linkem et al. 2011), but only 14 species can be found in China mainland. The slender forest skink (Scincella modesta) studied is a small-sized [to 55 mm snout-vent length (SVL)] oviparous diurnal sincid lizard that is widely distributed in the eastern and central provinces of China (Zhao and Adler 1993). Adult S. modesta are morphologically similar to a medium-sized sympatric viviparous skink (Sphenomorphus indicus) that they are often regarded wrongly as juveniles of the latter species. Despite the fact that it is taxonomically and zoogeographically well known, the biology and ecology of this species remain almost unknown. Most previous studies on S. modesta were about its sexual size dimorphism (Yang et al. 2012), reproductive traits and thermal biology (Li et al. 2012) and so on. In order to do so, further research on molecular levels about S. modesta and other skinks in the genus Scincella, it is necessary to analyze its complete mitochondrial genome.

The specimen of S. modesta was collected from Zijin mountain in Nanjing, Jiangsu province, China (N 32°3′48.35″, E 118°50′9.6″). The specimen is stored in the College of Life Sciences, Nanjing Normal University in China (Voucher No. 0216). Whole genomic DNA was extracted from the tail tissues of the specimens using the Animal Genomic DNA Extraction Kit (Roche, Germany). For amplification of the S. modesta mitochondrial genome, specific PCR primers were designed based on the mitochondrial genome sequences obtained from Sphenomorphus incognitus (MH329292). The complete mitochondrial (17,511 bp in length) genome of S. modesta (GenBank: MN786972) contained 22 tRNA genes, 2 rRNA genes (12S rRNA and 16S rRNA), 13 protein-coding genes, and 2 non-coding regions. In the 13 protein-coding genes: 12 protein-coding genes had ATG as the start codon, while COXI started with GTG. Five protein-coding genes (ND1, ATP8, ATP6, ND4L, and ND5) regarded TAA as stop codon; ND2 and CYTB used TGG as stop codon; ND6 used AGG as stop codon and COXI used AGA as stop codon; the others terminated with T as an incomplete stop codon, which was presumably completed as TAA by post-transcriptional polyadenylation (Anderson et al. 1981). The 22 tRNA genes range in size from 65 bp in tRNACys to 75 bp in tRNALeu. The 12S rRNA and 16S rRNA genes were 976 bp and 1513 bp in size, respectively. Two ribosomal subunit genes were separated by the tRNAVal. Two non-coding regions with lengths of 2100 bp and 25 bp, respectively. The overall base composition of the H-strand for the mitogenome sequence of S. modesta was as follows: A = 31.9%, T = 27.2%, G = 14.5%, and C = 26.5%. Phylogenetic analysis revealed that there were evolutionary relationships within Scincidae (Figure 1). The three skink species showed a close phylogenetic relationship with other species in Scincidae, which clustered in a monophyletic group.

Figure 1.

Phylogenetic tree inferred by maximum likelihood analyses and Bayesian inference based on PCG123 showing the relationship between Scincella modesta and other Scincidae mitochondrial genomes. GenBank accession numbers of mitogenome sequences used are shown in parentheses. Node labels indicate bootstrap values and posterior probabilities.