Vertebrate mitochondrial genomes (mitogenomes) are valuable for studying phylogeny, evolutionary genetics and genomics. To date, however, compared to other vertebrate groups, our knowledge about the mitogenomes of skinks (the family Scincidae), even of reptile, has been relatively limited. In the present study, we determined the complete mitogenome of a blue-tailed skink Plestiodon capito for the first time, and compared it with other skinks available in GenBank. The circular genome is 17,344 bp long, showing a typical vertebrate pattern with 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one control region (CR). The gene organization, nucleotide composition, and codon usage are similar to those from skinks previously published. Twelve out of 13 PCGs initiates with canonical start codon (ATG), while COX1 starts with GTG. The codon usage analysis revealed a preferential use of the LeuCUN (Leu1), Pro, and Thr codons with the A/U ending. All tRNAs in P. capito were predicted to fold into typical clover-leaf secondary structure, except tRNA-Ser AGY. The secondary structures of 12S rRNA and 16S rRNA comprises 34 helices and 56 helices, respectively. The alignment of the Plesitodon species CRs exhibited high genetic variability and rich A + T content. Besides, variable types and numbers of tandem repeat units were also identified in the CR of Plestiodon. Phylogenetic analyses recovered P. capito as the sister species to P. tunganus; monophyly of the Scincidae is well supported. Our results will help to better understand structure and evolution of the mitochondrial DNA control region in reptiles as well as the evolutionary status of P. capito, and to lay foundation for further phylogenetic study of skinks in a mitogenomic framework.

中文翻译：

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蓝尾石龙子 Plesiodon capito（爬行动物、有鳞、Scincidae）的完整线粒体基因组以及与其他 Scincidae 蜥蜴的比较

脊椎动物线粒体基因组（有丝分裂基因组）对于研究系统发育、进化遗传学和基因组学很有价值。然而，迄今为止，与其他脊椎动物群相比，我们对石龙子（Scincidae 科），甚至爬行动物的有丝分裂基因组的了解相对有限。在本研究中，我们首次确定了蓝尾石龙子 Plestiodon capito 的完整有丝分裂基因组，并将其与 GenBank 中的其他石龙子进行了比较。环状基因组长 17,344 bp，显示出典型的脊椎动物模式，具有 13 个蛋白质编码基因 (PCG)、22 个转移 RNA (tRNA) 基因、两个核糖体 RNA (rRNA) 基因和一个控制区 (CR)。基因组织、核苷酸组成和密码子使用与之前发表的石龙子相似。13 个 PCG 中有 12 个以规范起始密码子 (ATG) 启动，而 COX1 以 GTG 开头。密码子使用分析显示优先使用以 A/U 结尾的 LeuCUN (Leu1)、Pro 和 Thr 密码子。除 tRNA-Ser AGY 外，P. capito 中的所有 tRNA 都被预测为折叠成典型的三叶草二级结构。12S rRNA和16S rRNA的二级结构分别包含34个螺旋和56个螺旋。Plesitodon 物种 CR 的比对表现出高遗传变异性和丰富的 A + T 含量。此外，在 Plesiodon 的 CR 中还确定了串联重复单元的可变类型和数量。系统发育分析恢复了 P. capito 作为 P. tunganus 的姊妹种；Scincidae 的单系性得到了很好的支持。我们的研究结果将有助于更好地了解爬行动物线粒体 DNA 控制区的结构和进化以及 P. capito 的进化状态，