Complete mitochondrial genome of a blue-tailed skink Plestiodon capito (Reptilia, Squamata, Scincidae) and comparison with other Scincidae lizards

• Published in: Genetica 2020-12, Vol.148 (5-6), p.229-241
• Main Authors: Chen, Minli, Liu, Jinlong, Chen, Dali, Guo, Xianguang
• Format: Article
• Language: English
• Subjects: Animal Genetics and Genomics; Animals; Base Composition; Biological evolution; Biomedical and Life Sciences; Codons; Deoxyribonucleic acid; DNA; Evolutionary Biology; Evolutionary genetics; Genes; Genetic variability; Genetics; Genome, Mitochondrial; Genomes; Genomics; Helices; Human Genetics; Life Sciences; Lizards; Lizards - classification; Lizards - genetics; Microbial Genetics and Genomics; Mitochondrial DNA; Nucleotides; Open Reading Frames; Original Paper; Phylogenetics; Phylogeny; Plant Genetics and Genomics; Protein structure; Reptiles; Ribonucleic acid; RNA; RNA, Ribosomal - genetics; RNA, Transfer - genetics; rRNA 12S; rRNA 16S; Scincidae; Secondary structure; Sequence Homology; Sibling species; Transfer RNA; tRNA Ser; Vertebrates
• ISSN: 0016-6707; 1573-6857
• DOI: 10.1007/s10709-020-00107-1

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 Leu CUN (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.