Comparative Analyses of Two Nearly Complete Mitochondrial Genomes of the Liu’s Skink, Plestiodon liui, from South and North Sides of the Yangtze River

Abstract

In this study we amplified and sequenced the nearly complete mitochondrial DNA of an individual of the Liu’s skink, Plestiodon liui, from south of the Yangtze River. The obtained mitochondrial genome was 17, 945 bp in length, comprising 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and an incomplete control region (D-loop). Another nearly complete mitogenome of P. liui, from north of the Yangtze River, was retrieved from GenBank and used for comparative analyses. The results showed that the genome organization, base composition, codon usage, and gene arrangement of the mitochondrial genomes for the two individuals of P. liui were highly similar to each other. Twelve out of 13 PCGs initiated with canonical start codon (ATG), while COX1 started with GTG. The codon usage analysis revealed a preferential use of the LeuCUN, Pro, and Thr codons with the A/U ending. Among the 22 tRNA genes, only tRNA-SerAGY was not folded into a typical cloverleaf secondary structure and had no recognizable DHU stem. The phylogenetic tree inferred from Bayesian inference and maximum likelihood approaches strongly supported that the two individuals of P. liui clustered together, and formed the sister taxon to a clade of P. capito and P. tunganus. All PCGs had undergone a strong purifying selection, whereas 27 residues of the ATP6, COX2, Cytb, ND3, ND4, ND5, ND6 genes might have undergone positive selection. Bayesian molecular dating indicated that the split between P. liui and P. capito – P. tunganus was approximately 9.62 million years ago (Ma). Meanwhile, the coalescence time of the two individuals of P. liui was estimated to be 2.26 Ma with 95% highest posterior density of 1.32 – 3.28 Ma, which fell within the timeframe for the Yangtze River run-through between the late Pliocene to the middle Pleistocene. This finding implied that the Yangtze River run-through had played an important role in the diversification of the Liu’s skink.