A comparison of gene organisations and phylogenetic relationships of all 22 squamate species listed in South Korea using complete mitochondrial DNA

Abstract

Studies using complete mitochondrial genome data have the potential to increase our understanding on gene organisations and evolutionary species relationships. In this study, we compared complete mitochondrial genomes between all 22 squamate species listed in South Korea. In addition, we constructed Maximum Parsimony (MP), Maximum Likelihood (ML) and Bayesian Inference (BI) phylogenetic trees using 13 mitochondrial protein-coding genes. The mitochondrial genes for all six species in the suborder Sauria followed the same organisation as the sequenced Testudines (turtle) outgroup. In contrast, 16 snake species in the suborder Serpentes contained some gene organisational variations. For example, all snake species contained a second control region (CR2), while three species in the family Viperidae had a translocated tRNA-Pro gene region. In addition, the snake species, Elapheschrenckii, carried a tRNA-Pro pseudogene. We were also able to identify a translocation of a tRNA-Asn gene within the five tRNA (WANCY gene region) gene clusters for two true sea snake species in the subfamily Hydrophiinae. Our BI phylogenetic tree was also well fitted against currently known Korean squamate phylogenetic trees, where each family and genus unit forms monophyletic clades and the suborder Sauria is paraphyletic to the suborder Serpentes. Our results may form the basis for future northeast Asian squamate phylogenetic studies.

Keywords: Full mitochondrial genome; Korea; Squamata; WANCY; phylogeny; rearrangement; tRNA-Pro.

Figure 1.

Comparison of the mitochondrial gene organisation for all 22 squamate species listed in South Korea. Two sea turtle species (Carettacaretta and Cheloniamydas), served as outgroups. L1, L2, S1, S2. P* represent the following genes: tRNA-Leu (UUR), tRNA-Leu (CUN), tRNA-Ser (AGY), tRNA-Ser (UCN) and a pseudo tRNA-Pro gene, respectively. tRNA genes are abbreviated by the corresponding one-letter amino acid codes, such as F, V, I, M etc.

Figure 2.

Maximum Parsimony (MP) tree (left) and Maximum Likelihood (ML) tree (right) for all 22 squamates listed in South Korea. Both MP and ML trees are based on 13 mitochondrial protein-coding genes. Carettacaretta and Cheloniamydas are outgroup species. Bootstrap values are denoted on each tree branch.

Figure 3.

The constructed Bayesian Inference (BI) tree for all 22 squamate species listed in South Korea, based on 13 mitochondrial protein-coding genes. Two cheloniid species (Carettacaretta and Cheloniamydas) were used as outgroups. Bayesian posterior probabilities are denoted on each tree branch.

Figure 4.

Intergenic spacers located in the cluster of five tRNA genes (WANCY gene region) of two sea snake species (Hydrophisplaturus and H.melanocephalus) found off South Korean coastal waters A intergenic spacers located in the WANCY gene region of two sea krait species (Laticaudalaticaudata and L.semifasciata), four terrestrial cobras (Bungarusfasciatus, Micrurusfulvius, Najanaja and Sinomicrurusmacclellandi) B and two true sea snake species downloaded from GenBank (H.curtus and Emydocephalusijimae) C intergenic spacer lengths amongst Hydrophiinae species are above the intergenic spacer in the same order as the species are listed. The hypothesised tRNA genes lost due to random deletions are written below the intergenic spacers. The tRNA genes are abbreviated by the corresponding one-letter amino acid codes, such as W, A, N etc.