Characterization of Two Mitogenomes of Hyla sanchiangensis (Anura: Hylidae), with Phylogenetic Relationships and Selection Pressure Analyses of Hylidae

Abstract

Hyla sanchiangensis (Anura: Hylidae) is endemic to China and is distributed across Anhui, Zhejiang, Fujian, Guangdong, Guangxi, Hunan, and Guizhou provinces. The mitogenomes of H. sanchiangensis from two different sites (Jinxiu, Guangxi, and Wencheng, Zhejiang) were sequenced. Phylogenetic analyses were conducted, including 38 mitogenomes of Hylidae from the NCBI database, and assessed the phylogenetic relationship of H. sanchiangensis within the analyzed dataset. Two mitogenomes of H. sanchiangensis showed the typical mitochondrial gene arrangement with 13 protein-coding genes (PCGs), two ribosomal RNA genes (12S rRNA and 16S rRNA), 22 transfer RNA (tRNA) genes, and one non-coding control region (D-loop). The lengths of the 12S rRNA and 16S rRNA genes from both samples (Jinxiu and Wencheng) were 933 bp and 1604 bp, respectively. The genetic distance (p-distance transformed into percent) on the basis of the mitogenomes (excluding the control region) of the two samples was calculated as 4.4%. Hyla sanchiangensis showed a close phylogenetic relationship with the clade of (H. annectans + H. tsinlingensis), which was supported by ML and BI analyses. In the branch-site model, five positive selection sites were found in the clade of Hyla and Dryophytes: Cytb protein (at position 316), ND3 protein (at position 85), and ND5 protein (at position 400) have one site, respectively, and two sites in ND4 protein (at positions 47 and 200). Based on the results, we hypothesized that the positive selection of Hyla and Dryophytes was due to their experience of cold stress in historical events, but more evidence is needed to support this conclusion.

Comparative Mitogenome of Phylogenetic Relationships and Divergence Time Analysis within Potamanthidae (Insecta: Ephemeroptera)

“…Research has already demonstrated that the 13 PCGs within the mt genome may be subject to positive selection under the influence of low temperatures [57,118]. In the present study, we found that the 258th site in ATP8 and the 2265th site in ND2 had higher evolutionary rates using the site model, which utilizes various site class-specific models and assumes that all branches have the same ω ratio but differ among sites in alignment [100].…”

Complete Mitochondrial Genome and Phylogenetic Analysis of Tarsiger indicus (Aves: Passeriformes: Muscicapidae)

“…To further understand the role of selective pressure on the mitochondrial PCGs among the Muscicapidae species, we calculated and compared the average Ka/Ks ratio for each PCG (Figure 6B). Ka/Ks ratio = 1 denotes neutral mutations, Ka/Ks ratio < 1 denotes negative selection, and Ka/Ks ratio > 1 denotes positive selection [82,83]. Here, the average Ka/Ks ratio for all PCGs were consistently far lower than 1, indicating that all PCGs of Muscicapidae mitogenomes had experienced purifying selection.…”

Differential Mitochondrial Genome Expression of Four Hylid Frog Species under Low-Temperature Stress and Its Relationship with Amphibian Temperature Adaptation

“…A non-coding region with a length of about 35 bp was found between trnS1 and ND5 in the five Hylidae sequences evaluated in this study. This non-coding region has been found in many species of Hylidae [ 62 , 63 , 64 , 65 , 66 , 67 , 68 ], but did not exist in D. versicolor [ 54 ]. Whether this is the feature of all members of Hylidae will require more sequences to be assessed.…”

“…In fact, there are many more species that show genetic differences in ND gene expression in response to various stresses. The proteins encoded by these genes are concentrated in mitochondrial complex I, and positive selection sites in previous studies were also concentrated mostly in mitochondrial complex I [ 65 ]. Mitochondrial complex I is a large enzyme and is the main entry point for electrons delivered from nicotinamide adenine dinucleotide (NADH) into the respiratory chain [ 72 ].…”