The complete mitochondrial genome of the toad-headed lizard subspecies,Phrynocephalus theobaldi orientalis(Reptilia, Squamata, Agamidae)

Comparative Analysis of Mitochondrial Genomes in Two Subspecies of the Sunwatcher Toad-Headed Agama (Phrynocephalus helioscopus): Prevalent Intraspecific Gene Rearrangements in Phrynocephalus

Intraspecific rearrangements of mitochondrial genomes are rarely reported in reptiles, even in vertebrates. The sunwatcher toad-headed agama, Phryncoephalus helioscopus, can serve as an excellent model for investigating the dynamic mitogenome structure at intraspecific level. To date, seven subspecies of P. helioscopus are well recognized, but little is known about the mitogenomic evolution among different subspecies. In this study, complete mitogenomes of subspecies P. helioscopus varius II and P. helioscopus cameranoi were determined by next-generation sequencing, and another P. helioscopus varius I retrieved from GenBank was compiled for comparative analysis. The nucleotide composition and the codon usage are similar to those previously published from toad-headed agamas. P. helioscopus varius II and P. helioscopus cameranoi have 23 tRNA genes, including standard 22 tRNA genes and one extra tRNA-Phe (tRNA-Phe duplication). Gene order and phylogenetic analyses in the genus Phrynocephalus support prevalent intraspecific gene rearrangement in P. helioscopus and other congener species including P. erythrurus, P. vlangalii, and P. forsythii. Six different mitochondrial gene arrangements are observed in Phrynocephalus. Overall, the occurrence of rearrangements may result from multiple independent structural dynamic events. The split of the two subspecies in P. helioscopus was dated at approximately 2.34 million years ago (Ma). Two types of gene rearrangements are found in the three mitogenomes of P. helioscopus, and this intraspecific rearrangement phenomenon can be explained by the tandem duplication/random loss (TDRL) model. Post duplication, the alternative loss types can occur in 0.23–0.72 Ma, suggesting that the duplication and fixation of these rearrangements can occur quite quickly. These findings highlight the need for more mitogenomes at the population level in order to better understand the potentially rampant intraspecific mitogenomic reorganization in Phrynocephalus.

Evolutionary analysis of mitochondrially encoded proteins of toad-headed lizards, Phrynocephalus, along an altitudinal gradient

Background

Animals living at high altitude must adapt to environments with hypoxia and low temperatures, but relatively little is known about underlying genetic changes. Toad-headed lizards of the genus Phrynocephalus cover a broad altitudinal gradient of over 4000 m and are useful models for studies of such adaptive responses. In one of the first studies to have considered selection on mitochondrial protein-coding regions in an ectothermic group distributed over such a wide range of environments, we analysed nineteen complete mitochondrial genomes from all Chinese Phrynocephalus (including eight genomes sequenced for the first time). Initial analyses used site and branch-site model (program: PAML) approaches to examine nonsynonymous: synonymous substitution rates across the mtDNA tree.

Results

Ten positively selected sites were discovered, nine of which corresponded to subunits ND2, ND3, ND4, ND5, and ND6 within the respiratory chain enzyme mitochondrial Complex I (NADH Coenzyme Q oxidoreductase). Four of these sites showed evidence of general long-term selection across the group while the remainder showed evidence of episodic selection across different branches of the tree. Some of these branches corresponded to increases in altitude and/or latitude. Analyses of physicochemical changes in protein structures revealed that residue changes at sites that were under selection corresponded to major functional differences. Analyses of coevolution point to coevolution of selected sites within the ND4 subunit, with key sites associated with proton translocation across the mitochondrial membrane.

Conclusions

Our results identify mitochondrial Complex I as a target for environment-mediated selection in this group of lizards, a complex that frequently appears to be under selection in other organisms. This makes these lizards good candidates for more detailed future studies of molecular evolution.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4569-1) contains supplementary material, which is available to authorized users.

The complete mitochondrial genome of the lizard subspecies, Phrynocephalus vlangalii vlangalii (Reptilia, Squamata, Agamidae)

The complete mitochondrial genome was sequenced from the toad-headed lizard, Phrynocephalus vlangalii vlangalii. The overall length of mitogenome is 16,319 bp, including 22 tRNA, 13 protein coding genes, 2 rRNA genes, and 2 control regions. The gene order and content were same with the published congeneric mitogenomes, besides the small portion between tRNA-Pro and tRNA-Phe.

The complete mitochondrial genome of Phrynocephalus forsythii (Reptilia, Squamata, Agamidae), a toad-headed agama endemic to the Taklamakan Desert

The complete mitochondrial genome was sequenced from a viviparous toad-headed agama, Phrynocephalus forsythii, which is endemic to the Taklamakan Desert. The mitogenome sequence was 17,542 bp in size, containing 13 protein-coding genes, 22 tRNA genes, two rRNA genes and a control region (D-loop). The gene arrangement and composition of P. forsythii is identical to the mitogenome of P. theobaldi in that tRNA-Pro was translocated immediately downstream of tRNA-Phe. The D-loop comprised two parts, one existing between tRNA-Thr and tRNA-Phe, and another containing 12 copies of 36-bp tandem repeats inserting between tRNA-Pro and 12S rRNA. The complete mitogenome sequence of P. forsythii may provide fundamental data for unveiling the phylogenetic origin and adaptive evolution related to Phrynocephalus viviparity.

The complete mitochondrial genome of Phrynocephalus guinanensis (Reptilia, Squamata, Agamidae)

Recent phylogenetic researches discovered no reciprocal monophyly between morphological species of Phrynocephalus putjatia and P. guinanensis, P. guinanensis exhibits extensive sexual color dimorphism, whereas P. putjatia does not have. The complete mitochondrial genome of the putative taxa, Phrynocephalus guinanensis, was determined in order to compare the mitogenomes of both ecological forms. The mitogenome sequence was 16,279 bp in size. It consists of 13 protein-coding, 22 tRNA, 2 rRNA genes and 3 control region, and its gene order and gene content were identical with the mitogenome of P. putjatia.

The complete mitochondrial genome of an agama, Phrynocephalus putjatia (Reptilia, Squamata, Agamidae)

The complete mitochondrial genome was sequenced from the toad-headed viviparous lizard, Phrynocephalus putjatia. The mitogenome was 16,283 bp in length; it contained 13 protein coding, 22 tRNA, 2 rRNA genes and 2 control regions. The gene order and compositions were identical with all published congeneric mitogenomes for the fragment between 12 s RNA and tRNA-Thr, but with some differences for the remaining sequences including CR, tRNA-Pro and tRNA-Phe. The characteristics of the mitogenome was analyzed and discussed in detail.