Bioinformatics Analysis the Complete Sequences of Cytochrome b of Takydromus sylvaticus and Modeling the Tertiary Structure of Encoded Protein

Abstract

Cytochrome b (cyt b) gene complete sequences (1143bp) of Takydromus sylvaticus were sequenced. In order to clarify the phylogenetic position of the Takydromus sylvaticus, we investigated the phylogeny of 15 Takydromus spp. distributed in East-Asia by Maximum Parsimony (MP), Bayesian Inference (BI), and Maximum Likelihood (ML) methods using DNA fragments of cyt b genes. The results supported that the Platyplacopus merged into Takydromus and negated the validity of Platyplacopus. Furthermore, the prediction of tertiary structures of cyt b exhibited the CD loop region contain two short helices forming a hairpin arrangement, namely cd1 and cd2. Thermostability analysis shows that the CD-loop region is unstable thermodynamically and may provide mobility to amino acids located at the heme, and might provide high flexibility to the top of ISP (iron-sulfur protein) and the cavity region of Qo binding site. It suggested that the two short helices of CD loop region of cyt b was a dominating portion for ISP binding site.

Phylogenetic and biogeographical relationships of theSanderpikeperches (Percidae: Perciformes): patterns across North America and Eurasia

“…The control region of mtDNA is non‐coding, houses its replication origin, and is less conserved than the other two mtDNA regions analysed here (summarized by Simon et al ., ). Cyt b and COI encode proteins that form part of the electron transport in cellular respiration (summarized by Lunt et al ., ; Chen et al ., ). COI additionally is involved in translocating proteins across the mitochondrial membrane (summarized by Lunt et al ., ).…”

Climate‐driven mitochondrial selection in lacertid lizards

“…For example, the phylogeny inferred from cyt b gene supports the idea that the genus Platyplacopus should be merged into the genus Takydromus (Chen et al, 2009).…”

“…Phylogenetic relationships within the family Lacertidae were once unclear because of the indistinguishable morphological characteristics such as the relationship between the genera Takydromus and Platyplacopus (Arnold, 1997 ). The phylogenetic analyses of the mitochondrial DNA (mtDNA) sequences have provided new insight into the evolutionary relationships within Lacertidae (Arnold et al., 2007 ; Chen et al., 2009 ; Guo et al., 2011 ). For example, the phylogeny inferred from cyt b gene supports the idea that the genus Platyplacopus should be merged into the genus Takydromus (Chen et al., 2009 ).…”

“…The phylogenetic analyses of the mitochondrial DNA (mtDNA) sequences have provided new insight into the evolutionary relationships within Lacertidae (Arnold et al., 2007 ; Chen et al., 2009 ; Guo et al., 2011 ). For example, the phylogeny inferred from cyt b gene supports the idea that the genus Platyplacopus should be merged into the genus Takydromus (Chen et al., 2009 ).…”

A New Species of the Genus Takydromus (Squamata: Lacertidae) from Northeastern Guangxi, China

“…The interrelationships and evolution of Asian grass lizards, Takydromus (Squamata: Lacertidae), are still in dispute and, due to the inconsistencies in the molecular and/or morphological data, different conclusions have been drawn [1,7,[16][17][18][19]. For example, our phylogenetic tree of two concatenated mtDNA genes (CO1 and cyt b) differs from the trees based on CO1 [5] or cyt b [6] in the positions of T. smaragdinus, T. kuehnei and T. sexlineatus within the genus Takydromus (Figure 2).…”