title: The complete mitochondrial genome of a tree frog, Polypedates megacephalus (Amphibia: Anura: Rhacophoridae), and a novel gene organization in living amphibians.
abstract: In this study, we have determined the complete sequence of the mitochondrial genome of an Old World tree frog Polypedates megacephalus (Anura: Rhacophoridae) by using a long polymerase chain reaction (PCR) technique and shotgun strategy of sequencing. The entire mtDNA sequence is 16,473 nt long with a novel mitogenomic gene organization in amphibians. Unlike other neobatrachian frogs, the transfer ribonucleic acid (tRNA)-Leu(CUN) and tRNA-Thr genes exchange their positions in P. megacephalus and form a Thr-Leu(CUN)-Pro-Phe tRNA gene tetrad. Moreover, we found that the ATP8 gene was replaced by a noncoding sequence of 853 nt long and that the ND5 gene was absent in the new mitogenome. These peculiar features of P. megacephalus mtDNA were further studied among related anuran species by PCR amplification. The new sequence data was used to assess the phylogenetic relationships of the three living amphibian orders using neighbor-joining, maximum likelihood, and Bayesian methods. In agreement with most morphological studies, phylogenetic analyses of a whole mitochondrial genome data set suggest a close relationship between salamanders and frogs. Moreover, using a molecular clock-independent Bayesian approach for inferring dating information from molecular phylogenies, we have provided a rough timescale for living amphibian evolution. This timescale provides a working framework for future paleontological researches on amphibian evolution and improves our understanding of the evolutionary history of modern amphibians.
authors.affiliation: Key Laboratory of Gene Engineering of the Ministry of Education, Biotechnology Research Center, Zhongshan University, Guangzhou 510275, PR China.
authors.forename: Peng
authors.initials: P
authors.lastname: Zhang
authors.forename: Hui
authors.initials: H
authors.lastname: Zhou
authors.forename: Dan
authors.initials: D
authors.lastname: Liang
authors.forename: Yi-Fei
authors.initials: YF
authors.lastname: Liu
authors.forename: Yue-Qin
authors.initials: YQ
authors.lastname: Chen
authors.forename: Liang-Hu
authors.initials: LH
authors.lastname: Qu
mesh_terms: D000818:Animals; D001001:Anura / Q000235:genetics*; D001483:Base Sequence; D017931:DNA Primers; D004272:DNA, Mitochondrial / Q000235:genetics*; D016678:Genome; D008969:Molecular Sequence Data; D010802:Phylogeny; D012343:RNA, Transfer / Q000235:genetics
chemical_list: D017931:DNA Primers; D004272:DNA, Mitochondrial; D012343:RNA, Transfer