Complete Nucleotide Sequence And Gene Organization Of The Mitochondrial Genome Of Paa Spinosa

Mitochndrial genome is used as a useful model for structural, functional and evolutionary genomics studies, which has already made a great progress. Paa spinosa is a species of genus Paa, belongs to the Ranidae of the order Anura. P. spinosa has both medicinal and nutritious value. However, this species is believed to have undergone a dramatic decline as a result of over-harvesting, observed shrinkage in distribution, and ongoing habitat destruction and degradation. In this study, the complete nucleotide sequence of the mitochondrial genome of P. spinosa has been the only complete mtDNA sequence available in genus Paa until now.In order to describe and analyze the complete nucleotide sequence of the mitochondrial genome of P. spinosa, we amplified overlapping fragments by normal PCR and long-and-accurate PCR (LA-PCR) methods. The mt genome of P. spinosa is a circular molecule of 18,012 bp in length, containing 13 protein-coding genes, 2 rRNA genes and 23 tRNA genes (including an extra copy of tRNA-Met gene), and non-coding regions (including the control region). This mt genome was characterized by three distinctive features: a cluster of rearranged tRNA genes (LTPF tRNA gene cluster), a tandem duplication of tRNA-Met gene (Metl and Met2), and distinct repeat regions at both 5' and 3' -sides in the control region. In the known anurans, most mt genomes had only one tRNA-Met gene except 5 frogs (all belonged to Ranoidae). Comparing the locations and the sequences of 16 tRNA-Met genes among Ranoidae, and constructing NJ tree of the nucleotide of those tRNA-Met genes, we suggested a tandem duplication of tRNA-Met gene can be regarded as a synapomorphy of Dicroglossinae. To further investigate the phylogenetic relationships of anurans, we constructed the phylogenetic trees (BI, ML and MP) based on the concatenated 11 mt protein-coding genes (except ND5 and ATP8). The results were as follows: the BI, ML and MP phylogenetic trees had the similar topology, and they were similar to the traditional classifications; the monophyly of Anura, Archeobatrachia, Neobatrachia, Dicroglossinae and Raninae was well supported, however, the monophyly of Mesobatrachia was failed to recover; the relationship between Bufonidae and Hylidae was closer than that between Bufonidae and other frogs; Ranidae was found as a sister clade to (Mantellidae + Rhacophoridae); P. spinosa (Dicroglossinae) was found as a sister clade to Limnonectes fujianensis, which indicated the close relationship between Paa and Limnonectes.