| The complete mitochondrial genome and phylogeography of the rice frog from China (Fejervarya limnocharis) were studied in the present research.1 Review The rice frog Fejervarya limnocharis is one of the most common species in the south China, and distributed throughout the east, southeast and south of Asia. It was determined as Rana limnocharis by Peter in 1863, and name has been adopted by herpetologists since then. Even though its taxonomic status of this species remains controversial. In present review, the study developments of the rice frog were summarized at morphological, taxonomic, physiological, biochemical, genetic, molecular biological and population biogeographical levels.2 Gene organization in mitochondrial genome of the rice frog from China The complete nucleotide sequence (17, 717 bp) of mitochondrial genome of the rice frog from China, Fejervarya limnocharis (Anura, Amphibia) was determined. Besides it encodes for 13 protein-coding, 22 tRNA and 2 rRNA genes, this molecule is characterized by three distinctive genomic features: 1) a unique ND5 gene order and a cluster of rearranged tRNA genes (tRNAThr, tRNAPro, tRNALeu(CUN)); 2) eight large 89-bp tandem repeats in the control region; and 3) one pseudogene of tRNAMet. Gene rearrangement of ND5 and a pseudogene of tRNAMet in the rice frog mitochondrial genome are first observed in vertebrate. We have also analyzed the nucleotide and deduced amino acid sequences of mitochondrial genes, the formation cause of a pseudogene for tRNAMel, and proposed the secondary structures of 22 tRNA genes. Moreover, we also explore the mechanisms of gene rearrangements and taxonomic status of the rice frog. Basing on the characteristics of the morphology and mitochondrial genome, we agree with the opinion of separating F. limnocharis from original genus Rana.3 The comparison of mitochondrial genomes and phylogentic relationships of Amphibian There still is a lack of consensus regarding living amphibian phylogenetic relationships. The most widely accepted hypothesis, based on morphological data, supports the monophyletic origin in the Late Paleozoic (300 mya) of the three living orders in the class Amphibia and a sister-group relationship between Caudata and Anura (the Batrachia hypothesis) to the exclusion of the Gymnophiona. However, both the monophyly of living amphibians and the close phylogenetic relationships of frogs with salamanders are still debated. The complete nucleotide sequence of the mitochondrial genome of F. limnocharis was detailedly compared with those of 5 other amphibians. The nucleotide sequences of 22 tRNA encoded by 6 amphibians mitochondrial genomes were combined and aligned to the homologous sequences of the 11 veterbrate taxa. Using teleosts as outgroup, the phylogenetic analyses results show that MP, NJ and ML trees all strongly support the monophyly of living amphibians with respect to other living tetrapods and favor a sister group relationship for caecilians and salamanders. Robustness of our results was confirmed by high bootstrap support of all nodes in the trees. This result contradicts the Batrachia hypothesis (a salamander + frog grouping), and is consistent with Bolt's hypothesis (1991) basing on the morphological data. The result was also supported by previous molecular studies based on mitochondrial and nuclear rRNA data. In addition, we also analyse the reason why our result is not consistent with previous work, and detailedly discuss the pitfalls of phylogenetic analyses based on the complete mitochondrial genomes.4 Gene rearrangements and proposed mechanisms of vertebrate mtDNA Vertebrate mitochondrial gene order was initially considered completely conserved. DNA sequences of the entire mitochondrial genome from mammals and African clawed frog suggested that all vertebrates shared a common gene order. However, with the mtDNA sequences have been increasingly determined for vertebrate genomes, the rearranged and repeated genes had been found in many taxa. Based on the complete mitochondri...
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