The complete mitochondrial genome of the large-headed frog, Limnonectes bannaensis (Amphibia: Anura), and a novel gene organization in the vertebrate mtDNA.

We determined the complete nucleotide sequence of the mitochondrial (mt) genome of the large-headed frog, Limnonectes bannaensis (Amphibia, Anura) by using polymerase chain reaction (PCR). The entire mtDNA sequence is 16,867 bp in length with a novel case of tRNAs in vertebrates. This mt genome is characterized by three distinctive features: (1) a tandem duplication of tRNA(Met) gene is observed, (2) the tRNA(Ala), tRNA(Asn), tRNA(Cys) and tRNA(Glu) genes coded on the L-strand are absent from the L. bannaensis mtDNA, the tRNA(Cys) and tRNA(Glu) genes change into tRNA pseudogenes by reason of degenerative anticodon, and a noncoding sequence of 206 nt long (NC1) has replaced the original position of other two tRNAs, (3) besides NC1, another three noncoding spacers (NC2-4) longer than 50 bp are found in the broken WANCY region and the region NC3-ND5-NC4-ND6-PsiE-Cytb-CR of the new sequence. These features could be explained by a model of gene duplication and deletion. The new sequence data was used to assess the phylogenetic relationships among 25 species of Anura using neighbor-joining, Bayesian, and maximum likelihood methods, and the phylogenetic tree shows the rice frog Fejervarya limnocharis is closest to L. bannaensis in the study.