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 tRNAMet gene is observed, (2) the tRNAAla, tRNAAsn, tRNACys and tRNAGlu genes coded on the L-strand are absent from the L. bannaensis mtDNA, the tRNACys and tRNAGlu 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-ΨE-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.