Abstract
BackgroundComplete mitochondrial (mt) genomes have been used extensively to test hypotheses about microevolution and to study population structure, phylogeography, and phylogenetic relationships of Anura at various taxonomic levels. Large-scale mt genomic reorganizations have been observed among many fork-tongued frogs (family Dicroglossidae). The relationships among Dicroglossidae and validation of the genus Feirana are still problematic. Hence, we sequenced the complete mt genomes of Nanorana taihangnica (=F. taihangnica) and N. yunnanensis as well as partial mt genomes of six Quasipaa species (dicroglossid taxa), two Odorrana and two Amolops species (Ranidae), and one Rhacophorus species (Rhacophoridae) in order to identify unknown mt gene rearrangements, to investigate the validity of the genus Feirana, and to test the phylogenetic relationship of Dicroglossidae.ResultsIn the mt genome of N. taihangnica two trnM genes, two trnP genes and two control regions were found. In addition, the trnA, trnN, trnC, and trnQ genes were translocated from their typical positions. In the mt genome of N. yunnanensis, three control regions were found and eight genes (ND6, trnP, trnQ, trnA, trnN, trnC, trnY and trnS genes) in the L-stand were translocated from their typical position and grouped together. We also found intraspecific rearrangement of the mitochondrial genomes in N. taihangnica and Quasipaa boulengeri. In phylogenetic trees, the genus Feirana nested deeply within the clade of genus Nanorana, indicating that the genus Feirana may be a synonym to Nanorana. Ranidae as a sister clade to Dicroglossidae and the clade of (Ranidae + Dicroglossidae) as a sister clade to (Mantellidae + Rhacophoridae) were well supported in BI analysis but low bootstrap in ML analysis.ConclusionsWe found that the gene arrangements of N. taihangnica and N. yunnanensis differed from other published dicroglossid mt genomes. The gene arrangements in N. taihangnica and N. yunnanensis could be explained by the Tandem Duplication and Random Loss (TDRL) and the Dimer-Mitogenome and Non-Random Loss (DMNR) models, respectively. The invalidation of the genus Feirana is supported in this study.
Highlights
Complete mitochondrial genomes have been used extensively to test hypotheses about microevolution and to study population structure, phylogeography, and phylogenetic relationships of Anura at various taxonomic levels
The trnT-trnP-trnF transfer RNAs (tRNAs) cluster moved from the typical neobatrachian LTPF tRNA cluster to a position between the CR1 and NADH dehydrogenase subunit 1 (ND1) genes
The trnQ gene moved from the typical dicroglossid IQMM tRNA cluster to a location between a 209 bp noncoding region (NCR) and a 208 bp NCR (Fig. 1) and within the former IQMM tRNA cluster the trnQ gene was replaced by a 40 bp NCR between the trnI and tandem transfer ribonucleic acid M (trnM) genes
Summary
Complete mitochondrial (mt) genomes have been used extensively to test hypotheses about microevolution and to study population structure, phylogeography, and phylogenetic relationships of Anura at various taxonomic levels. We sequenced the complete mt genomes of Nanorana taihangnica (=F. taihangnica) and N. yunnanensis as well as partial mt genomes of six Quasipaa species (dicroglossid taxa), two Odorrana and two Amolops species (Ranidae), and one Rhacophorus species (Rhacophoridae) in order to identify unknown mt gene rearrangements, to investigate the validity of the genus Feirana, and to test the phylogenetic relationship of Dicroglossidae. Complete mt genomes have been extensively used to test hypotheses about microevolution, to study population structure, phylogeography, and phylogenetic relationships at various taxonomic levels, and to identify cryptic species [2, 5, 6]. Gene rearrangements in the mitochondrial genome can be mainly explained by six available models: the recombination model [8, 19], the Tandem Duplication and Random Loss model (TDRL) [20], the Tandem Duplication and Non-Random Loss model (TDNL) [21], the tRNA miss-priming model [22], the Dimer-Mitogenome and Non-Random Loss model (DMNR) [23] and/or the Double Replications and Random Loss model (DRRL) [24]
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