Project description:BACKGROUND: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. 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. RESULTS:In 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. CONCLUSIONS:We 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.
Project description:In this study, the complete mitogenome sequence of <i>Rana amurensis</i> (Anura: Ranidae) is determined using long PCR. It is a circular molecule of 20,571?bp in length (GenBank accession no. MF370348). The complete mtDNA sequence of <i>R. amurensis</i> contained 2 rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, 13 protein-coding genes (PCGs) and 2 control regions (D-loops). The nucleotide composition was 28.6% A, 26.8% C, 14.0% G and 30.6% T. Mitochondrial genome analyses based on NJ method yield phylogenetic trees, including that 20 reported family Ranidae frogs. These molecular data presented here provide a useful tool for systematic analyses of genus <i>Rana</i>.
Project description:In this study, the complete mitogenome sequence of <i>Rugosa emeljanovi</i> (Anura: Ranidae) is first determined using long PCR. It is a circular molecule of 17,733?bp in length (GenBank accession no. KU641020). Similar to the typical mtDNA of amphibians, the complete mtDNA sequence of <i>R. emeljanovi</i> contained 2 rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, 13 protein-coding genes (PCGs), and a control region (D-loop). The nucleotide composition was 28.1% A, 26.8% C, 14.8% G, and 30.3% T. Mitochondrial genome analyses based on the NJ method yield phylogenetic trees, including the 13 already reported Ranidae family frogs. The molecular data presented here provide a useful tool for systematic analyses of genus <i>Rugosa</i> and <i>Glandirana</i>.
2017-01-01 | S-EPMC7801011 | BioStudies
Project description:The complete mitochondrial genome of the Amolops mantzorum northern lineage (Anura: Ranidae)
Project description:The complete mitochondrial DNA (mtDNA) for <i>Odorrana exiliversabilis</i>Li, Ye and Fei 2001 (Anura: Ranidae) was determined in this study. The length of complete mtDNA was 17,122?bp, including 13 PCGs (COI-III, ND1-6, ND4L, ATP6, ATP8 and CYTB), 25 tRNA genes, 2 rRNA genes, 2 non-coding regions of a L-strand replication origin and a control region. The overall base composition of the sequence is 28.27% T, 28.27% C, 28.52% A, and 14.94% G, with a total A?+?T content of 56.79%. The phylogenetic tree showed that <i>O. exiliversabilis</i> was the sister species of <i>O. tormota</i>, and formed a monophyletic clade with other <i>Odorrana</i> species. These data provide a powerful tool for evolutionary biology and population genetics of genus <i>Odorrana</i>.
Project description:The complete mitochondrial genome of the Wuchuan Odorous Frog was 18,256?bp in length including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region and was similar to that of typical vertebrates. The base composition was 27.89% A, 29.00% C, 15.34% G, and 27.78% T. All genes were encoded on the H-strand except <i>ND6</i> and eight tRNA genes (<i>tRNAPro</i>, <i>tRNAGln</i>, <i>tRNAAla</i>, <i>tRNAAsn</i>, <i>tRNACys</i>, <i>tRNATyr</i>, <i>tRNASer</i>, and <i>tRNAGlu</i>), which were encoded on the L-strand. The phylogenetic relationship of Anura based on complete mitochondrial genomes showed that <i>O. wuchuanesis</i> is closest to <i>O. margaretae</i> with strong support and the genetic distance between Ranidae, Dicroglossidae, and Rhacophoridae was closer than others.
Project description:Recent improvements in next-generation sequencing (NGS) technologies can facilitate the obtainment of mitochondrial genomes. However, it is not clear whether NGS could be effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly and alignment errors. Here, we choose two frogs with rearranged gene order, Amolops chunganensis and Quasipaa boulengeri, to test whether gene rearrangements affect the mitogenome assembly and alignment by using NGS. The mitogenomes with gene rearrangements are sequenced through Illumina MiSeq genomic sequencing and assembled effectively by Trinity v2.1.0 and SOAPdenovo2. Gene order and contents in the mitogenome of A. chunganensis and Q. boulengeri are typical neobatrachian pattern except for rearrangements at the position of "WANCY" tRNA genes cluster. Further, the mitogenome of Q. boulengeri is characterized with a tandem duplication of trnM. Moreover, we utilize 13 protein-coding genes of A. chunganensis, Q. boulengeri and other neobatrachians to reconstruct the phylogenetic tree for evaluating mitochondrial sequence authenticity of A. chunganensis and Q. boulengeri. In this work, we provide nearly complete mitochondrial genomes of A. chunganensis and Q. boulengeri.
Project description:The mitochondrial genome of one <i>Rana pseudo-rana</i> species <i>Rana sangzhiensis</i> Shen was sequenced and annotated. The mitogenome is 19,207?bp in length, containing 37 typical genes. The A?+?T content of the whole mitogenome is 56.6%. All of the protein-condoning genes (PCGs) started with ATG and stopped with TGA. The tRNA-Pro, tRNA-Gln, tRNA-Ala, tRNA-Asn, tRNA-Cys, tRNA-Tyr, tRNA-Ser, tRNA-Glu, andND5 are located in the circular mitochondrial L chain. The phylogeny tree is monophyletic among 14 related <i>Rana</i> species. The <i>R. sangzhiensis</i> Shen cluster was more closely related to <i>R. amurensis</i> Boulenger and <i>R. kunyuensis</i> Lu, Y.-Y., and P.-P. Li. This mitochondrial genome can be used for further analyses of <i>Ranidae</i> mitochondrial comparative genomics to improve the understanding of diverse <i>Ranidae</i> species.
Project description:Frogs (Lissamphibia: Anura) use adhesive tongues to capture fast moving, elusive prey. For this, the tongues are moved quickly and adhere instantaneously to various prey surfaces. Recently, the functional morphology of frog tongues was discussed in context of their adhesive performance. It was suggested that the interaction between the tongue surface and the mucus coating is important for generating strong pull-off forces. However, despite the general notions about its importance for a successful contact with the prey, little is known about the surface structure of frog tongues. Previous studies focused almost exclusively on species within the Ranidae and Bufonidae, neglecting the wide diversity of frogs. Here we examined the tongue surface in nine different frog species, comprising eight different taxa, i.e., the Alytidae, Bombinatoridae, Megophryidae, Hylidae, Ceratophryidae, Ranidae, Bufonidae, and Dendrobatidae. In all species examined herein, we found fungiform and filiform papillae on the tongue surface. Further, we observed a high degree of variation among tongues in different frogs. These differences can be seen in the size and shape of the papillae, in the fine-structures on the papillae, as well as in the three-dimensional organization of subsurface tissues. Notably, the fine-structures on the filiform papillae in frogs comprise hair-like protrusions (Megophryidae and Ranidae), microridges (Bufonidae and Dendrobatidae), or can be irregularly shaped or absent as observed in the remaining taxa examined herein. Some of this variation might be related to different degrees of adhesive performance and may point to differences in the spectra of prey items between frog taxa.