Isolation and characterization of 113 polymorphic microsatellite loci for the Tibetan frog (Nanorana parkeri) using next generation sequencing

Wang, Cuimin; Hu, Xiaoju; Xie, Xinglong; Liu, Pengfei; Merilä, Juha; Zhang, Qiong; Li, Menghua

doi:10.1007/s12686-013-9932-6

Cited by 3 publications

(3 citation statements)

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“…The software avoided repeated SSRs (simple sequences repeats), and those very short, imperfect or compound. There are previous studies using NGS in amphibians (Drechsler et al, 2013;Wang et al, 2013) and reptiles (Castoe et al, 2010;Geser et al, 2013) in which the authors express the advantages of NGS, such as reducing cost and time through more efficient microsatellites obtaining. Our results are similar to those reported by other authors working in reptiles regarding the number of microsatellites designed (Geser et al, 2013) employing NGS approach.…”

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confidence: 99%

Isolation and characterization of new microsatellite markers for application in population genetic studies of Caiman latirostris and related species

et al. 2015

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Wild populations ofCaiman latirostrisare subject to sustainable use programs in Argentina, becoming a species with important impact in the regional economy, based in their skin and meat. Genetic studies are fundamental to acquire information on important parameters for conservation and management, which may be obtained from analysis of molecular markers. Some microsatellites have been previously isolated in this species, but due to some difficulties in using them, we obtained new ones using Next Generation Sequencing approach. This study reports eight new microsatellites forC. latirostrisand tests their utility in a related species,Caiman yacare, with successful application in population genetics and mating systems studies. In addition, we shared data about a novel and fast bioinformatics tool to find microsatellites and to design their corresponding primers.

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confidence: 99%

Isolation and characterization of new microsatellite markers for application in population genetic studies of Caiman latirostris and related species

et al. 2015

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“…The development of markers associated with high-throughput sequencing (HTS) approaches have increased the comprehension of genetic variability in population studies, since it makes access to genomes of non-model organisms feasible (Ekblom and Galindo, 2011). Recently, this approach made viable the development of microsatellite markers for various anuran species, for example: Nanorana parkeri with 113 new microsatellite markers (Wang et al, 2013), Leptodactylus bufonius with 17 markers, Leptodactylus chaquensi with 16 markers (Faggioni et al, 2014), Bokermannohyla sp. with 22 markers (Nali et al, 2014), Quasipaa boulengeri with 32 markers (Yuan et al, 2015), Telmatobius chusmisensis with 22 markers (Fabres et al, 2018), and Bufotes viridis with 12 markers (Vences et al, 2019).…”

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confidence: 99%

Research Article Isolation and development of microsatellite markers for the Brazilian Cerrado endemic tree frog <i>Ololygon</i> <i>centralis</i> (Anura: Hylidae)

Castro¹,

Targueta²,

Guerra³

et al. 2020

Genet. Mol. Res.

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“…Mitochondrial genes such as the COX I, Cytochrome b (Cytb), D‐loop, tRNA, and NADH have been used for previous phylogenetic and phylogeographic studies on the genetic divergence of Nanorana (Che et al., ; Liu et al., ; Wang et al., ; Zhang et al., ; Zhou et al., ). Here, we use complete mitochondrial genomes to analyze the phylogenetic relationships of the three Nanorana species ( N. parkeri , N. ventripunctata , and N. pleskei ) and other related species.…”

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confidence: 99%

The first complete mitochondrial genome sequence of Nanorana parkeri and Nanorana ventripunctata (Amphibia: Anura: Dicroglossidae), with related phylogenetic analyses

Jiang

You

et al. 2018

Ecology and Evolution

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Members of the Nanorana genus (family Dicroglossidae) are often referred to as excellent model species with which to study amphibian adaptations to extreme environments and also as excellent keystone taxa for providing insights into the evolution of the Dicroglossidae. However, a complete mitochondrial genome is currently only available for Nanorana pleskei. Thus, we analyzed the complete mitochondrial genomes of Nanorana parkeri and Nanorana ventripunctata to investigate their evolutionary relationships within Nanorana and their phylogenetic position in the family Dicroglossidae. Our results showed that the genomes of N. parkeri (17,837 bp) and N. ventripunctata (18,373 bp) encode 13 protein‐coding genes (PCGs), two ribosomal RNA genes, 23 transfer RNA (tRNA) genes, and a noncoding control region. Overall sequences and genome structure of the two species showed high degree of similarity with N. pleskei, although the motif structures and repeat sequences of the putative control region showed clear differences among these three Nanorana species. In addition, a tandem repeat of the tRNA‐Met gene was found located between the tRNA‐Gln and ND2 genes. On both the 5′ and 3′‐sides, the control region possessed distinct repeat regions; however, the CSB‐2 motif was not found in N. pleskei. Based on the nucleotide sequences of 13 PCGs, our phylogenetic analyses, using Bayesian inference and maximum‐likelihood methods, illustrate the taxonomic status of Nanorana with robust support showing that N. ventripunctata and N. pleskei are more closely related than they are to N. parkeri. In conclusion, our analyses provide a more robust and reliable perspective on the evolutionary history of Dicroglossidae than earlier analyses, which used only a single species (N. pleskei).

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Isolation and characterization of 113 polymorphic microsatellite loci for the Tibetan frog (Nanorana parkeri) using next generation sequencing

Cited by 3 publications

References 5 publications

Isolation and characterization of new microsatellite markers for application in population genetic studies of Caiman latirostris and related species

Isolation and characterization of new microsatellite markers for application in population genetic studies of Caiman latirostris and related species

Research Article Isolation and development of microsatellite markers for the Brazilian Cerrado endemic tree frog <i>Ololygon</i> <i>centralis</i> (Anura: Hylidae)

The first complete mitochondrial genome sequence of Nanorana parkeri and Nanorana ventripunctata (Amphibia: Anura: Dicroglossidae), with related phylogenetic analyses

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