A novel mitogenomic rearrangement for Odorrana schmackeri (Anura: Ranidae) and phylogeny of Ranidae inferred from thirteen mitochondrial protein-coding genes

Li, Yongmin; Zhang, Huabin; Wu, Xiaoyou; Xue, Hui; Yan, Peng; Wu, Xiaobing

doi:10.1163/15685381-00002958

Cited by 10 publications

(6 citation statements)

References 54 publications

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“…BI and ML analyses were performed with 59 anuran mt genomes including Pyxicephalus adspersus . In total this included 55 species as the ingroup from Ranidae, Dicroglossidae, Rhacophoridae, Mantellidae, Pyxicephalidae, Petropedetidae, Ptychadenidae, Ceratobatrachidae, and Phrynobatrachidae (Alam et al, 2010; Chen et al, 2011; Hofman et al, 2012; Huang et al, 2016a, 2016b; Jiang et al, 2017; Kakehashi et al, 2013; Kurabayashi et al, 2006, 2010; Li et al, 2014b, 2016b; Lin et al, 2014; Liu, Wang & Zhao, 2017a; Liu et al, 2017b; Liu, Wang & Su, 2005; Ni et al, 2015; Ren et al, 2009; Sano et al, 2004, 2005; Xia et al, 2014; Yan et al, 2016; Yang et al, 2018; Yu, Zhang & Zheng, 2012a; Yu et al, 2012b, 2015; Zhang, Xia & Zeng, 2016; Zhang et al, 2005, 2009, 2013, 2018a; Zhao, Meng & Su, 2018; Zhou et al, 2009) and four species as outgroups from Microhylidae (Chen et al, 2016; Wang et al, 2018; Zhao, Meng & Su, 2018). We used the nucleotide data to assess BI and ML topology to discuss the phylogenetic position of Pyxicephalus .…”

Section: Methodsmentioning

confidence: 99%

The complete mitochondrial genome ofPyxicephalus adspersus: high gene rearrangement and phylogenetics of one of the world’s largest frogs

Cai

Shen

et al. 2019

PeerJ

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The family Pyxicephalidae including two subfamilies (Cacosterninae and Pyxicephalinae) is an ecologically important group of frogs distributed in sub-Saharan Africa. However, its phylogenetic position among the Anura has remained uncertain. The present study determined the complete mitochondrial genome sequence of Pyxicephalus adspersus, the first representative mitochondrial genome from the Pyxicephalinae, and reconstructed the phylogenetic relationships within Ranoidae using 10 mitochondrial protein-coding genes of 59 frog species. The P. adspersus mitochondrial genome showed major gene rearrangement and an exceptionally long length that is not shared with other Ranoidae species. The genome is 24,317 bp in length, and contains 15 protein-coding genes (including extra COX3 and Cyt b genes), four rRNA genes (including extra 12S rRNA and 16S rRNA genes), 29 tRNA genes (including extra tRNALeu (UAG), tRNALeu (UUR), tRNAThr, tRNAPro, tRNAPhe, tRNAVal, tRNAGln genes) and two control regions (CRs). The Dimer-Mitogenome and Tandem duplication and random loss models were used to explain these gene arrangements. Finally, both Bayesian inference and maximum likelihood analyses supported the conclusion that Pyxicephalidae was monophyletic and that Pyxicephalidae was the sister clade of (Petropedetidae + Ptychadenidae).

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Section: Methodsmentioning

confidence: 99%

The complete mitochondrial genome ofPyxicephalus adspersus: high gene rearrangement and phylogenetics of one of the world’s largest frogs

Cai

Shen

et al. 2019

PeerJ

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“…A 1151 base pairs (bp) fragment of mitochondrial DNA containing the complete mitochondrial NADH dehydrogenase subunit 2 (ND2) gene and two flanking transfer RNA (tRNA) genes was amplified with the primer pair Ile-LND2 (5’-ATAGGGAGACTTATAGGGGTTC-3’) and Asn-HND2 (5’-CTAAGTCATTACGGGATCGAGGCC-3’) designed according to the complete mitochondrial genome of O . schmackeri from Li et al [ 52 ] (GenBank accession no. KJ149452).…”

Section: Methodsmentioning

confidence: 99%

Vicariance and Its Impact on the Molecular Ecology of a Chinese Ranid Frog Species-Complex (Odorrana schmackeri, Ranidae)

Zhang

et al. 2015

PLoS ONE

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Paleogeological events and Pleistocene climatic fluctuations have had profound influences on the genetic patterns and phylogeographic structure of species in southern China. In this study, we investigated the population genetic structure and Phylogeography of the Odorrana schmackeri species complex, mountain stream-dwelling odorous frogs, endemic to southern China. We obtained mitochondrial sequences (1,151bp) of the complete ND2 gene and two flanking tRNAs of 511 individuals from 25 sites for phylogeographic analyses. Phylogenetic reconstruction revealed seven divergent evolutionary lineages, with mean pairwise (K2P) sequence distances from 7.8% to 21.1%, except for a closer ND2 distance (3.4%). The complex geological history of southern China drove matrilineal divergence in the O. schmackeri species complex into highly structured geographical units. The first divergence between lineage A+B and other lineages (C-G) had likely been influenced by the uplift of coastal mountains of Southeast China during the Mio-Pliocene period. The subsequent divergences between the lineages C-G may have followed the formation of the Three Gorges and the intensification of the East Asian summer monsoon during the late Pliocene and early Pleistocene. Demographic analyses indicated that major lineages A and C have been experienced recent population expansion (c. 0.045–0.245 Ma) from multiple refugia prior to the Last Glacial Maximum (LGM). Molecular analysis suggest that these seven lineages may represent seven different species, three described species and four cryptic species and should at least be separated into seven management units corresponding to these seven geographic lineages for conservation.

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“…So far, combined with the 38 mitochondrial genome sequences in GenBank database, our phylogenetic analyses revealed that the subfamily Dicroglossinae's monophyly was well supported (Li et al., , ; Roelants et al., ; Yuan et al., ). The subfamily Dicroglossinae is the sister clade to the Occidozyginae (Figure ).…”

Section: Resultsmentioning

confidence: 77%

“…In addition, a tandem repeat of tRNA‐Met gene was easy to find in the three Nanorana species, located between the tRNA‐Gln and ND2 genes. Extra tRNA‐Met was also found in Quasipaa boulengeri , Fejervarya cancrivora , Hoplobatrachus rugulosus , Euphlyctis hexadactylus , Limnonectes bannaensis , and Occidozyga martensii (Alam et al., ; Chen et al., ; Li et al., , ; Ren et al., ; Shan, Xia, Zheng, Zou, & Zeng, ; Zhang et al., ). But this phenomenon is different to that seen in Amolops tormotus and other typical vertebrates (Su, Wu, Yan, Cao, & Hu, ).…”

Section: Resultsmentioning

confidence: 97%

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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A novel mitogenomic rearrangement for Odorrana schmackeri (Anura: Ranidae) and phylogeny of Ranidae inferred from thirteen mitochondrial protein-coding genes

Cited by 10 publications

References 54 publications

The complete mitochondrial genome ofPyxicephalus adspersus: high gene rearrangement and phylogenetics of one of the world’s largest frogs

The complete mitochondrial genome ofPyxicephalus adspersus: high gene rearrangement and phylogenetics of one of the world’s largest frogs

Vicariance and Its Impact on the Molecular Ecology of a Chinese Ranid Frog Species-Complex (Odorrana schmackeri, Ranidae)

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

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