The complete mitochondrial genome of
            <i>Lithobates sylvaticus</i>
            (Anura: Ranidae)

Ni, Ningning; Yu, Dan‐Na; Storey, Kenneth B.; Zheng, Rongquan; Zhang, Jia‐Yong

doi:10.3109/19401736.2015.1033697

Cited by 14 publications

(19 citation statements)

References 14 publications

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“…Gene order, lengths and codon compositions are shown in Table 1. The overall base composition of the heavy strand is 27.7% for A, 28.3% for T, 14.9% for G and 29.1% for C, with an A þ T bias of 59.9%, similar to other ranid species (Hofman et al 2014, Li et al 2014a, 2014b, Ni et al 2015. The genome shows a similar gene organization as other ranids (Kurabayashi et al 2010;Xia et al 2014), but it is the only anuran known so far lacking the tRNA Phe .…”

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confidence: 77%

The complete mitochondrial genome of the Endangered European brown frog Rana pyrenaica through RNAseq

Peso-Fernández

Ponti

Ponz‐Segrelles

et al. 2016

Mitochondrial DNA Part B

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We sequenced the complete mitogenome of the Pyrenean frog Rana pyrenaica , which was determined from an Illumina Hi-seq RNAseq run (Illumina Inc., San Diego, CA). The genome is 17,213 bp in size, including 13 protein-coding genes, 21 transfer RNAs, two ribosomal RNAs and a control region. It shows the typical gene order of previously available frog mitogenomes, although it lacks the tRNA Phe . This is the first complete mitogenome described for a Western Palearctic brown frog species.

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mentioning

confidence: 77%

The complete mitochondrial genome of the Endangered European brown frog Rana pyrenaica through RNAseq

Peso-Fernández

Ponti

Ponz‐Segrelles

et al. 2016

Mitochondrial DNA Part B

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“…This study included ten species that we sequenced ourselves and five species from GenBank; detailed information is shown in Table 1 and Fig 1. Within Table 1, The sequences with superscript numbers among the GenBank accession numbers are referenced as follows: 1, Zhou et al [17]; 2, Che et al [3]; 3; Zhou et al [18]; 4, Yan et al [11]; 5, Sumida et al [19]; 6, Lin et al [20]; 7, Ni et al [21]. This study was conducted in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health.…”

Section: Methodsmentioning

confidence: 99%

“…catesbeiana and L . sylvatica ) from GenBank [20, 21] were selected as outgroups for phylogeny and divergent time analyses. P-distances were calculated using MEGA v.7.0.…”

Section: Methodsmentioning

confidence: 99%

Phylogeny and biogeography of South Chinese brown frogs (Ranidae, Anura)

et al. 2017

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Few studies have explored the role of Cenozoic tectonic evolution in shaping the patterns and processes of extant animal distributions in and around East Asia. In this study, we selected South Chinese brown frogs as a model to examine the phylogenetic and biogeographical consequences of Miocene tectonic events within South China and its margins. We used mitochondrial and nuclear molecular data to reconstruct phylogenetic interrelationships among Chinese brown frogs using Bayesian and maximum likelihood analyses. The phylogeny results show that there are four main clades of Chinese brown frogs. Excepting the three commonly known Chinese brown frog species groups, R. maoershanensis forms an independent clade nearest to the R. japonica group. Phylogeny and P-distance analyses confirmed R. maoershanensis as a valid species. Among South Chinese brown frogs, there are four subclades associated with four geographical areas: (I) R. maoershanensis; (II) R. japonica; (III) R. chaochiaoensis; and (IV) other species of the R. longicrus species group. Divergence times, estimated using mitochondrial sequences, place the vicariance events among the four subclades in the middle to late Miocene epoch. Our results suggest that (1) South Chinese brown frogs originated due to a vicariance event separating them from the R. chensinensis species group at the time of the Geological movement (~18 million years ago, Ma) in southern Tibet and the Himalayan region; (2) the separation and speciation of R. maoershanensis from the R. japonica group occurred due to the dry climate at approximately 16 Ma; (3) South Chinese brown frogs migrated from South China to Japan at the time (~10.8 Ma) that the global sea-level fell and the East China Sea Shelf Basin was swamp facies, when a land gallery may have formed across the sea to connect the two areas; and (4) R. chaochiaoensis separated from other species of the R. longicrus species group during the uplift of the Tibetan Plateau at approximately 9.5 Ma.

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“…Comparative analysis showed that the longest IGN between A. americanus and Bufotes pewzowi had a high similarity (76.9%). In many vertebrates, there is usually a trnL (CUN) gene following the trnS (AGY) gene (Cheng et al, 2018;Lin et al, 2014;Ni et al, 2016;Ye et al, 2016;. However, when the trnL (CUN) gene is translocated, an IGN is left in its original position (Zhou et al, 2009).…”

Section: Control Region and Intergenic Regionsmentioning

confidence: 99%

Characterization of the mitochondrial genomes of two toads, Anaxyrus americanus (Anura: Bufonidae) and Bufotes pewzowi (Anura: Bufonidae), with phylogenetic and selection pressure analyses

Cai

Qin

Zhang

et al. 2020

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Mitogenomes are useful in analyzing phylogenetic relationships and also appear to influence energy metabolism, thermoregulation and osmoregulation. Much evidence has accumulated for positive selection acting on mitochondrial genes associated with environmental adaptation. Hence, the mitogenome is a likely target for environmental selection. The family Bufonidae (true toads) has only nine complete and four partial mitogenomes published compared to the 610 known species of this family. More mitogenomes are needed in order to obtain a clearer understanding of the phylogenetic relationships within Bufonidae that are currently controversial. To date, no mitogenomes have been reported from the genera Anaxyrus and Bufotes. Anaxyrus americanus can live in low temperature environments and Bufotes pewzowi can live in high salinity environments. We sequenced the mitogenomes of these two species to discuss the phylogenetic relationships within Bufonidae and the selection pressures experienced by specimens living in low temperature or saline environments. Like other toads, the circular mitogenomes of both species contained the typical 37 genes. Anaxyrus americanus had the highest A+T content of the complete mitogenome among the Bufonidae. In addition, A. americanus showed a negative AT-skew in the control region, whereas Bufotes pewzowi showed a positive AT-skew. Additionally, both toad species had unique molecular features in common: an ND1 gene that uses TTG as the start codon, an extra unpaired adenine (A) in the anticodon arm of trnS (AGY), and the loss of the DHU loop in trnC. The monophyly of Bufonidae was corroborated by both BI and ML trees. An analysis of selective pressure based on the 13 protein coding genes was conducted using the EasyCodeML program. In the branch model analysis, we found two branches of A. americanus and Bufotes pewzowi that were under negative selection. Additionally, we found two positively selected sites (at positions 115 and 119, BEB value > 0.90) in the ND6 protein in the site model analysis. The residue D (119) was located only in A. americanus and may be related to adaptive evolution in low temperature environments. However, there was no evidence of a positively selected site in Bufotes pewzowi in this study.

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The complete mitochondrial genome of Lithobates sylvaticus (Anura: Ranidae)

Cited by 14 publications

References 14 publications

The complete mitochondrial genome of the Endangered European brown frog Rana pyrenaica through RNAseq

The complete mitochondrial genome of the Endangered European brown frog Rana pyrenaica through RNAseq

Phylogeny and biogeography of South Chinese brown frogs (Ranidae, Anura)

Characterization of the mitochondrial genomes of two toads, Anaxyrus americanus (Anura: Bufonidae) and Bufotes pewzowi (Anura: Bufonidae), with phylogenetic and selection pressure analyses

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