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Li SZ, Chen JJ, Su HJ, Liu J, Tang XJ, Wang B. A new odorous frog species of Odorrana (Amphibia, Anura, Ranidae) from Guizhou Province, China. Zookeys 2024; 1192:57-82. [PMID: 38419744 PMCID: PMC10897836 DOI: 10.3897/zookeys.1192.114315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
The frog genus Odorrana is distributed across east and southeastern Asia. Based on morphological differences and molecular phylogenetics, a new species of the genus occurring from Leigong Mountain in Guizhou Province, China is described. Phylogenetic analyses based on DNA sequences of the mitochondrial 12S rRNA, 16S rRNA, and ND2 genes supported the new species as an independent lineage. The uncorrected genetic distances between the 12S rRNA, 16S rRNA, and ND2 genes between the new species and its closest congener were 5.0%, 4.9%, and 16.3%, respectively. The new species is distinguished from its congeners by a combination of the following characters: body size moderate (SVL 39.1-49.4 mm in males, 49.7 mm in female); head width larger than head length; tympanum distinctly visible; small rounded granules scattered all over dorsal body and limbs; dorsolateral folds absent; heels overlapping when thighs are positioned at right angles to the body; tibiotarsal articulation reaching the level between eye to nostril when leg stretched forward; vocal sacs absent in male and nuptial pads present on the base of finger I.
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Affiliation(s)
- Shi-Ze Li
- Department of Food Science and Engineering, Moutai Institute, Renhuai 564500, China Chengdu Institute of Biology, Chinese Academy of Sciences Chengdu China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China Moutai Institute Renhuai China
| | - Ji-Jun Chen
- Leigongshan National Nature Reserve Administration, Leishan 557100, China Leigongshan National Nature Reserve Administration Leishan China
| | - Hai-Jun Su
- College of Forestry, Guizhou University, Guiyang 550025, China Guizhou University Guiyang China
| | - Jing Liu
- Department of Food Science and Engineering, Moutai Institute, Renhuai 564500, China Chengdu Institute of Biology, Chinese Academy of Sciences Chengdu China
- College of Forestry, Guizhou University, Guiyang 550025, China Guizhou University Guiyang China
| | - Xiu-Jun Tang
- Leigongshan National Nature Reserve Administration, Leishan 557100, China Leigongshan National Nature Reserve Administration Leishan China
| | - Bin Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China Moutai Institute Renhuai China
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Yang T, Liu Y, Ning Z. Comparative Mitogenomic Analysis of Two Snake Eels Reveals Irregular Gene Rearrangement and Phylogenetic Implications of Ophichthidae. Animals (Basel) 2023; 13:ani13030362. [PMID: 36766251 PMCID: PMC9913227 DOI: 10.3390/ani13030362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/15/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
The family Ophichthidae has the largest number and the most various species (about 359 valid species) in the order Anguilliformes worldwide. Both morphological and molecular characteristics have been used to assess their taxonomic status. However, due to the ambiguous morphological features, molecular data such as mitochondrial DNA sequences have been implemented for the correct identification and classification of these fishes. In this study, the gene arrangement and structure characteristics of two Ophichthidae mitochondrial genomes were investigated for the first time. The total mitogenome lengths of O. evermanni and O. erabo were 17,759 bp and 17,856 bp, respectively. Comparing with the ancestral mitochondrial gene order, the irregular gene rearrangement happened between ND6 and tRNA-Pro (P) genes with another similar control region emerging between tRNA-Thr (T) and ND6 genes, which could be explained by the tandem duplication and random loss (TDRL) model appropriately. ML phylogenetic tree demonstrated that the family Ophichthidae was monophyletic origin, but genus Ophichthus might be polyphyletic because of the confused cluster relationships among different species.
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Zhong JJ, Ma L, Lin ZH, Ding GH, Luo ST. The complete mitochondrial DNA for the Fujian Bamboo-leaf Frog Odorrana exiliversabilis (Anura: Ranidae) by next-generation sequencing. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:570-571. [PMID: 33628933 PMCID: PMC7889110 DOI: 10.1080/23802359.2021.1875906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The complete mitochondrial DNA (mtDNA) for Odorrana exiliversabilisLi, 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 O. exiliversabilis was the sister species of O. tormota, and formed a monophyletic clade with other Odorrana species. These data provide a powerful tool for evolutionary biology and population genetics of genus Odorrana.
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Affiliation(s)
- Jun-Jie Zhong
- Laboratory of Amphibian Diversity Investigation, College of Ecology, Lishui University, Zhejiang, China
| | - Li Ma
- Laboratory of Amphibian Diversity Investigation, College of Ecology, Lishui University, Zhejiang, China
| | - Zhi-Hua Lin
- Laboratory of Amphibian Diversity Investigation, College of Ecology, Lishui University, Zhejiang, China
| | - Guo-Hua Ding
- Laboratory of Amphibian Diversity Investigation, College of Ecology, Lishui University, Zhejiang, China
| | - Si-Te Luo
- School of Life Sciences, Xiamen University, Xiamen, Fujian, China
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Jiang L, Zhang M, Deng L, Xu Z, Shi H, Jia X, Lai Z, Ruan Q, Chen W. Characteristics of the mitochondrial genome of Rana omeimontis and related species in Ranidae: Gene rearrangements and phylogenetic relationships. Ecol Evol 2020; 10:12817-12837. [PMID: 33304496 PMCID: PMC7713938 DOI: 10.1002/ece3.6824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/16/2020] [Accepted: 08/20/2020] [Indexed: 12/01/2022] Open
Abstract
The Omei wood frog (Rana omeimontis), endemic to central China, belongs to the family Ranidae. In this study, we achieved detail knowledge about the mitogenome of the species. The length of the genome is 20,120 bp, including 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a noncoding control region. Similar to other amphibians, we found that only nine genes (ND6 and eight tRNA genes) are encoded on the light strand (L) and other genes on the heavy strand (H). Totally, The base composition of the mitochondrial genome included 27.29% A, 28.85% T, 28.87% C, and 15.00% G, respectively. The control regions among the Rana species were found to exhibit rich genetic variability and A + T content. R. omeimontis was clustered together with R. chaochiaoensis in phylogenetic tree. Compared to R. amurensis and R. kunyuensi, it was more closely related to R. chaochiaoensis, and a new way of gene rearrangement (ND6-trnE-Cytb-D-loop-trnL2 (CUN)-ND5-D-loop) was also found in the mitogenome of R. amurensis and R. kunyuensi. Our results about the mitochondrial genome of R. omeimontis will contribute to the future studies on phylogenetic relationship and the taxonomic status of Rana and related Ranidae species.
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Affiliation(s)
- Lichun Jiang
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangChina
| | - Min Zhang
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Lu Deng
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Zhongwen Xu
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Hongyan Shi
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Xiaodong Jia
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Zhenli Lai
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Qiping Ruan
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Wei Chen
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangChina
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Zhang JY, Luu BE, Yu DN, Zhang LP, Al-attar R, Storey KB. The complete mitochondrial genome of Dryophytes versicolor: Phylogenetic relationship among Hylidae and mitochondrial protein-coding gene expression in response to freezing and anoxia. Int J Biol Macromol 2019; 132:461-469. [DOI: 10.1016/j.ijbiomac.2019.03.220] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/28/2019] [Accepted: 03/28/2019] [Indexed: 11/17/2022]
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Oh DJ, Yoon WJ, Park SY, Jung YH. Complete mitochondrial genome of cocktail wrasse Pteragogus flagellifer. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1546143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Dae-Ju Oh
- Jeju Biodiversity Research Institute, Jeju Technopark, Seogwipo, Republic of Korea
| | - Weon-Jong Yoon
- Jeju Biodiversity Research Institute, Jeju Technopark, Seogwipo, Republic of Korea
| | - Soo-Yeong Park
- Jeju Biodiversity Research Institute, Jeju Technopark, Seogwipo, Republic of Korea
| | - Yong-Hwan Jung
- Jeju Biodiversity Research Institute, Jeju Technopark, Seogwipo, Republic of Korea
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Jiang L, You Z, Yu P, Ruan Q, Chen W. The first complete mitochondrial genome sequence of Nanorana parkeri and Nanorana ventripunctata (Amphibia: Anura: Dicroglossidae), with related phylogenetic analyses. Ecol Evol 2018; 8:6972-6987. [PMID: 30073060 PMCID: PMC6065340 DOI: 10.1002/ece3.4214] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 04/20/2018] [Accepted: 04/24/2018] [Indexed: 11/24/2022] Open
Abstract
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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Affiliation(s)
- Lichun Jiang
- Ecological Security and Protection Key Laboratory of Sichuan Province Mianyang Normal University Mianyang Sichuan China.,Key Laboratory for Molecular Biology and Biopharmaceutics School of Life Science and Technology Mianyang Normal University Mianyang Sichuan China
| | - Zhangqiang You
- Ecological Security and Protection Key Laboratory of Sichuan Province Mianyang Normal University Mianyang Sichuan China
| | - Peng Yu
- Key Laboratory for Molecular Biology and Biopharmaceutics School of Life Science and Technology Mianyang Normal University Mianyang Sichuan China
| | - Qiping Ruan
- Key Laboratory for Molecular Biology and Biopharmaceutics School of Life Science and Technology Mianyang Normal University Mianyang Sichuan China
| | - Wei Chen
- Ecological Security and Protection Key Laboratory of Sichuan Province Mianyang Normal University Mianyang Sichuan China
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The complete mitochondrial genome of Odorrana hainanensis (Anura: Ranidae). CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-017-0775-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Zhang JY, Zhang LP, Yu DN, Storey KB, Zheng RQ. Complete mitochondrial genomes of Nanorana taihangnica and N. yunnanensis (Anura: Dicroglossidae) with novel gene arrangements and phylogenetic relationship of Dicroglossidae. BMC Evol Biol 2018; 18:26. [PMID: 29486721 PMCID: PMC6389187 DOI: 10.1186/s12862-018-1140-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 02/15/2018] [Indexed: 02/06/2023] Open
Abstract
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.
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Affiliation(s)
- Jia-Yong Zhang
- Key lab of wildlife biotechnology, conservation and utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang Province, 321004, China
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, 321004, China
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Le-Ping Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, 321004, China
| | - Dan-Na Yu
- Key lab of wildlife biotechnology, conservation and utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang Province, 321004, China.
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, 321004, China.
| | - Kenneth B Storey
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Rong-Quan Zheng
- Xingzhi College, Zhejiang Normal University, Jinhua, Zhejiang Province, 321004, China
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Jiang L, Zhao L, Cheng D, Zhu L, Zhang M, Ruan Q, Chen W. The complete mitochondrial genome sequence of the Sichuan Digging Frog, Kaloula rugifera (Anura: Microhylidae) and its phylogenetic implications. Gene 2017; 626:367-375. [PMID: 28536079 DOI: 10.1016/j.gene.2017.05.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 04/30/2017] [Accepted: 05/19/2017] [Indexed: 10/19/2022]
Abstract
The Sichuan Digging Frog (Kaloula rugifera) belongs to the family Dicroglossidae, which is endemic to northeastern Sichuan and southernmost Gansu provinces, in southwestern China. In this study, the complete mitochondrial genome of K. rugifera was sequenced. The mitogenome was 17,074bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a non-coding control region. As in other vertebrates, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes which are encoded on the light strand. The overall base composition of the K. rugifera is 30.32% A, 25.76% C, 29.72% T, and 14.20% G, which is consistent with the lowest frequency for G content in typical amphibian animals' mitochondrial genomes. The alignment of the Kaloula species control regions exhibited high genetic variability and rich A+T content. Besides, 3 types of tandem repeat units were also identified in the control region. Phylogenetic tree demonstrated that K. rugifera was clustered together with K. borealis and K. verrucosa and they had a close relationship with each other. The complete mitogenome of K. rugifera can provide an important data for the studies on phylogenetic relationship to further explore the taxonomic status of Kaloula species.
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Affiliation(s)
- Lichun Jiang
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan 621000, PR China; Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, Mianyang, Sichuan 621000, PR China
| | - Li Zhao
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, Mianyang, Sichuan 621000, PR China
| | - Dongmei Cheng
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, Mianyang, Sichuan 621000, PR China
| | - Lilan Zhu
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, Mianyang, Sichuan 621000, PR China
| | - Min Zhang
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, Mianyang, Sichuan 621000, PR China
| | - Qiping Ruan
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, Mianyang, Sichuan 621000, PR China.
| | - Wei Chen
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan 621000, PR China.
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Huang Y, Zhao W, Bao X, Lin Y, Ran J. Sequence and analysis of the complete mitochondrial genome of the Wuchuan Odorous Frog Odorrana wuchuanensis (Anura: Ranidae). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:757-758. [PMID: 33473617 PMCID: PMC7799677 DOI: 10.1080/23802359.2016.1219624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
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 ND6 and eight tRNA genes (tRNAPro, tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer, and tRNAGlu), which were encoded on the L-strand. The phylogenetic relationship of Anura based on complete mitochondrial genomes showed that O. wuchuanesis is closest to O. margaretae with strong support and the genetic distance between Ranidae, Dicroglossidae, and Rhacophoridae was closer than others.
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Affiliation(s)
- Yongjie Huang
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing, China
| | - Wei Zhao
- School of Life Science, Lanzhou University, Lanzhou, China
| | - Xinkang Bao
- School of Life Science, Lanzhou University, Lanzhou, China
| | - Yinghua Lin
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing, China
| | - Jingcheng Ran
- Guizhou Management Station of Wildlife, Guiyang, Guizhou Province, P.R. China
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Bu X, Zhang L, He K, Jiang Y, Nie L. The complete mitochondrial genome of the Odorrana schmackeri (Anura, Ranidae). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:162-163. [PMID: 33473447 PMCID: PMC7800420 DOI: 10.1080/23802359.2016.1144112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The complete mitochondrial genome of O. schmackeri has been sequenced and characterized in this study. The mitogenome is a circular molecule of 18 610 bp in length, containing 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 21 transfer RNA (tRNA) genes and a non-coding D-loop region (control region). Its gene arrangements are identical to the typical neobatrachian-type except for the loss of tRNAHis gene. Our data provide a useful resource for the phylogenetic studies of genus Odorrana.
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Affiliation(s)
- Xingjiang Bu
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, PR China
| | - Lijuan Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, PR China
| | - Kexin He
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, PR China
| | - Yanmei Jiang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, PR China
| | - Liuwang Nie
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, PR China
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Ding C, Zhou B, Guo H, Duan Y, Wang Z. Sequencing and analysis of mitochondrial genome of Elaphe carinata (Reptilia, Squamata, Colubridae). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:41-42. [PMID: 33473400 PMCID: PMC7800545 DOI: 10.1080/23802359.2015.1137813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The complete mitochondrial genome of Elaphe carinata was sequenced and analysed using muscle tissue for the first time. The genome is 17 154 bp in length. The complete mitochondrial genome contains 22 tRNA genes, 13 protein-coding genes (PCGs), two rRNA genes, two control regions (CRI and CRII) and one putative origin of L-strand replication. The gene order and nucleotide composition of E. carinata are very similar with E. davidi, E. schrenckii, E. anomala and E. bimaculata. A phylogenetic tree of mitochondrial genomes analyses of 16 species snakes of Colubridae was made based on the Neighbour-Joining (NJ) method, E. carinata has the most closely relationship with E. davidi, while E. poryphyracea and Euprepiophis perlacea are special species.
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Affiliation(s)
- Changhong Ding
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, P.R. China
| | - Bo Zhou
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, P.R. China
| | - Hui Guo
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, P.R. China
| | - Yunbao Duan
- College of Forestry, Southwest Forestry University, Kunming, P.R. China
| | - Zhenyue Wang
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, P.R. China
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Zhou B, Ding C, Duan Y, Hui G. The complete mitochondrial genome sequence of Ptyas mucosus. Mitochondrial DNA B Resour 2016; 1:193-194. [PMID: 33473451 PMCID: PMC7799689 DOI: 10.1080/23802359.2015.1137848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The complete mitochondrial genome sequence of the Ptyas mucosus was sequenced and reported for the first time using muscle tissue. The total length is 17 151 bp and sequence analysis showed its structure is in accordance with other snakes. The complete mitochondrial genome contains 2 rRNA genes, 21 tRNA genes, 13 protein-coding genes (PCGs), 2 control regions and 1 putative origin of L-strand replication. The gene order and nucleotide composition of P. mucosus are very similar with E. bimaculata, E. anomala and E. schrenckii. A phylogenetic tree of mitochondrial genomes indicated P. mucosus had the most closely relationship with E. bimaculata, and formed a monophyletic group with E. bimaculata, E. anomala and E. schrenckii.
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Affiliation(s)
- Bo Zhou
- Pharmacy College, Heilongjiang University of Chinese Medicine, Harbin, People's Republic of China
| | - Changhong Ding
- Pharmacy College, Heilongjiang University of Chinese Medicine, Harbin, People's Republic of China
| | - Yubao Duan
- College of Forestry, Southwest Forestry University, Kunming, People's Republic of China
| | - Guo Hui
- Pharmacy College, Heilongjiang University of Chinese Medicine, Harbin, People's Republic of China
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Yu D, Zhang J, Li P, Zheng R, Shao C. Do cryptic species exist in Hoplobatrachus rugulosus? An examination using four nuclear genes, the cyt b gene and the complete MT genome. PLoS One 2015; 10:e0124825. [PMID: 25875761 PMCID: PMC4395372 DOI: 10.1371/journal.pone.0124825] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 03/18/2015] [Indexed: 11/18/2022] Open
Abstract
he Chinese tiger frog Hoplobatrachus rugulosus is widely distributed in southern China, Malaysia, Myanmar, Thailand, and Vietnam. It is listed in Appendix II of CITES as the only Class II nationally-protected frog in China. The bred tiger frog known as the Thailand tiger frog, is also identified as H. rugulosus. Our analysis of the Cyt b gene showed high genetic divergence (13.8%) between wild and bred samples of tiger frog. Unexpected genetic divergence of the complete mt genome (14.0%) was also observed between wild and bred samples of tiger frog. Yet, the nuclear genes (NCX1, Rag1, Rhod, Tyr) showed little divergence between them. Despite this and their very similar morphology, the features of the mitochondrial genome including genetic divergence of other genes, different three-dimensional structures of ND5 proteins, and gene rearrangements indicate that H. rugulosus may be a cryptic species complex. Using Bayesian inference, maximum likelihood, and maximum parsimony analyses, Hoplobatrachus was resolved as a sister clade to Euphlyctis, and H. rugulosus (BT) as a sister clade to H. rugulosus (WT). We suggest that we should prevent Thailand tiger frogs (bred type) from escaping into wild environments lest they produce hybrids with Chinese tiger frogs (wild type).
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Affiliation(s)
- Danna Yu
- Institute of Ecology, Zhejiang Normal University, Jinhua, 321004, Zhejiang Province, China
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu Province, China
| | - Jiayong Zhang
- Institute of Ecology, Zhejiang Normal University, Jinhua, 321004, Zhejiang Province, China
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang Province, China
| | - Peng Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu Province, China
| | - Rongquan Zheng
- Institute of Ecology, Zhejiang Normal University, Jinhua, 321004, Zhejiang Province, China
- Institute of Special Aquaculture Source, Zhejiang Normal University, Jinhua, 321004, Zhejiang Province, China
| | - Chen Shao
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang Province, China
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16
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Huang Z, Yang C, Ke D. DNA barcoding and molecular phylogeny in Ranidae. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:4003-4007. [PMID: 25543914 DOI: 10.3109/19401736.2014.989522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The family Ranidae has the widest distribution compared with other frog family. The phylogeny of the Ranidae is still a matter of dispute. In the present study, we analyzed the COI barcodes of 29 species from six genera belonging to the family Ranidae. Twenty-seven species (93.10% of all the species) were correctly identified by their DNA barcodes. Pelophylax lessonae and Pelophylax ridibundus shared the same one barcode sequence. Kimura two-parameter distances were calculated between barcodes. Pair-wise comparisons among-species were distributed from 0.16% (between Pelophylax lessonae and Pelophylax esculenta) to 29.13% (between Rana warszewitschii and Rana dybowskii). The average genetic distance between species was 28 times higher than the average genetic distance within species. The neighbor-joining method was used to construct a phylogenetic tree, which grouped all the genera into two divergent clades. The results indicated that some currently recognized genera of Ranidae may not be monophyletic. COI gene data supported the hypothesis of polyphyly for Rana, Amolops, Babina, and Hylarana. DNA barcoding is an effective molecular tool for Ranidae species identification and phylogenetic inference.
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Affiliation(s)
- Zuhao Huang
- a School of Life Sciences, Jinggangshan University , Ji'an , Jiangxi Province , China and
| | - Chengzhong Yang
- b Chongqing Key Laboratory of Animal Biology , College of Life Sciences, Chongqing Normal University , Chongqing , China
| | - Dianhua Ke
- a School of Life Sciences, Jinggangshan University , Ji'an , Jiangxi Province , China and
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17
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Complete nucleotide sequence and gene rearrangement of the mitochondrial genome of Occidozyga martensii. J Genet 2014; 93:631-41. [DOI: 10.1007/s12041-014-0418-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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18
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Huang M, Duan R, Kong X, Wang H, Zhu H. The complete mitochondrial genome of Amolops wuyiensis (Anura: Ranidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1705-6. [PMID: 25238108 DOI: 10.3109/19401736.2014.961131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In the organisms, mitochondrial DNA plays an important role in the evolutionary studies, which can serve as a powerful molecular marker. Amolops wuyiensis, belongs to the family Ranidae that is known to occur in southeast China. The complete mitochondrial genome of A. wuyiensis was sequenced (17,797 bp in length, GenBank accession number KM386618). Similar to the typical mtDNA of amphibians, the complete mtDNA sequence of A. wuyiensis contained 13 protein-coding genes, 2 rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes and 1 control region. The nucleotide composition was 25.9% A, 33.8% T, 28.0% C and 12.3% G.
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Affiliation(s)
- Minyi Huang
- a College of Life Science, Anqing Normal University , Anqing , Anhui , P.R. China
| | - Renyan Duan
- a College of Life Science, Anqing Normal University , Anqing , Anhui , P.R. China
| | - Xiaoquan Kong
- a College of Life Science, Anqing Normal University , Anqing , Anhui , P.R. China
| | - Huanhuan Wang
- a College of Life Science, Anqing Normal University , Anqing , Anhui , P.R. China
| | - Haiyan Zhu
- a College of Life Science, Anqing Normal University , Anqing , Anhui , P.R. China
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Xia Y, Zheng Y, Miura I, Wong PBY, Murphy RW, Zeng X. The evolution of mitochondrial genomes in modern frogs (Neobatrachia): nonadaptive evolution of mitochondrial genome reorganization. BMC Genomics 2014; 15:691. [PMID: 25138662 PMCID: PMC4153901 DOI: 10.1186/1471-2164-15-691] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Accepted: 08/12/2014] [Indexed: 11/25/2022] Open
Abstract
Background Although mitochondrial (mt) gene order is highly conserved among vertebrates, widespread gene rearrangements occur in anurans, especially in neobatrachians. Protein coding genes in the mitogenome experience adaptive or purifying selection, yet the role that selection plays on genomic reorganization remains unclear. We sequence the mitogenomes of three species of Glandirana and hot spots of gene rearrangements of 20 frog species to investigate the diversity of mitogenomic reorganization in the Neobatrachia. By combing these data with other mitogenomes in GenBank, we evaluate if selective pressures or functional constraints act on mitogenomic reorganization in the Neobatrachia. We also look for correlations between tRNA positions and codon usage. Results Gene organization in Glandirana was typical of neobatrachian mitogenomes except for the presence of pseudogene trnS (AGY). Surveyed ranids largely exhibited gene arrangements typical of neobatrachian mtDNA although some gene rearrangements occurred. The correlation between codon usage and tRNA positions in neobatrachians was weak, and did not increase after identifying recurrent rearrangements as revealed by basal neobatrachians. Codon usage and tRNA positions were not significantly correlated when considering tRNA gene duplications or losses. Change in number of tRNA gene copies, which was driven by genomic reorganization, did not influence codon usage bias. Nucleotide substitution rates and dN/dS ratios were higher in neobatrachian mitogenomes than in archaeobatrachians, but the rates of mitogenomic reorganization and mt nucleotide diversity were not significantly correlated. Conclusions No evidence suggests that adaptive selection drove the reorganization of neobatrachian mitogenomes. In contrast, protein-coding genes that function in metabolism showed evidence for purifying selection, and some functional constraints appear to act on the organization of rRNA and tRNA genes. As important nonadaptive forces, genetic drift and mutation pressure may drive the fixation and evolution of mitogenomic reorganizations. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-691) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Xiaomao Zeng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
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20
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Wu X, Li Y, Zhang H, Jiang Z, Xue H, Yan P, Wu X. The complete mitochondrial genome of Hylarana guentheri (Amphidia, Anura, Ranidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1223-4. [PMID: 25101852 DOI: 10.3109/19401736.2014.945528] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of Hylarana guentheri was determined. This mitogenome was 19,053 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region (CR). The following three distinctive features were observed: there was an additional non-coding region of 561 bp between nad5 and nad6; four different tandem repeats were characteristic of the CR region for this species; a pseudogene of tRNA-His (trnH) was found in the CR downstream region.
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Affiliation(s)
- Xiaoyou Wu
- a Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource , College of Life Sciences, Anhui Normal University , Wuhu , P.R. China
| | - Yongmin Li
- a Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource , College of Life Sciences, Anhui Normal University , Wuhu , P.R. China .,b School of Life Sciences, Fuyang Teachers College , Fuyang , P.R. China , and
| | - Huabin Zhang
- a Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource , College of Life Sciences, Anhui Normal University , Wuhu , P.R. China .,c Jiangsu Key Laboratory for Bioresources of Saline Soils , Yancheng Teachers College , Yancheng , P.R. China
| | - Zhiyong Jiang
- a Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource , College of Life Sciences, Anhui Normal University , Wuhu , P.R. China
| | - Hui Xue
- a Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource , College of Life Sciences, Anhui Normal University , Wuhu , P.R. China
| | - Peng Yan
- a Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource , College of Life Sciences, Anhui Normal University , Wuhu , P.R. China
| | - Xiaobing Wu
- a Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource , College of Life Sciences, Anhui Normal University , Wuhu , P.R. China
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21
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Li E, Sun F, Zhang R, Chen J, Wu X. The complete mitochondrial genome of the striped-tailed rat-snake, Orthriophis taeniurus (Reptilia, Serpentes, Colubridae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:599-600. [PMID: 24730609 DOI: 10.3109/19401736.2014.908364] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome (mitogenome) of the striped-tailed rat-snake Orthriophis taeniurus was determined in the present study. The genome is 17,183 bp in size, containing 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and 2 control regions (CRI and CRII). The gene order and orientation in O. taeniurus mitogenome are basically identical to that of other alethinophidian snakes. Nucleotide composition is very similar with other vertebrates, showing an AT bias.
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Affiliation(s)
- En Li
- a Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource , College of Life Sciences, Anhui Normal University , Wuhu , P.R. China
| | - Fuxiao Sun
- a Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource , College of Life Sciences, Anhui Normal University , Wuhu , P.R. China
| | - Ruidong Zhang
- a Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource , College of Life Sciences, Anhui Normal University , Wuhu , P.R. China
| | - Jing Chen
- a Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource , College of Life Sciences, Anhui Normal University , Wuhu , P.R. China
| | - Xiaobing Wu
- a Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource , College of Life Sciences, Anhui Normal University , Wuhu , P.R. China
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22
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Li Y, Wu X, Zhang H, Yan P, Xue H, Wu X. The complete mitochondrial genome of Amolops ricketti (Amphidia, Anura, Ranidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:242-3. [PMID: 24521496 DOI: 10.3109/19401736.2014.883606] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The complete mitochondrial genome from the South China torrent frog Amolops ricketti was determined. This mitogenome was 17,771 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region (CR). All the protein-coding genes in A. ricketti were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand.
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Affiliation(s)
- Yongmin Li
- a Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource , College of Life Sciences, Anhui Normal University , Wuhu , China .,b School of Life Sciences, Fuyang Teachers College , Fuyang , China , and
| | - Xiaoyou Wu
- a Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource , College of Life Sciences, Anhui Normal University , Wuhu , China
| | - Huabin Zhang
- a Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource , College of Life Sciences, Anhui Normal University , Wuhu , China .,c Jiangsu Key Laboratory for Bioresources of Saline Soils , Yancheng Teachers University , Yancheng , China
| | - Peng Yan
- a Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource , College of Life Sciences, Anhui Normal University , Wuhu , China
| | - Hui Xue
- a Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource , College of Life Sciences, Anhui Normal University , Wuhu , China
| | - Xiaobing Wu
- a Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource , College of Life Sciences, Anhui Normal University , Wuhu , China
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23
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Wu X, Li Y, Zhang H, Yan L, Wu XB. The complete mitochondrial genome of Microhyla pulchra (Amphidia, Anura, Microhylidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:40-1. [PMID: 24438273 DOI: 10.3109/19401736.2013.869685] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of Microhyl pulchra was determined in this work. This mitogenome was 16,744 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region (CR). The following four distinctive features were observed: a protein-coding gene (ND1) began with GTG as start codon; eight protein-coding genes (ND1, COII, ATP6, COIII, ND3, ND4, ND5 and Cytb) ended with incomplete stop codon T; four tRNA genes positions (tRNA-Leu (CUN)/tRNA-Thr/Trna-Pro/tRNA-Phe) located between CR and 12S rRNA genes, which was a novel mtDNA gene rearrangement in amphibians; there was no significant repeat regions in the CR.
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Affiliation(s)
- Xiaoyou Wu
- a Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource , College of Life Sciences, Anhui Normal University , Wuhu , China
| | - Yongmin Li
- a Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource , College of Life Sciences, Anhui Normal University , Wuhu , China .,b College of Life Sciences, Fuyang Normal University , Fuyang , China , and
| | - Huabin Zhang
- a Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource , College of Life Sciences, Anhui Normal University , Wuhu , China .,c Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection , Yancheng Normal University , Yancheng , China
| | - Long Yan
- a Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource , College of Life Sciences, Anhui Normal University , Wuhu , China
| | - Xiao-Bing Wu
- a Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource , College of Life Sciences, Anhui Normal University , Wuhu , China
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24
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Li E, Feng D, Yan P, Xue H, Chen J, Wu XB. The complete mitochondrial genome of Oocatochus rufodorsatus (Reptilia, Serpentes, Colubridae). ACTA ACUST UNITED AC 2013; 25:449-50. [PMID: 23901930 DOI: 10.3109/19401736.2013.814116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome from the red-backed ratsnake Oocatochus rufodorsatus was determined. The following four distinctive features are observed: duplicate control regions that have nearly identical sequences at two different locations of mitogenome, translocation of tRNA-Leu (UUR), a pseudogene for tRNA-Pro and truncations of TΨC arm for most tRNA genes.
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Affiliation(s)
- En Li
- College of Life Sciences, Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, Anhui Normal University , Wuhu , P.R. China
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25
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Zeng L, Wang J, Sheng J, Gu Q, Hong Y. Molecular characteristics of mitochondrial DNA and phylogenetic analysis of the loach (Misgurnus anguillicaudatus) from the Poyang Lake. ACTA ACUST UNITED AC 2012; 23:187-200. [PMID: 22651231 DOI: 10.3109/19401736.2012.668893] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The goal of our study was to investigate the molecular characteristics of mitochondrial DNA (mtDNA) and phylogenetic construction of the weather loach (Misgurnus anguillicaudatus) in Poyang Lake. The complete mitochondrial genome was 16,634 bp, and the gene order was identical to that of teleost fishes. Compared with the previous reported weather loach in China, there were numerous nucleotide substitutions and length polymorphisms on the structural genes of mitochondrial DNA in the loach from the Poyang Lake. The Phylogenetic tree indicated that the loach had its own molecular characteristics and was somewhat different from those in other regions of China. Fourteen unique haplotypes of the cytochrome b (cyt b) gene were obtained from 300 weather loaches. The Phylogenetic tree based on the cyt b gene showed that the loaches were substructured into two different populations in The Poyang Lake. Results indicated that the loaches in Poyang Lake not only showed the same phylogeny as the loaches in other areas of China, but also generated its own unique phylogenetic relationships.
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Affiliation(s)
- Liugen Zeng
- Key Laboratory of Molecular Biology and Genetic Engineering in Jiangxi, College of Life Science and Food Engineering, Nanchang University, Nanchang, PR China
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26
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Yu D, Zhang J, Zheng R, Shao C. The complete mitochondrial genome ofHoplobatrachusrugulosus (Anura: Dicroglossidae). ACTA ACUST UNITED AC 2012; 23:336-7. [DOI: 10.3109/19401736.2012.690748] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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27
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Hofman S, Pabijan M, Dziewulska-Szwajkowska D, Szymura JM. Mitochondrial genome organization and divergence in hybridizing central European waterfrogs of the Pelophylax esculentus complex (Anura, Ranidae). Gene 2011; 491:71-80. [PMID: 21951340 DOI: 10.1016/j.gene.2011.08.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2011] [Revised: 08/02/2011] [Accepted: 08/10/2011] [Indexed: 01/08/2023]
Abstract
Natural transfer of mitochondrial DNA has occurred between three western Palaearctic waterfrog taxa: Pelophylax lessonae, Pelophylax ridibundus and their hybridogenetic hybrid, Pelophylax kl. esculentus. The transfer is asymmetric with most P. kl. esculentus and approximately one third of all central European P. ridibundus having mtDNA derived from P. lessonae (L-mtDNA). We obtained complete nucleotide sequences of multiple mitochondrial genomes (15,376-78 bp without control regions) from all 3 taxa, including a P. ridibundus frog with introgressed L-mtDNA. The gene content and organization of the mitogenomes correspond to those typical of neobatrachians. Divergence between the mtDNAs of P. lessonae and P. ridibundus is high with an uncorrected p-distance of 11.9% across the entire mitogenome. However, the rate of nucleotide substitution depends on the degree of functional constraint with up to 30-fold differences in levels of divergence. In general, mitochondrial genes encoding the translational machinery evolve very slowly, whereas genes encoding polypeptides of the electron transport system, especially the ND genes, evolve rapidly. Only 25 of 211-213 observed amino acid replacements could be classified as radical and are therefore more likely to be exposed to selection. A disproportionately high number of amino acid substitutions has occurred in the ND4, ND4L and cytb genes of the P. lessonae lineage (including 36% of all radical changes). In contrast to the interspecific divergence, nucleotide polymorphism within L- and R-mtDNA is very low: L-mtDNA haplotypes differed on average by only 19 nucleotides, while there was no variation within two mtDNAs derived from P. ridibundus. This is an expected finding considering that we have sampled a post-glacial expansion area. Moreover, the introgressed L-mtDNA on a P. ridibundus background differed from other L-mtDNAs by only a few substitutions, indicative of a very recent introgression event. We discuss our findings in the context of natural selection acting on L-mtDNA and its potential significance in cytonuclear epistasis.
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Affiliation(s)
- Sebastian Hofman
- Department of Comparative Anatomy, Institute of Zoology, Jagiellonian University, ul. Gronostajowa 9, 30-387 Kraków, Poland.
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Zhang J, Wu X, Xie M, Xu X, Li A. The mitochondrial genome ofPolylabris halichoeres(Monogenea: Microcotylidae). ACTA ACUST UNITED AC 2011; 22:3-5. [DOI: 10.3109/19401736.2011.588223] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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29
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The diversity of arbuscular mycorrhizal fungi in the subtropical forest of Huangshan (Yellow Mountain), East-Central China. World J Microbiol Biotechnol 2011. [DOI: 10.1007/s11274-011-0702-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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30
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Kurabayashi A, Yoshikawa N, Sato N, Hayashi Y, Oumi S, Fujii T, Sumida M. Complete mitochondrial DNA sequence of the endangered frog Odorrana ishikawae (family Ranidae) and unexpected diversity of mt gene arrangements in ranids. Mol Phylogenet Evol 2010; 56:543-53. [DOI: 10.1016/j.ympev.2010.01.022] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 12/21/2009] [Accepted: 01/20/2010] [Indexed: 11/29/2022]
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31
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Tang B, Pan H, Zhang Q, Ding L. Cloning and expression of cellulase gene EG1 from Rhizopus stolonifer var. reflexus TP-02 in Escherichia coli. BIORESOURCE TECHNOLOGY 2009; 100:6129-6132. [PMID: 19640700 DOI: 10.1016/j.biortech.2009.06.091] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Revised: 06/08/2009] [Accepted: 06/09/2009] [Indexed: 05/28/2023]
Abstract
A novel gene, EG encoding enzymes involved in carboxymethyl cellulose (CMC) degradation was isolated, sequenced from the filamentous fungus Rhizopus stolonifer var. reflexus TP-02, and expressed in Escherichia coli BL21. The results showed that the gene amplified from the cDNA of the strain could be classified as the family of endoglucanase. During the fermentation process, the maximum endoglucanase activity (i.e. 0.715 IU/ml) of the recombinant bacteria was obtained at 36 h. The SDS-PAGE analysis on purified samples showed that a band with apparent molecular weight of about 40 kDa was detected after staining with Coomassie brilliant blue.
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Affiliation(s)
- Bin Tang
- Department of Biochemical Engineering, Anhui University of Technology and Science, Wuhu 241000, China.
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32
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Complete nucleotide sequence and gene organization of the mitochondrial genome of Paa spinosa (Anura: Ranoidae). Gene 2009; 447:86-96. [PMID: 19631263 DOI: 10.1016/j.gene.2009.07.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Revised: 03/28/2009] [Accepted: 07/14/2009] [Indexed: 11/22/2022]
Abstract
The mt genome of Paa spinosa (Anura: Ranoidae) is a circular molecule of 18,012 bp in length, containing 38 genes (including an extra copy of tRNA-Met gene). This mt genome is characterized by three distinctive features: a cluster of rearranged tRNA genes (LTPF tRNA gene cluster), a tandem duplication of tRNA-Met gene (Met1 and Met2), and distinct repeat regions at both 5' and 3'-sides in the control region. Comparing the locations and the sequences of all tRNA-Met genes among Ranoidae, and constructing NJ tree of the nucleotide of those tRNA-Met genes, we suggested a tandem duplication of tRNA-Met gene can be regarded as a synapomorphy of Dicroglossinae. To further investigate the phylogenetic relationships of anurans, phylogenetic analyses (BI, ML and MP) based on the nucleotide dataset and the corresponding amino acid dataset of 11 protein-coding genes (except ND5 and ATP8) arrived at the similar topology.
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The complete mitochondrial genome of the large-headed frog, Limnonectes bannaensis (Amphibia: Anura), and a novel gene organization in the vertebrate mtDNA. Gene 2009; 442:119-27. [PMID: 19397958 DOI: 10.1016/j.gene.2009.04.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2008] [Revised: 04/16/2009] [Accepted: 04/17/2009] [Indexed: 11/20/2022]
Abstract
We determined the complete nucleotide sequence of the mitochondrial (mt) genome of the large-headed frog, Limnonectes bannaensis (Amphibia, Anura) by using polymerase chain reaction (PCR). The entire mtDNA sequence is 16,867 bp in length with a novel case of tRNAs in vertebrates. This mt genome is characterized by three distinctive features: (1) a tandem duplication of tRNA(Met) gene is observed, (2) the tRNA(Ala), tRNA(Asn), tRNA(Cys) and tRNA(Glu) genes coded on the L-strand are absent from the L. bannaensis mtDNA, the tRNA(Cys) and tRNA(Glu) genes change into tRNA pseudogenes by reason of degenerative anticodon, and a noncoding sequence of 206 nt long (NC1) has replaced the original position of other two tRNAs, (3) besides NC1, another three noncoding spacers (NC2-4) longer than 50 bp are found in the broken WANCY region and the region NC3-ND5-NC4-ND6-PsiE-Cytb-CR of the new sequence. These features could be explained by a model of gene duplication and deletion. The new sequence data was used to assess the phylogenetic relationships among 25 species of Anura using neighbor-joining, Bayesian, and maximum likelihood methods, and the phylogenetic tree shows the rice frog Fejervarya limnocharis is closest to L. bannaensis in the study.
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Abstract
Vertebrates can modulate the sound levels entering their inner ears in the face of intense external sound or during their own vocalizations. Middle ear muscle contractions restrain the motion of the middle ear ossicles, attenuating the transmission of low-frequency sound and thereby protecting the hair cells in the inner ear. Here we show that the Chinese concave-eared torrent frog, Odorrana tormota, can tune its ears dynamically by closing its normally open Eustachian tubes. Contrary to the belief that the middle ear in frogs permanently communicates with the mouth, O. tormota can close this connection by contraction of the submaxillary and petrohyoid muscles, drastically reducing the air volume behind the eardrums. Mathematical modeling and laser Doppler vibrometry revealed that the reduction of this air volume increases the middle ear impedance, resulting in an up to 20 dB gain in eardrum vibration at high frequencies (10-32 kHz) and 26 dB attenuation at low frequencies (3-10 kHz). Eustachian tube closure was observed in the field during calling and swallowing. Besides a potential role in protecting the inner ear from intense low-frequency sound and high buccal air pressure during calling, this previously unrecognized vertebrate mechanism may unmask the high-frequency calls of this species from the low-frequency stream noise which dominates the environment. This mechanism also protects the thin tympanic membranes from injury during swallowing of live arthropod prey.
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