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Comparison and Phylogenetic Analysis of Mitochondrial Genomes of Talpidae Animals. Animals (Basel) 2023; 13:ani13020186. [PMID: 36670726 PMCID: PMC9854984 DOI: 10.3390/ani13020186] [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: 11/11/2022] [Revised: 12/30/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
Talpidae is a model group for evolutionary studies due to their highly specialized morphologies and diverse lifestyles. Mitochondrial genomes are molecular markers commonly used in species evolution and phylogenetic studies. In this study, the complete mitochondrial genome sequence of Scaptochirus moschatus was obtained by Illumina NovaSeq sequencing. The complete mitochondrial genomes of 14 Talpidae species (including Scaptochirus moschatus obtained in the present study) and the cytochrome b (Cyt b) gene sequences of 48 Talpidae species were downloaded from the NCBI database for comparison and phylogenetic studies to analyze the phylogenetic relationships and to find the possible reasons of the niche differentiation and ecotype specialization of Talpidae animals. The results showed that the mitochondrial genome sequences of 14 species belonging to the family Talpidae were 16,528 to 16,962 bp, all containing 13 protein-coding genes, 22 tRNA, two rRNA, and a non-coding region (control region). The difference in the number of repetitive repeats in the control region is responsible for the difference in the length of Talpidae mitochondrial genome sequences. Combining the divergence time of Talpidae animals with the geological history, it is found that the niche differentiation and ecotype divergence of Talpidae is closely related to historically global climate changes. Semi-aquatic groups diverged in the early Oligocene (about 31.22 MYA), probably in response to the global climate transition from warm to cool. During the early Miocene (about 19.54 MYA), some species of Talpidae moved to underground habitats and formed fossorial groups that were adept at digging due to the effects of the glaciation. In the middle Miocene (about 16.23 MYA), some Talpidae animals returned to the ground and formed semi-fossorial shrew moles as global climate warming again.
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Demirtaş S, Budak M, Korkmaz EM, Searle JB, Bilton DT, Gündüz İ. The complete mitochondrial genome of Talpa martinorum (Mammalia: Talpidae), a mole species endemic to Thrace: genome content and phylogenetic considerations. Genetica 2022; 150:317-325. [PMID: 36029420 DOI: 10.1007/s10709-022-00162-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 08/04/2022] [Indexed: 11/04/2022]
Abstract
The complete mitogenome sequence of Talpa martinorum, a recently described Balkan endemic mole, was assembled from next generation sequence data. The mitogenome is similar to that of the three other Talpa species sequenced to date, being 16,835 bp in length, and containing 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, an origin of L-strand replication, and a control region or D-loop. Compared to other Talpa mitogenomes sequenced to date, that of T. martinorum differs in the length of D-loop and stop codon usage. TAG and T-- are the stop codons for the ND1 and ATP8 genes, respectively, in T. martinorum, whilst TAA acts as a stop codon for both ND1 and ATP8 in the other three Talpa species sequenced. Phylogeny reconstructions based on Maximum Likelihood and Bayesian inference analyses yielded phylogenies with similar topologies, demonstrating that T. martinorum nests within the western lineage of the genus, being closely related to T. aquitania and T. occidentalis.
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Affiliation(s)
- Sadık Demirtaş
- Department of Biology, Faculty of Arts and Sciences, Ondokuz Mayis University, Samsun, Turkey
| | - Mahir Budak
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
| | - Ertan M Korkmaz
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853-2701, USA
| | - David T Bilton
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, Devon, PL4 8AA, UK.,Department of Zoology, University of Johannesburg, Auckland Park, PO Box 524, Johannesburg, 2006, South Africa
| | - İslam Gündüz
- Department of Biology, Faculty of Arts and Sciences, Ondokuz Mayis University, Samsun, Turkey.
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Tu F, Huang X, Zhang Y, Feng Y. Complete mitochondrial genome of captive Chinese porcupine Hystrix hodgsoni (Rodentia: Hystricidae). Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1756488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Feiyun Tu
- Institute of Wildlife Conservation, Jiangxi Academy of Forestry, Nanchang, Jiangxi Province, China
| | - Xiaofeng Huang
- Institute of Wildlife Conservation, Jiangxi Academy of Forestry, Nanchang, Jiangxi Province, China
| | - Yixuan Zhang
- Institute of Wildlife Conservation, Jiangxi Academy of Forestry, Nanchang, Jiangxi Province, China
| | - Yingying Feng
- Institute of Wildlife Conservation, Jiangxi Academy of Forestry, Nanchang, Jiangxi Province, China
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Gutiérrez J, Lamelas L, Aleix-Mata G, Arroyo M, Marchal JA, Palomeque T, Lorite P, Sánchez A. Complete mitochondrial genome of the Iberian Mole Talpa occidentalis (Talpidae, Insectivora) and comparison with Talpa europaea. Genetica 2018; 146:415-423. [PMID: 30145730 DOI: 10.1007/s10709-018-0033-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 08/01/2018] [Indexed: 12/23/2022]
Abstract
The complete mitogenome of Talpa occidentalis, the Iberian mole, was sequenced using a combination of the Illumina and Sanger methods. The 16,962 bp genome obtained contains 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a control region. Thirty-seven identical repetitions of a 10-nucleotide (CACACGTACG) repeat element were identified in the non-coding control region (D-loop). The number, order, and orientation of the mitochondrial genes are the same as in T. europaea, the only mitogenome published so far for this genus. These two mitogenomes differ only at the repeat element included in the control region. The phylogeny obtained for the Talpidae species using the protein-coding genes of these mitogenomes agrees with the current classification of this family.
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Affiliation(s)
- Juana Gutiérrez
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - Luz Lamelas
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - Gaël Aleix-Mata
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - María Arroyo
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - Juan Alberto Marchal
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - Teresa Palomeque
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - Pedro Lorite
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - Antonio Sánchez
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain.
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The complete mitochondrial genome of Chinese Shrew, Sorex sinalis (Soricidae). CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-017-0780-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Tu F, Tang S, Yan C, Huang X. Complete mitogenome of Intermediate Egret Ardea intermedia (Ciconiiformes: Ardeidae). Mitochondrial DNA B Resour 2017; 2:510-511. [PMID: 33473879 PMCID: PMC7799489 DOI: 10.1080/23802359.2017.1361352] [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: 11/15/2022] Open
Abstract
The Intermediate Egret Ardea intermedia belongs to family Ardeidae, and it is widely distributed over east Africa across the Indian subcontinent to Southeast Asia and Australia. In the present study, the total mitochondrial genome of A. intermedia was determined. The genome is 18,578 bases in length and contains 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes and 2 non-coding regions (CR and CRR), with a base composition of A 30.8%, G 14.0%, T 24.3% and C 30.9%. The dn/ds values of ten PCGs (ND1, ND2, ATP8, ATP6, Cox3, ND3, ND4L, ND4, ND5 and ND6) are below 1. Bayesian inference (BI) and maximum likelihood (ML) methods generated similar topologies. Phylogenies showed that Ardea novaehollandiae and A. intermedia should be assign to Egretta and Ardea, respectively. The mitogenomic data of A. intermedia will be useful in the conservation genetics and phylogeny of the species.
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Affiliation(s)
- Feiyun Tu
- Institute of Wildlife Conservation, Jiangxi Academy of Forestry, Nanchang, Jiangxi Province, China
| | - Shan Tang
- Institute of Wildlife Conservation, Jiangxi Academy of Forestry, Nanchang, Jiangxi Province, China
| | - Chaochao Yan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan Province, China
| | - Xiaofeng Huang
- Institute of Wildlife Conservation, Jiangxi Academy of Forestry, Nanchang, Jiangxi Province, China
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Xu Y, Hu Y, Tu F. Mitogenome of a cryptic species within Uropsilus and divergence time estimation. Mitochondrial DNA B Resour 2017; 2:685-686. [PMID: 33473947 PMCID: PMC7800900 DOI: 10.3109/19401736.2015.1060440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 06/06/2015] [Indexed: 11/13/2022] Open
Abstract
Uropsilus sp. 4 is a new cryptic species, collected in Changyang county, Hubei province, China. In this study, the whole mitochondrial genome of Uropsilus sp. 4 was first determined and characterized. The genome is 16,542 bp in length, containing 13 protein coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Base on NJ, ML, and BI methods, we obtained the same topologies. U. sp. 4 clustered with U. gracilis and the divergence time was 1.78 Ma (95% CI 1.24-2.32 Ma), in concordance with the third period of last orogenic push of the Qinghai-Tibetan Plateau, might contribute to the speciation of U. sp. 4.
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Affiliation(s)
- Yu Xu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yunting Hu
- Guizhou Normal University Library, Guizhou Normal University, Guiyang, China
| | - Feiyun Tu
- Institute of Wildlife Conservation, Jiangxi Academy of Forestry, Nanchang, China
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Li B, Song X, Yan C, Ran J, Zhang X, Yue B. Complete mitochondrial genome sequence of Arboreal Brown-toothed Shrew, Episoriculus macrurus. Mitochondrial DNA B Resour 2016; 1:332-333. [PMID: 33644374 PMCID: PMC7871864 DOI: 10.1080/23802359.2016.1172047] [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: 11/03/2022] Open
Abstract
The Arboreal Brown-toothed Shrew (Episoriculus macrurus) belongs to the family Soricidae, and distributes in China, Nepal, India, Myanma, and Vietnam. In this study, the complete mitochondrial genome sequence of E. macrurus was determined. The mitogenome is 16,943 bp in length. Phylogenetic trees were constructed by the methods of Bayesian inference and maximum likelihood. The results showed that in the family of Soricidae, Crocidurinae differentiated earlier than Soricinae. Episoriculus was more close to Nectogale or Neomys rather than Sorex, and Blarinella was close to Sorex. This study contributes to illuminating the taxonomic status of E. macrurus.
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Affiliation(s)
- Bo Li
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Xuhao Song
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Chaochao Yan
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Jianghong Ran
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiuyue Zhang
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Bisong Yue
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
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Xu Y, Huang X, Hu Y, Tu F. Description of the mitogenome of Gansu mole (Scapanulus oweni). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:2083-4. [PMID: 25391035 DOI: 10.3109/19401736.2014.982567] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Gansu mole Scapanulus oweni belongs to family Talpidae, and is distributed in the Central and Southwest China. In this study, the total mitochondrial genome of S. oweni was firstly determined. The genome is 16,826 bases in length and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a displacement loop region, with a base composition of A 34.0%, G 13.5%, T 28.7% and C 23.9%. All of the protein-coding genes initiate with the orthodox ATG start codon execpt for Nd2 and Nd3 begin with ATT, Nd4 and Nd5, start with GTG and ATA, respectively. Four types of stop codons are used by the coding genes, including TAA for Nd1, Cox1, Cox2, Atp8, Atp6, Nd4L, Nd5, Nd6, TAG for Nd2, AGA for Cytb, and an incomplete stop codon T for Cox3, Nd3 and Nd4. The mito-genomic data of Gansu mole, S. oweni will be useful in determining its taxonomic status within Talpidae.
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Affiliation(s)
- Yu Xu
- a School of Resources and Environmental Sciences, Pingdingshan University , Pingdingshan , Henan , China
| | - Xiaofeng Huang
- b Institute of Wildlife Conservation, Jiangxi Academy of Forestry , Nanchang , China , and
| | - Yunting Hu
- c Pingdingshan University Library, Pingdingshan University , Pingdingshan , Henan , China
| | - Feiyun Tu
- b Institute of Wildlife Conservation, Jiangxi Academy of Forestry , Nanchang , China , and
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Tu F, Fan Z, Murphy RW, Chen S, Zhang X, Yan C, Liu Y, Sun Z, Fu J, Liu S, Yue B. Molecular phylogenetic relationships among Asiatic shrewlike moles inferred from the complete mitogenomes. J ZOOL SYST EVOL RES 2014. [DOI: 10.1111/jzs.12081] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Feiyun Tu
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife; College of Life Sciences; Sichuan University; Chengdu China
- Jiangxi Academy of Forestry; Nanchang China
| | - Zhenxin Fan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife; College of Life Sciences; Sichuan University; Chengdu China
| | - Robert W. Murphy
- Centre for Biodiversity and Conservation Biology; Royal Ontario Museum; Toronto M5S, 2C6 Canada
| | - Shunde Chen
- College of Life Sciences; Sichuan Normal University; Chengdu China
| | - Xiuyue Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife; College of Life Sciences; Sichuan University; Chengdu China
| | - Chaochao Yan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife; College of Life Sciences; Sichuan University; Chengdu China
| | - Yang Liu
- Sichuan Academy of Forestry; Chengdu China
| | - Zhiyu Sun
- Sichuan Academy of Forestry; Chengdu China
| | | | | | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife; College of Life Sciences; Sichuan University; Chengdu China
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Li Q, Wang Q, Chen G, Fu C, Chen S. The complete mitogenome of Chinese Mole Shrew, Anourosorex squamipes (Soricidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:553-4. [PMID: 24708118 DOI: 10.3109/19401736.2014.905854] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Chinese Mole Shrew, Anourosorex squamipes belongs to the family Soricidae, and widely distributes in central and southern China, northern and south Burma, east India, northern Vietnam and Thailand. In this study, the complete mitochondrial genome sequence of Anourosorex squamipes was determined. The mitogenome is 17,121 base pairs in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region, with base composition of 34.0% A, 31.3% T, 22.0% C, and 12.7% G. The genome organization, nucleotide composition and codon usage did not differ significantly from those of other shrews. The study contributes to illuminating taxonomic status of Chinese Mole Shrew Anourosorex squamipes.
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Affiliation(s)
- Qun Li
- a College of Life Sciences, Sichuan Normal University , Chengdu , People's Republic of China
| | - Qiong Wang
- a College of Life Sciences, Sichuan Normal University , Chengdu , People's Republic of China
| | - Guiying Chen
- a College of Life Sciences, Sichuan Normal University , Chengdu , People's Republic of China
| | - Changkun Fu
- a College of Life Sciences, Sichuan Normal University , Chengdu , People's Republic of China
| | - Shunde Chen
- a College of Life Sciences, Sichuan Normal University , Chengdu , People's Republic of China
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Wang Q, Fu C, Chen S, Yong B, Chen G, Zong H. The complete mitogenome of Asiatic Short-tailed ShrewBlarinella quadraticauda(Soricidae). ACTA ACUST UNITED AC 2014; 27:282-3. [DOI: 10.3109/19401736.2014.892078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Tu F, Liu S, Liu Y, Sun Z, Yin Y, Yan C, Lu L, Yue B, Zhang X. Complete mitogenome of Chinese shrew moleUropsilus soricipes(Milne-Edwards, 1871) (Mammalia: Talpidae) and genetic structure of the species in the Jiajin Mountains (China). J NAT HIST 2014. [DOI: 10.1080/00222933.2013.842012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Chen S, Tu F, Zhang X, Li W, Chen G, Zong H, Wang Q. The complete mitogenome of Stripe-Backed Shrew,Sorex cylindricauda(Soricidae). ACTA ACUST UNITED AC 2014; 26:477-8. [DOI: 10.3109/19401736.2013.855756] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Huang T, Yan C, Tan Z, Tu F, Yue B, Zhang X. Complete mitochondrial genome sequence of Nectogale elegans. ACTA ACUST UNITED AC 2013; 25:253-4. [PMID: 23795853 DOI: 10.3109/19401736.2013.800490] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The elegant water shrew (Nectogale elegans) belongs to the family Soricidae, and distributes in northern South Asia, central and southern China and northern Southeast Asia. In this study, the complete mitochondrial genome of N. elegans was sequenced. It was determined to be 17,460 bases, and included 13 protein-coding genes (PCGs), 22 tRNA genes, 2 ribosomal RNA genes and one non-coding region, which is similar to other mammalian mitochondrial genomes. Bayesian inference and maximum likelihood methods were used to construct phylogenetic trees based on 12 heavy-strand concatenated PCGs. Phylogenetic analyses further confirmed that Crocidurinae diverged prior to Soricinae, and Sorex unguiculatus differentiated earlier than N. elegans.
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Affiliation(s)
- Ting Huang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University , Chengdu , P.R. China and
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Lu L, Tu F, Yan C, Zhang X, Yue B, Zeng T. The complete mitochondrial genome sequence of Shrew Gymnure,Neotetracus sinensis. ACTA ACUST UNITED AC 2012. [DOI: 10.3109/19401736.2012.744976] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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