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Bernacki LE, Kilpatrick CW. Structural Variation of the Turtle Mitochondrial Control Region. J Mol Evol 2020; 88:618-640. [PMID: 32808073 DOI: 10.1007/s00239-020-09962-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 08/05/2020] [Indexed: 11/25/2022]
Abstract
The present study describes the most comprehensive comparison of turtle mtD-loop regions to date. The primary structure was compared from DNA sequences accessed from GenBank from 48 species in 13 families of extant turtles, and secondary structures of the mtD-loop region were inferred from thermal stabilities, using the program Mfold, for each superfamiliy of turtles. Both primary and secondary structures were found to be highly variable across the order. The Cryptodira showed conservation in the primary structure at conserved sequence blocks (CSBs), but the Pleurodira displayed limited conservation of primary structural characters, other than the coreTAS, a binding site for the helicase TWINKLE, which was highly conserved in the Central and Right Domains across the order. No secondary structure was associated with a TAS, but an AT-rich fold (secondary structure) near the 3' terminus of the mtD-loop region was detected in all turtle superfamilies. Mapping of character states of structural features of the mtD-loop region revealed that most character states were autapomorphies and inferred a number of homoplasies. The Left Domain of turtles, containing no highly conserved structural elements, likely does not serve a functional role; therefore, the Central Domain in turtles is likely equivalent to the Left Domain of mammals. The AT-rich secondary structural element near the 3' terminus of the mtD-loop region may be conserved across turtles because of a functional role, perhaps containing the Light Strand Promotor, or perhaps interacting with the TWINKLE-coreTAS complex in the Central and Right Domains to regulate mtDNA replication and transcription.
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Affiliation(s)
- Lucas E Bernacki
- Department of Sciences, Saint Joseph's College, Mercy Hall, Rm 122, 278 Whites Bridge Road, Standish, ME, 04084, USA.
- Department of Biology, University of Vermont, Burlington, VT, USA.
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Whole mitochondrial genome of long-clawed mole vole (Prometheomys schaposchnikowi) from Turkey, with its phylogenetic relationships. Genomics 2020; 112:3247-3255. [PMID: 32512144 DOI: 10.1016/j.ygeno.2020.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/27/2020] [Accepted: 06/03/2020] [Indexed: 11/21/2022]
Abstract
The mitogenome of Prometheomys schaposchnikowi was characterized for the first time as a circular DNA molecule (16.284 bp), containing 37 coding and 2 non-coding regions. In the mitogenome, ND6 and 8 tRNA genes were encoded on the light chain, while 12 PCGs, 14 tRNAs, 2 rRNAs, D-loop and OL were encoded on the heavy chain. The most common initiation codon in PCGs was ATG. As in many mammals, incomplete stop codons in P. schaposchnikowi were in the COX3, ND1 and ND4. Phylogenetic relationships were revealed using Bayesian method and the 13 PCGs. Seven genera (Arvicola, Dicrostonyx, Lasiopodomys, Myodes, Ondatra, Proedromys and Prometheomys) formed a monophyletic group, while Eothenomys, Microtus and Neodon were paraphyletic. P. schaposchnikowi constituted the most basal group within Arvicolinae. Divergence time estimation suggested that P. schaposchnikowi diversified during the Miocene (16.28 Mya). Further molecular studies are needed to test the distinctiveness and diversity of the genus Prometheomys.
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53
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The first complete mitochondrial genome sequence of the endangered mountain anoa (Bubalus quarlesi) (Artiodactyla: Bovidae) and phylogenetic analysis. JOURNAL OF ASIA-PACIFIC BIODIVERSITY 2020. [DOI: 10.1016/j.japb.2020.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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54
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Mukundan LP, Sukumaran S, Sebastian W, Gopalakrishnan A. Characterization of the Whole Mitogenome of Largehead Hairtail Trichiurus lepturus (Trichiuridae): Insights into Special Characteristics. Biochem Genet 2020; 58:430-451. [DOI: 10.1007/s10528-020-09956-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/05/2020] [Indexed: 12/01/2022]
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Cruz-Salazar B, García-Bautista M, Ruiz-Montoya L. Genetic Structure Associated with the Ecological Traits of Four Species of Phyllostomid Bats Inhabiting Selva El Ocote Biosphere Reserve, Chiapas, México. ACTA CHIROPTEROLOGICA 2020. [DOI: 10.3161/15081109acc2019.21.2.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Bárbara Cruz-Salazar
- Consejo Nacional de Ciencia y Tecnología, Universidad Autónoma de Tlaxcala, Carretera Federal Puebla-Tlaxcala Km 1.5, La Loma Xicohténcatl, CP 90062, Tlaxcala de Xicohténcatl, Tlaxcala, México
| | - Maricela García-Bautista
- Consejo Nacional de Ciencia y Tecnología, Universidad Autónoma de Tlaxcala, Carretera Federal Puebla-Tlaxcala Km 1.5, La Loma Xicohténcatl, CP 90062, Tlaxcala de Xicohténcatl, Tlaxcala, México
| | - Lorena Ruiz-Montoya
- Consejo Nacional de Ciencia y Tecnología, Universidad Autónoma de Tlaxcala, Carretera Federal Puebla-Tlaxcala Km 1.5, La Loma Xicohténcatl, CP 90062, Tlaxcala de Xicohténcatl, Tlaxcala, México
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56
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Cuppari A, Fernández-Millán P, Battistini F, Tarrés-Solé A, Lyonnais S, Iruela G, Ruiz-López E, Enciso Y, Rubio-Cosials A, Prohens R, Pons M, Alfonso C, Tóth K, Rivas G, Orozco M, Solà M. DNA specificities modulate the binding of human transcription factor A to mitochondrial DNA control region. Nucleic Acids Res 2020; 47:6519-6537. [PMID: 31114891 PMCID: PMC6614842 DOI: 10.1093/nar/gkz406] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 04/30/2019] [Accepted: 05/15/2019] [Indexed: 12/18/2022] Open
Abstract
Human mitochondrial DNA (h-mtDNA) codes for 13 subunits of the oxidative phosphorylation pathway, the essential route that produces ATP. H-mtDNA transcription and replication depends on the transcription factor TFAM, which also maintains and compacts this genome. It is well-established that TFAM activates the mtDNA promoters LSP and HSP1 at the mtDNA control region where DNA regulatory elements cluster. Previous studies identified still uncharacterized, additional binding sites at the control region downstream from and slightly similar to LSP, namely sequences X and Y (Site-X and Site-Y) (Fisher et al., Cell 50, pp 247-258, 1987). Here, we explore TFAM binding at these two sites and compare them to LSP by multiple experimental and in silico methods. Our results show that TFAM binding is strongly modulated by the sequence-dependent properties of Site-X, Site-Y and LSP. The high binding versatility of Site-Y or the considerable stiffness of Site-X tune TFAM interactions. In addition, we show that increase in TFAM/DNA complex concentration induces multimerization, which at a very high concentration triggers disruption of preformed complexes. Therefore, our results suggest that mtDNA sequences induce non-uniform TFAM binding and, consequently, direct an uneven distribution of TFAM aggregation sites during the essential process of mtDNA compaction.
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Affiliation(s)
- Anna Cuppari
- Structural MitoLab, Structural Biology Department, Maria de Maeztu Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
| | - Pablo Fernández-Millán
- Structural MitoLab, Structural Biology Department, Maria de Maeztu Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
| | - Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Aleix Tarrés-Solé
- Structural MitoLab, Structural Biology Department, Maria de Maeztu Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
| | - Sébastien Lyonnais
- Structural MitoLab, Structural Biology Department, Maria de Maeztu Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
| | - Guillermo Iruela
- BioNMR Laboratory, Inorganic and Organic Chemistry Department, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Elena Ruiz-López
- Structural MitoLab, Structural Biology Department, Maria de Maeztu Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
| | - Yuliana Enciso
- Structural MitoLab, Structural Biology Department, Maria de Maeztu Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
| | - Anna Rubio-Cosials
- Structural MitoLab, Structural Biology Department, Maria de Maeztu Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
| | - Rafel Prohens
- Unitat de Polimorfisme i Calorimetria, Centres Científics i Tecnològics, University of Barcelona, 08028 Barcelona, Spain
| | - Miquel Pons
- BioNMR Laboratory, Inorganic and Organic Chemistry Department, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain
| | - Katalin Tóth
- Deutsches Krebsforschungszentrum, Division Biophysics of Macromolecules, Heidelberg, Germany
| | - Germán Rivas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.,Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona 08028, Spain
| | - Maria Solà
- Structural MitoLab, Structural Biology Department, Maria de Maeztu Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
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The complete mitochondrial genome of Talpa aquitania (Talpidae; Insectivora), a mole species endemic to northern Spain and southern France. Mol Biol Rep 2020; 47:2397-2403. [PMID: 32034626 DOI: 10.1007/s11033-020-05296-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/08/2020] [Accepted: 01/30/2020] [Indexed: 10/25/2022]
Abstract
The complete mitogenome sequence of Talpa aquitania, a recently described Talpa species, was assembled using whole-genome sequencing data. It varies in length from 16,776 to 16,846 bp, contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, one origin of L-strand replication, and a control region. In the control region, which varied from 1320 to 1390 bp, we identified the extended termination-associated sequence (ETAS-1 and ETAS-2) and the conserved sequence blocks (CSB-1, 2, 3, B, C, D, E, F). In addition, this region includes a 10 bp tandem repeat DNA sequence, with a variable number of repeats that suggest the existence of heteroplasmy. Phylogeny reconstructions based on Maximum Likelihood, Neighbor-joining and Bayesian inference analyses yielded phylogenies with similar topologies demonstrating that T. aquitania and T. occidentalis are sister species.
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58
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Ding L, Zhou Q, Sun Y, Feoktistova NY, Liao J. Two novel cricetine mitogenomes: Insight into the mitogenomic characteristics and phylogeny in Cricetinae (Rodentia: Cricetidae). Genomics 2019; 112:1716-1725. [PMID: 31669701 DOI: 10.1016/j.ygeno.2019.09.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 09/06/2019] [Accepted: 09/18/2019] [Indexed: 01/30/2023]
Abstract
Both Cricetus cricetus and Phodopus sungorus mitochondrial genomes (mitogenomes) were sequenced and elaborated for the first time in the present study. Their mitogenomes contained 37 genes and showed typical characteristics of the vertebrate mitogenome. Comparative analysis of 10 cricetine mitogenomes indicated that they shared similar characteristics with those of other cricetines in terms of genes arrangement, nucleotide composition, codon usage, tRNA structure, nucleotide skew and the origin of replication of light strand. Phylogenetic relationship of the subfamily Cricetinae was reconstructed using mitogenomes data with the methods of Bayesian Inference and Maximum Likelihood. Phylogenetic analysis indicated that Cricetulus kamensis was at basal position and phylogenetically distant from all other Cricetulus species but had a close relationship with the group of Phodopus, and supported that the genus Urocricetus deserved as a separate genus rank. The phylogenetic status of Tscherskia triton represented a separate clade corresponding to a diversified cricetine lineage (Cricetulus, Allocricetulus, and Cricetus).
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Affiliation(s)
- Li Ding
- School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China.
| | - Quan Zhou
- School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China
| | - Yuanhai Sun
- School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China
| | - Natalia Yu Feoktistova
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow 119071, Russia
| | - Jicheng Liao
- School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China.
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59
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Kornienko IV, Faleeva TG, Oreshkova NV, Grigoriev SE, Grigorieva LV, Putintseva YA, Krutovsky KV. Structural and Functional Organization of the Mitochondrial DNA Control Region in the Woolly Mammoth (Mammuthus primigenius). Mol Biol 2019. [DOI: 10.1134/s002689331904006x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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60
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Complete mitochondrial genomes confirm the generic placement of the plateau vole, Neodon fuscus. Biosci Rep 2019; 39:BSR20182349. [PMID: 31262975 PMCID: PMC6689105 DOI: 10.1042/bsr20182349] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 05/25/2019] [Accepted: 05/31/2019] [Indexed: 11/22/2022] Open
Abstract
The plateau vole, Neodon fuscus is endemic to China and is distributed mainly in Qinghai Province. It is of public health interest, as it is, a potential reservoir of Toxoplasma gondii and the intermediate host of Echinococcus multilocularis. However, genetic data of this species are lacking, and its name and taxonomy are still a controversy. In the present study, we determined the nucleotide sequence of the entire mitochondrial (mt) genome of N. fuscus and analyzed its evolutionary relationship. The mitogenome was 16328 bp in length and contained 13 protein-coding genes, 22 genes for transfer RNAs (tRNA), two ribosomal RNA genes and two major noncoding regions (OL region and D-loop region). Most genes were located on the heavy strand. All tRNA genes had typical cloverleaf structures except for tRNASer (GCU). The mt genome of N. fuscus was rich in A+T (58.45%). Maximum likelihood (ML) and Bayesian methods yielded phylogenetic trees from 33 mt genomes of Arvicolinae, in which N. fuscus formed a sister group with Neodon irene and Neodon sikimensis to the exclusion of species of Microtus and other members of the Arvicolinae. Further phylogenetic analyses (ML only) based on the cytb gene sequences also demonstrated that N. fuscus had a close relationship with N. irene. The complete mitochondrial genome was successfully assembled and annotated, providing the necessary information for the phylogenetic analyses. Although the name Lasiopodomys fuscus was used in the book ‘Wilson & Reeder’s Mammal Species of the World’, we have confirmed here that its appropriate name is N. fuscus through an analysis of the evolutionary relationships.
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61
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Jiang L, Peng L, Tang M, You Z, Zhang M, West A, Ruan Q, Chen W, Merilä J. Complete mitochondrial genome sequence of the Himalayan Griffon, Gyps himalayensis (Accipitriformes: Accipitridae): Sequence, structure, and phylogenetic analyses. Ecol Evol 2019; 9:8813-8828. [PMID: 31410282 PMCID: PMC6686361 DOI: 10.1002/ece3.5433] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 11/12/2022] Open
Abstract
This is the first study to describe the mitochondrial genome of the Himalayan Griffon, Gyps himalayensis, which is an Old World vulture belonging to the family Accipitridae and occurring along the Himalayas and the adjoining Tibetan Plateau. Its mitogenome is a closed circular molecule 17,381 bp in size containing 13 protein-coding genes, 22 tRNA coding genes, two rRNA-coding genes, a control region (CR), and an extra pseudo-control region (CCR) that are conserved in most Accipitridae mitogenomes. The overall base composition of the G. himalayensis mitogenome is 24.55% A, 29.49% T, 31.59% C, and 14.37% G, which is typical for bird mitochondrial genomes. The alignment of the Accipitridae species control regions showed high levels of genetic variation and abundant AT content. At the 5' end of the domain I region, a long continuous poly-C sequence was found. Two tandem repeats were found in the pseudo-control regions. Phylogenetic analysis with Bayesian inference and maximum likelihood based on 13 protein-coding genes indicated that the relationships at the family level were (Falconidae + (Cathartidae + (Sagittariidae + (Accipitridae + Pandionidae))). In the Accipitridae clade, G. himalayensis is more closely related to Aegypius monachus than to Spilornis cheela. The complete mitogenome of G. himalayensis provides a potentially useful resource for further exploration of the taxonomic status and phylogenetic history of Gyps species.
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Affiliation(s)
- Lichun Jiang
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and TechnologyMianyang Normal UniversityMianyangSichuanChina
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangSichuanChina
| | - Liqing Peng
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangSichuanChina
| | - Min Tang
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangSichuanChina
| | - Zhangqiang You
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangSichuanChina
| | - Min Zhang
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and TechnologyMianyang Normal UniversityMianyangSichuanChina
| | - Andrea West
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVicAustralia
| | - Qiping Ruan
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and TechnologyMianyang Normal UniversityMianyangSichuanChina
| | - Wei Chen
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and TechnologyMianyang Normal UniversityMianyangSichuanChina
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangSichuanChina
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty Biological & Environmental SciencesUniversity of HelsinkiHelsinkiFinland
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Deletion of OGG1 Results in a Differential Signature of Oxidized Purine Base Damage in mtDNA Regions. Int J Mol Sci 2019; 20:ijms20133302. [PMID: 31284385 PMCID: PMC6651574 DOI: 10.3390/ijms20133302] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/28/2019] [Accepted: 07/02/2019] [Indexed: 02/06/2023] Open
Abstract
Mitochondrial oxidative stress accumulates with aging and age-related diseases and induces alterations in mitochondrial DNA (mtDNA) content. Since mtDNA qualitative alterations are also associated with aging, repair of mtDNA damage is of great importance. The most relevant form of DNA repair in this context is base excision repair (BER), which removes oxidized bases such as 8-oxoguanine (8-oxoG) and thymine glycol through the action of the mitochondrial isoform of the specific 8-oxoG DNA glycosylase/apurinic or apyrimidinic (AP) lyase (OGG1) or the endonuclease III homolog (NTH1). Mouse strains lacking OGG1 (OGG1−/−) or NTH1 (NTH1−/−) were analyzed for mtDNA alterations. Interestingly, both knockout strains presented a significant increase in mtDNA content, suggestive of a compensatory mtDNA replication. The mtDNA “common deletion” was not detected in either knockout mouse strain, likely because of the young age of the mice. Formamidopyrimidine DNA glycosylase (Fpg)-sensitive sites accumulated in mtDNA from OGG1−/− but not from NTH1−/− mice. Interestingly, the D-loop region was most severely affected by the absence of OGG1, suggesting that this region may be a hotspot for oxidative damage. Thus, we speculate that mtDNA alterations may send a stress message to evoke cell changes through a retrograde mitochondrial–nucleus communication.
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Rapid divergence, molecular evolution, and morphological diversification of coastal host-parasite systems from southern Brazil. Parasitology 2019; 146:1313-1332. [PMID: 31142390 DOI: 10.1017/s0031182019000556] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This study assessed the role of historical processes on the geographic isolation, molecular evolution, and morphological diversification of host-parasite populations from the southern Brazilian coast. Adult specimens of Scleromystax barbatus and Scleromystax macropterus were collected from the sub-basin of the Nhundiaquara River and the sub-basin of the Paranaguá Bay, state of Paraná, Brazil. Four species of Gyrodactylus were recovered from the body surface of both host species. Morphometric analysis of Gyrodactylus spp. and Scleromystax spp. indicated that subpopulations of parasites and hosts could be distinguished from different sub-basins and locations, but the degree of morphological differentiation seems to be little related to geographic distance between subpopulations. Phylogenetic relationships based on DNA sequences of Gyrodactylus spp. and Scleromystax spp. allowed distinguishing lineages of parasites and hosts from different sub-basins. However, the level of genetic structuring of parasites was higher in comparison to host species. Evidence of positive selection in mtDNA sequences is likely associated with local adaptation of lineages of parasites and hosts. A historical demographic analysis revealed that populations of Gyrodactylus and Scleromystax have expanded in the last 250 000 years. The genetic variation of parasites and hosts is consistent with population-specific selection, population expansions, and recent evolutionary co-divergence.
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Yan C, Duanmu X, Zeng L, Liu B, Song Z. Mitochondrial DNA: Distribution, Mutations, and Elimination. Cells 2019; 8:E379. [PMID: 31027297 PMCID: PMC6523345 DOI: 10.3390/cells8040379] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 04/17/2019] [Accepted: 04/20/2019] [Indexed: 12/21/2022] Open
Abstract
Mitochondrion harbors its own DNA (mtDNA), which encodes many critical proteins for the assembly and activity of mitochondrial respiratory complexes. mtDNA is packed by many proteins to form a nucleoid that uniformly distributes within the mitochondrial matrix, which is essential for mitochondrial functions. Defects or mutations of mtDNA result in a range of diseases. Damaged mtDNA could be eliminated by mitophagy, and all paternal mtDNA are degraded by endonuclease G or mitophagy during fertilization. In this review, we describe the role and mechanism of mtDNA distribution and elimination. In particular, we focus on the regulation of paternal mtDNA elimination in the process of fertilization.
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Affiliation(s)
- Chaojun Yan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Xiaoying Duanmu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Ling Zeng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Bing Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Zhiyin Song
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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Zhong J, Yi S, Ma L, Wang W. Evolution and phylogeography analysis of diploid and polyploid Misgurnus anguillicaudatus populations across China. Proc Biol Sci 2019; 286:20190076. [PMID: 31014220 PMCID: PMC6501937 DOI: 10.1098/rspb.2019.0076] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/03/2019] [Indexed: 12/14/2022] Open
Abstract
The origin and evolution of polyploid organisms have been extensively studied in plants, but this topic remains only partially understood in vertebrates, where polyploidy is relatively rare. In this study, we used Misgurnus anguillicaudatus, a fish that comprises five ploidy levels in nature, as a model animal to improve our understanding of biogeographic history and evolution of polyploid vertebrates. After collecting samples from different geographical populations in China, their ploidy levels were determined using flow cytometry. Two mitochondrial markers ( cytochrome b and control region) were then used for phylogeographic analyses to unravel the possible origins of diploids and tetraploids in China. The results showed that diploids have wider geographical distribution than tetraploids and triploids. There was no clear allopatric geographical range or boundary to divide diploid and polyploid populations. Rather, the analysis of mitochondrial DNA sequences indicated that tetraploids were autopolyploids, with lower genetic diversity than diploids. This suggests that tetraploids originated from sympatric diploids via multiple independent polyploidization events. Genetic structure patterns were similar between diploids and tetraploids, whereas complex genetic differentiation was found among different regions. The potential origin of M. anguillicaudatus was deduced to be in the Pearl River basin, which exhibited the highest nucleotide diversity and genetic differentiation. These findings provide insights into the evolution of polyploidy in vertebrates.
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Affiliation(s)
| | | | | | - Weimin Wang
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
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66
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Coppedè F, Stoccoro A. Mitoepigenetics and Neurodegenerative Diseases. Front Endocrinol (Lausanne) 2019; 10:86. [PMID: 30837953 PMCID: PMC6389613 DOI: 10.3389/fendo.2019.00086] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 01/31/2019] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial impairment and increased oxidative stress are common features in neurodegenerative disorders, leading researchers to speculate that epigenetic changes in the mitochondrial DNA (mitoepigenetics) could contribute to neurodegeneration. The few studies performed so far to address this issue revealed impaired methylation levels of the mitochondrial regulatory region (D-loop region) in both animal models, postmortem brain regions, or circulating blood cells of patients with Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. Those studies also revealed that mtDNA D-loop methylation levels are subjected to a dynamic regulation within the progression of the neurodegenerative process, could be affected by certain neurodegenerative disease-causative mutations, and are inversely correlated with the mtDNA copy number. The methylation levels of other mtDNA regions than the D-loop have been scarcely investigated in human specimens from patients with neurodegenerative disorders or in animal models of the disease, and evidence of impaired methylation levels is often limited to a single study, making it difficult to clarify their correlation with mitochondrial dynamics and gene expression levels in these disorders. Overall, the preliminary results of the studies performed so far are encouraging making mitoepigenetics a timely and attractive field of investigation, but additional research is warranted to clarify the connections among epigenetic changes occurring in the mitochondrial genome, mitochondrial DNA dynamics and gene expression, and the neurodegenerative process.
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Querejeta M, Castresana J. Evolutionary history of the endemic water shrew Neomys anomalus: Recurrent phylogeographic patterns in semi-aquatic mammals of the Iberian Peninsula. Ecol Evol 2018; 8:10138-10146. [PMID: 30397453 PMCID: PMC6206195 DOI: 10.1002/ece3.4487] [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: 03/26/2018] [Revised: 07/27/2018] [Accepted: 08/08/2018] [Indexed: 11/10/2022] Open
Abstract
The Cabrera's water shrew (Neomys anomalus) is a small semi-aquatic mammal whose taxonomic status was recently elevated from subspecies to species; as a consequence of this change, this species is now endemic to the Iberian Peninsula. In this study, we looked at its evolutionary history by combining phylogeography, the spatial distribution of genetic diversity, and species distribution modeling. To perform these analyses, we used noninvasive samples collected across the species distribution range and sequenced partial mitochondrial cytochrome b and D-loop genes. Maximum-likelihood and Bayesian phylogenetic trees derived from these sequences indicated that N. anomalus is divided into two main phylogroups that correlate strongly with geography, with two contact zones between the groups that showed limited spatial mixing between them. River basins were responsible for only a small percentage of the structure of the genetic diversity of this species despite its riparian habitat. The nucleotide diversity variation map showed the highest genetic diversity to be in the north of the Iberian Peninsula. Finally, species distribution modeling allowed the inference of an optimal area during the Last Interglacial in the north of the Iberian Peninsula, and multiple glacial refugia during the Last Glacial Maximum. The phylogeographic pattern of N. anomalus is strikingly similar to that of another semi-aquatic Iberian mammal, the Pyrenean desman (Galemys pyrenaicus), revealing how Pleistocene glaciations could have had equivalent effects on species of similar ecology and distribution. This phylogeographic structure is consistent with N. anomalus having been isolated for long periods in multiple glacial refugia within the Iberian Peninsula, in agreement with the "refugia-within-refugia" hypothesis, and further supporting its status as a distinct species.
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Affiliation(s)
- Marina Querejeta
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
- Bavarian State Collection of ZoologyMünchenGermany
| | - Jose Castresana
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
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Li R, Wang G, Wen ZY, Zou YC, Qin CJ, Luo Y, Wang J, Chen GH. Complete mitochondrial genome of a kind of snakehead fish Channa siamensis and its phylogenetic consideration. Genes Genomics 2018; 41:147-157. [PMID: 30242740 DOI: 10.1007/s13258-018-0746-5] [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: 06/14/2018] [Accepted: 09/18/2018] [Indexed: 12/28/2022]
Abstract
The snakehead fish, Channa siamensis, belongs to the genus of Channa (perciformes: Channidae) and was first reported by Günther in 1861. Despite it has been described approximately for 15 decades, the genetic information is limited and the taxon status of this kind of fish is still unclear. The primary objective of this study is to get more genomic data and calculate the taxon location of this kind of fish. The next generation sequencing method was used to obtain the whole mitochondrial DNA information, and bioinformatic analysis was performed to investigate the evolutionary status and taxon location of C. siamensis. The circular mitochondrial DNA was 16,570 bp in length, and which showed typical piscine structure and arrangement. The overall nucleotide composition was 29.28% A, 24.72% T, 30.71% C, 15.29% G, with 54.1% AT, respectively. Phylogenetic analyses using concatenated amino acid and nucleotide sequences of the 13 protein-coding genes with two different methods (Maximum likelihood and Bayesian analysis) both highly supported C. siamensis belongs to the genus Channa and shows a close relationship with C. micropeltes. These data will provide more useful information for a better understanding of the mitochondrial genomic diversities and evolution in fish as well as novel genetic markers for studying population genetics and species identification.
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Affiliation(s)
- Rui Li
- Conservation and Utilization of Fishes Resources in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, Sichuan, China
| | - Gang Wang
- Conservation and Utilization of Fishes Resources in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, Sichuan, China
| | - Zheng-Yong Wen
- Conservation and Utilization of Fishes Resources in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, Sichuan, China. .,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.
| | - Yuan-Chao Zou
- Conservation and Utilization of Fishes Resources in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, Sichuan, China
| | - Chuan-Jie Qin
- Conservation and Utilization of Fishes Resources in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, Sichuan, China
| | - Yu Luo
- Institute of Aquaculture, Neijiang Academy of Agricultural Sciences, Neijiang, 641000, Sichuan, China
| | - Jun Wang
- Conservation and Utilization of Fishes Resources in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, Sichuan, China
| | - Gui-Hong Chen
- Conservation and Utilization of Fishes Resources in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, Sichuan, China
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Barshad G, Marom S, Cohen T, Mishmar D. Mitochondrial DNA Transcription and Its Regulation: An Evolutionary Perspective. Trends Genet 2018; 34:682-692. [DOI: 10.1016/j.tig.2018.05.009] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/19/2018] [Accepted: 05/31/2018] [Indexed: 12/15/2022]
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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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Ma H, Lee Y, Hayama T, Van Dyken C, Marti-Gutierrez N, Li Y, Ahmed R, Koski A, Kang E, Darby H, Gonmanee T, Park Y, Wolf DP, Jai Kim C, Mitalipov S. Germline and somatic mtDNA mutations in mouse aging. PLoS One 2018; 13:e0201304. [PMID: 30040856 PMCID: PMC6057648 DOI: 10.1371/journal.pone.0201304] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 07/11/2018] [Indexed: 12/13/2022] Open
Abstract
The accumulation of acquired mitochondrial genome (mtDNA) mutations with aging in somatic cells has been implicated in mitochondrial dysfunction and linked to age-onset diseases in humans. Here, we asked if somatic mtDNA mutations are also associated with aging in the mouse. MtDNA integrity in multiple organs and tissues in young and old (2-34 months) wild type (wt) mice was investigated by whole genome sequencing. Remarkably, no acquired somatic mutations were detected in tested tissues. However, we identified several non-synonymous germline mtDNA variants whose heteroplasmy levels (ratio of normal to mutant mtDNA) increased significantly with aging suggesting clonal expansion of inherited mtDNA mutations. Polg mutator mice, a model for premature aging, exhibited both germline and somatic mtDNA mutations whose numbers and heteroplasmy levels increased significantly with age implicating involvement in premature aging. Our results suggest that, in contrast to humans, acquired somatic mtDNA mutations do not accompany the aging process in wt mice.
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Affiliation(s)
- Hong Ma
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, Portland, Oregon, United States of America
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Yeonmi Lee
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, Portland, Oregon, United States of America
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
- Stem Cell Center, ASAN Institute for Life Sciences, ASAN Medical Center, Seoul, South Korea
| | - Tomonari Hayama
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, Portland, Oregon, United States of America
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Crystal Van Dyken
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, Portland, Oregon, United States of America
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Nuria Marti-Gutierrez
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, Portland, Oregon, United States of America
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Ying Li
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, Portland, Oregon, United States of America
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Riffat Ahmed
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, Portland, Oregon, United States of America
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Amy Koski
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, Portland, Oregon, United States of America
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Eunju Kang
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, Portland, Oregon, United States of America
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
- Stem Cell Center, ASAN Institute for Life Sciences, ASAN Medical Center, Seoul, South Korea
| | - Hayley Darby
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, Portland, Oregon, United States of America
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Thanasup Gonmanee
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, Portland, Oregon, United States of America
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Younjung Park
- Stem Cell Center, ASAN Institute for Life Sciences, ASAN Medical Center, Seoul, South Korea
| | - Don P. Wolf
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, Portland, Oregon, United States of America
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Chong Jai Kim
- Stem Cell Center, ASAN Institute for Life Sciences, ASAN Medical Center, Seoul, South Korea
| | - Shoukhrat Mitalipov
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, Portland, Oregon, United States of America
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
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Turanov SV, Lee YH, Kartavtsev YP. Structure, evolution and phylogenetic informativeness of eelpouts (Cottoidei: Zoarcales) mitochondrial control region sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:264-272. [PMID: 29991298 DOI: 10.1080/24701394.2018.1484117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Control region (CR) is a major non-coding domain of mitochondrial DNA in vertebrates which contains the promoters for replication and transcription of mitochondrial genome along with the binding sites for metabolic machinery and, hence, is a vital element for the integrity of mitochondrial genome as a biological replicator. The origin and diversity of structural elements within CR have been intensively studied in recent years with the involvement of new diverse taxa. In this paper, we provide new data on the nucleotide and structural patterns of CR evolution and phylogenetic suitability among eelpouts (Cottoidei: Zoarcales). To achieve this, we carried out a comparative phylogenetic and structural analysis of 29 CR sequences belonging to the long shanny Stichaeus grigorjewi together with nine sequences of other eelpouts taxa representing four families in contrast to mitochondrial protein-coding fragments. The CR organization within S. grigorjewi, as well as in all other eelpouts, is consistent with the common three-domain structure known from most vertebrates. We found a hidden CR variation constrains on the landscape level and a lack of nucleotide saturation. Finally, our results demonstrate the advantage of the length variation in CR sequences for phylogenetic reconstructions among eelpouts.
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Affiliation(s)
- Sergei V Turanov
- a Laboratory of Molecular Systematic, A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology, Far Eastern Branch , Russian Academy of Sciences , Vladivostok , Russia.,b Chair of Water Biological Resources and Aquaculture, Far Eastern State Technical Fisheries University , Vladivostok , Russia
| | - Youn-Ho Lee
- c Laboratory of Marine Genomics, Korean Institute of Ocean Science and Technology , Ansan , Republic of Korea
| | - Yuri Ph Kartavtsev
- a Laboratory of Molecular Systematic, A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology, Far Eastern Branch , Russian Academy of Sciences , Vladivostok , Russia.,d Chair of Biodiversity and Marine Bioresources, Far Eastern Federal University , Vladivostok , Russia
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73
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Hypomethylation of mitochondrial D-loop and ND6 with increased mitochondrial DNA copy number in the arsenic-exposed population. Toxicology 2018; 408:54-61. [PMID: 29940200 DOI: 10.1016/j.tox.2018.06.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 06/15/2018] [Accepted: 06/21/2018] [Indexed: 02/07/2023]
Abstract
Groundwater arsenic contamination has become a serious global concern due to its adverse effects on human health. Arsenic-induced reactive oxygen species trigger oxidative stress inside mitochondria, which initiate a cascade of events including altered mitochondrial (mt) membrane potential, uncoupling of electron transport chain, and mtDNA damage. A case-control study was conducted to examine the association between arsenic exposure and differences in mtDNA methylation and to assess the downstream consequences. We recruited 221 arsenic-exposed individuals, including 106 individuals with skin lesions (WSL) and 115 subjects without any skin lesions (WOSL) from the Murshidabad district, West Bengal, India. The unexposed group included 101 individuals from the arsenic unexposed area in East Midnapore. We analyzed the status of mtDNA methylation in D-loop region and ND6 gene by methylation-specific PCR. Gene expression was studied by quantitative real-time PCR. Significant hypomethylation in both D-loop and ND6 was observed with a consequent increase in their target gene expression and higher mtDNA copy number in arsenic-exposed populations compared to controls. Further mechanistic insights regarding mitochondrial epigenetic alteration in arsenic exposure will be of critical importance for the prevention of adverse health effects.
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74
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Coetzer WG, Turner TR, Schmitt CA, Grobler JP. Adaptive genetic variation at three loci in South African vervet monkeys ( Chlorocebus pygerythrus) and the role of selection within primates. PeerJ 2018; 6:e4953. [PMID: 29888138 PMCID: PMC5991302 DOI: 10.7717/peerj.4953] [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: 02/23/2018] [Accepted: 05/22/2018] [Indexed: 12/22/2022] Open
Abstract
Vervet monkeys (Chlorocebus pygerythrus) are one of the most widely distributed non-human primate species found in South Africa. They occur across all the South African provinces, inhabiting a large variety of habitats. These habitats vary sufficiently that it can be assumed that various factors such as pathogen diversity could influence populations in different ways. In turn, these factors could lead to varied levels of selection at specific fitness linked loci. The Toll-like receptor (TLR) gene family, which play an integral role in vertebrate innate immunity, is a group of fitness linked loci which has been the focus of much research. In this study, we assessed the level of genetic variation at partial sequences of two TLR loci (TLR4 and 7) and a reproductively linked gene, acrosin (ACR), across the different habitat types within the vervet monkey distribution range. Gene variation and selection estimates were also made among 11-21 primate species. Low levels of genetic variation for all three gene regions were observed within vervet monkeys, with only two polymorphic sites identified for TLR4, three sites for TLR7 and one site for ACR. TLR7 variation was positively correlated with high mean annual rainfall, which was linked to increased pathogen abundance. The observed genetic variation at TLR4 might have been influenced by numerous factors including pathogens and climatic conditions. The ACR exonic regions showed no variation in vervet monkeys, which could point to the occurrence of a selective sweep. The TLR4 and TLR7 results for the among primate analyses was mostly in line with previous studies, indicating a higher rate of evolution for TLR4. Within primates, ACR coding regions also showed signs of positive selection, which was congruent with previous reports on mammals. Important additional information to the already existing vervet monkey knowledge base was gained from this study, which can guide future research projects on this highly researched taxon as well as help conservation agencies with future management planning involving possible translocations of this species.
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Affiliation(s)
- Willem G Coetzer
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Trudy R Turner
- Department of Anthropology, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | | | - J Paul Grobler
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
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Li K, Liang AP. Hemiptera Mitochondrial Control Region: New Sights into the Structural Organization, Phylogenetic Utility, and Roles of Tandem Repetitions of the Noncoding Segment. Int J Mol Sci 2018; 19:E1292. [PMID: 29701634 PMCID: PMC5983824 DOI: 10.3390/ijms19051292] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/24/2018] [Accepted: 04/12/2018] [Indexed: 11/16/2022] Open
Abstract
As a major noncoding fragment, the control region (CR) of mtDNA is responsible for the initiation of mitogenome transcription and replication. Several structural features of CR sequences have been reported in many insects. However, comprehensive analyses on the structural organization and phylogenetic utility, as well as the role of tandem replications (TRs) on length variation, high A+T content, and shift of base skew of CR sequences are poorly investigated in hemipteran insects. In this study, we conducted a series of comparative analyses, using 116 samples covering all 11 infraorders of the five currently recognized monophyletic groups in the Hemiptera. Several structural elements (mononucleotide stretches containing conserved sequence blocks (CSBs), TRs, and GA-rich region) were identified in the mitochondrial control region in hemipteran insects, without showing a consistent location. The presence and absence of certain specific structural elements in CR sequences show the various structural organizations of that segment among the five monophyletic groups, which indicates the diversification of the control region’s structural organization in Hemiptera. Among the many groups within Hemiptera, eight monophyletic groups and three consistent phylogenetic trees were recovered, using CSBs datasets by maximum likelihood and Bayesian methods, which suggests the possible utility of CR sequences for phylogenetic reconstruction in certain groups of Hemiptera. Statistical analyses showed that TRs may contribute to the length variation, high AT content, and the shift of base skewing of CR sequences toward high AT content in the Hemiptera. Our findings enrich the knowledge of structural organization, phylogenetic utility, and roles of tandem replication of hemipteran CR, and provide a possible framework for mitochondrial control region analyses in hemimetabolous insects.
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Affiliation(s)
- Kui Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ai-Ping Liang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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76
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Wone BWM, Yim WC, Schutz H, Meek TH, Garland T. Mitochondrial haplotypes are not associated with mice selectively bred for high voluntary wheel running. Mitochondrion 2018; 46:134-139. [PMID: 29626644 DOI: 10.1016/j.mito.2018.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 03/30/2018] [Accepted: 04/02/2018] [Indexed: 10/17/2022]
Abstract
Mitochondrial haplotypes have been associated with human and rodent phenotypes, including nonshivering thermogenesis capacity, learning capability, and disease risk. Although the mammalian mitochondrial D-loop is highly polymorphic, D-loops in laboratory mice are identical, and variation occurs elsewhere mainly between nucleotides 9820 and 9830. Part of this region codes for the tRNAArg gene and is associated with mitochondrial densities and number of mtDNA copies. We hypothesized that the capacity for high levels of voluntary wheel-running behavior would be associated with mitochondrial haplotype. Here, we analyzed the mtDNA polymorphic region in mice from each of four replicate lines selectively bred for 54 generations for high voluntary wheel running (HR) and from four control lines (Control) randomly bred for 54 generations. Sequencing the polymorphic region revealed a variable number of adenine repeats. Single nucleotide polymorphisms (SNPs) varied from 2 to 3 adenine insertions, resulting in three haplotypes. We found significant genetic differentiations between the HR and Control groups (Fst = 0.779, p ≤ 0.0001), as well as among the replicate lines of mice within groups (Fsc = 0.757, p ≤ 0.0001). Haplotypes, however, were not strongly associated with voluntary wheel running (revolutions run per day), nor with either body mass or litter size. This system provides a useful experimental model to dissect the physiological processes linking mitochondrial, genomic SNPs, epigenetics, or nuclear-mitochondrial cross-talk to exercise activity.
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Affiliation(s)
- Bernard W M Wone
- Department of Biochemistry & Molecular Biology, University of Nevada, Reno, NV 89557, USA; Department of Biology, University of South Dakota, Vermillion, SD 57069, USA.
| | - Won C Yim
- Department of Biochemistry & Molecular Biology, University of Nevada, Reno, NV 89557, USA
| | - Heidi Schutz
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA; Biology Department, Pacific Lutheran University, Tacoma, WA 98447, USA
| | - Thomas H Meek
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA; In Vivo Pharmacology Research Unit, Novo Nordisk, Seattle, WA 98109, USA
| | - Theodore Garland
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA.
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Shinde P, Sarkar C, Jalan S. Codon based co-occurrence network motifs in human mitochondria. Sci Rep 2018; 8:3060. [PMID: 29449618 PMCID: PMC5814444 DOI: 10.1038/s41598-018-21454-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 02/05/2018] [Indexed: 11/09/2022] Open
Abstract
The nucleotide polymorphism in the human mitochondrial genome (mtDNA) tolled by codon position bias plays an indispensable role in human population dispersion and expansion. Herein, genome-wide nucleotide co-occurrence networks were constructed using data comprised of five different geographical regions and around 3000 samples for each region. We developed a powerful network model to describe complex mitochondrial evolutionary patterns among codon and non-codon positions. We found evidence that the evolution of human mitochondria DNA is dominated by adaptive forces, particularly mutation and selection, which was supported by many previous studies. The diversity observed in the mtDNA was compared with mutations, co-occurring mutations, network motifs considering codon positions as causing agent. This comparison showed that long-range nucleotide co-occurrences have a large effect on genomic diversity. Most notably, codon motifs apparently underpinned the preferences among codon positions for co-evolution which is probably highly biased during the origin of the genetic code. Our analysis also showed that variable nucleotide positions of different human sub-populations implemented the independent mtDNA evolution to its geographical dispensation. Ergo, this study has provided both a network framework and a codon glance to investigate co-occurring genomic variations that are critical in underlying complex mitochondrial evolution.
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Affiliation(s)
- Pramod Shinde
- Centre for Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Camellia Sarkar
- Centre for Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Sarika Jalan
- Centre for Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India.
- Complex Systems Lab, Discipline of Physics, Indian Institute of Technology Indore, Simrol, Indore, 453552, India.
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78
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Complete mitochondrial genome of freshwater goby Rhinogobius cliffordpopei (Perciformes, Gobiidae): genome characterization and phylogenetic analysis. Genes Genomics 2018; 40:1137-1148. [PMID: 30315517 DOI: 10.1007/s13258-018-0669-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 02/07/2018] [Indexed: 10/18/2022]
Abstract
Freshwater gobies Rhinogobius cliffordpopei and R. giurinus are invasive species with particular concern because they have become dominant and were fierce competitors in the invaded areas in Yunnan-Guizhou Plateau (southwest of China). Information about genetic characteristics of R. giurinus have been published, but there were still no relevant reports about R. cliffordpopei. In present study, the complete mitochondrial genome of R. cliffordpopei was determined, which was 16,511 bp in length with A + T content of 51.1%, consisting of 13 protein-coding genes, 22 tRNAs, 2 ribosomal RNAs, and a control region. The gene composition and the structural arrangement of the R. cliffordpopei complete mtDNA were identical to most of other teleosts. Phylogenetic analyses placed R. cliffordpopei in a well-supported monophyletic cluster with other Rhinogobius fish. But the phylogenetic relationship between genus Rhinogobius and Tridentiger remained to be resolved.
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79
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Lalitha R, Chandavar VR. Intraspecific variations in Cyt b and D-loop sequences of Testudine species, Lissemys punctata from south Karnataka. J Adv Res 2017; 9:87-95. [PMID: 30046490 PMCID: PMC6057446 DOI: 10.1016/j.jare.2017.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/21/2017] [Accepted: 10/23/2017] [Indexed: 11/17/2022] Open
Abstract
The freshwater Testudine species have gained importance in recent years, as most of their population is threatened due to exploitation for delicacy and pet trade. In this regard, Lissemys punctata, a freshwater terrapin, predominantly distributed in Asian countries has gained its significance for the study. A pilot study report on mitochondrial markers (Cyt b and D-loop) conducted on L. punctata species from southern Karnataka, India was presented in this investigation. A complete region spanning 1.14 kb and ∼1 kb was amplified by HotStart PCR and sequenced by Sanger sequencing. The Cyt b sequence revealed 85 substitution sites, no indels and 17 parsimony informative sites, whereas D-loop showed 189 variable sites, 51 parsimony informative sites with 5′ functional domains TAS, CSB-F, CSBs (1, 2, 3) preceding tandem repeat at 3′ end. Current data highlights the intraspecific variations in these target regions and variations validated using suitable evolutionary models points out that the overall point mutations observed in the region are transitions leading to no structural and functional alterations. The mitochondrial data generated uncover the genetic diversity within species and conservationist can utilize the data to estimate the effective population size or for forensic identification of animal or its seizures during unlawful trade activities.
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Affiliation(s)
- R Lalitha
- Molecular Endocrinology Laboratory, Department of Biotechnology, Yuvaraja's College, A Constituent Autonomous College of University of Mysore, Mysore 570005, India
| | - V R Chandavar
- Molecular Endocrinology Laboratory, Department of Biotechnology, Yuvaraja's College, A Constituent Autonomous College of University of Mysore, Mysore 570005, India
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80
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Yuhui X, Lijun Z, Yue H, Xiaoqi W, Chen Z, Zhang Huilun, Ruoran W, Da P, Hongying S. Complete mitochondrial genomes from two species of Chinese freshwater crabs of the genus Sinopotamon recovered using next-generation sequencing reveal a novel gene order (Brachyura, Potamidae). Zookeys 2017; 705:41-60. [PMID: 29118611 PMCID: PMC5674035 DOI: 10.3897/zookeys.705.11852] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/04/2017] [Indexed: 01/26/2023] Open
Abstract
Recent morphological and molecular evidence has challenged classical interpretations of eubrachyuran phylogeny and evolution. Complete mitochondrial genomes of two species of potamid freshwater crabs, Sinopotamon yaanense and Sinopotamon yangtsekiense were obtained using next-generation sequencing. The results revealed a novel gene order with translocations of a five-gene block and a tRNA gene in comparison to available brachyuran mitochondrial genomes. DNA sequence comparisons position the Potamidae, a primary freshwater crab family, outside of the clade for the traditional heterotreme families, and closer to the clade that includes the thoracotreme families of grapsoid and ocypodoid crabs. Mitogenomic comparisons using rapid next-generation sequencing and a much wider taxonomic sample are required for a high-resolution examination of the phylogenetic relationships within the Eubrachyura.
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Affiliation(s)
- Xing Yuhui
- Jiangsu Key Laboratory for Biodiversity and Biotechnology,
| | - Zhou Lijun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology,
| | - Hou Yue
- Jiangsu Key Laboratory for Biodiversity and Biotechnology,
| | - Wang Xiaoqi
- Jiangsu Key Laboratory for Biodiversity and Biotechnology,
| | - Zhang Chen
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Zhang Huilun
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Wang Ruoran
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Pan Da
- Jiangsu Key Laboratory for Biodiversity and Biotechnology,
| | - Sun Hongying
- Jiangsu Key Laboratory for Biodiversity and Biotechnology,
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81
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Lazo-Cancino D, Musleh SS, Hernandez CE, Palma E, Rodriguez-Serrano E. Does silvoagropecuary landscape fragmentation affect the genetic diversity of the sigmodontine rodent Oligoryzomys longicaudatus? PeerJ 2017; 5:e3842. [PMID: 28975057 PMCID: PMC5624292 DOI: 10.7717/peerj.3842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 09/01/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Fragmentation of native forests is a highly visible result of human land-use throughout the world. In this study, we evaluated the effects of landscape fragmentation and matrix features on the genetic diversity and structure of Oligoryzomys longicaudatus, the natural reservoir of Hantavirus in southern South America. We focused our work in the Valdivian Rainforest where human activities have produced strong change of natural habitats, with an important number of human cases of Hantavirus. METHODS We sampled specimens of O. longicaudatus from five native forest patches surrounded by silvoagropecuary matrix from Panguipulli, Los Rios Region, Chile. Using the hypervariable domain I (mtDNA), we characterized the genetic diversity and evaluated the effect of fragmentation and landscape matrix on the genetic structure of O. longicaudatus. For the latter, we used three approaches: (i) Isolation by Distance (IBD) as null model, (ii) Least-cost Path (LCP) where genetic distances between patch pairs increase with cost-weighted distances, and (iii) Isolation by Resistance (IBR) where the resistance distance is the average number of steps that is needed to commute between the patches during a random walk. RESULTS We found low values of nucleotide diversity (π) for the five patches surveyed, ranging from 0.012 to 0.015, revealing that the 73 sampled specimens of this study belong to two populations but with low values of genetic distance (γST ) ranging from 0.022 to 0.099. Likewise, we found that there are no significant associations between genetic distance and geographic distance for IBD and IBR. However, we found for the LCP approach, a significant positive relationship (r = 0.737, p = 0.05), with shortest least-cost paths traced through native forest and arborescent shrublands. DISCUSSION In this work we found that, at this reduced geographical scale, Oligoryzomys longicaudatus shows genetic signs of fragmentation. In addition, we found that connectivity between full growth native forest remnants is mediated by the presence of dense shrublands and native forest corridors. In this sense, our results are important because they show how native forest patches and associated routes act as source of vector species in silvoagropecuary landscape, increasing the infection risk on human population. This study is the first approach to understand the epidemiological spatial context of silvoagropecuary risk of Hantavirus emergence. Further studies are needed to elucidate the effects of landscape fragmentation in order to generate new predictive models based on vector intrinsic attributes and landscape features.
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Affiliation(s)
| | - Selim S. Musleh
- Departamento de Oceanografía, Universidad de Concepción, Concepción, Biobío, Chile
| | | | - Eduardo Palma
- Departamento de Ecología, Pontificia Universidad Católica de Chile, Santiago, Chile
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82
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Two mitochondrial genomes in Alcedinidae (Ceryle rudis/Halcyon pileata) and the phylogenetic placement of Coraciiformes. Genetica 2017; 145:431-440. [PMID: 28791584 DOI: 10.1007/s10709-017-9978-6] [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] [Received: 01/17/2017] [Accepted: 08/03/2017] [Indexed: 10/19/2022]
Abstract
Coraciiformes comprises 209 species belonging to ten families with significant divergence on external morphologies and life styles. The phylogenetic placement of Coraciiformes was still in debate. Here, we determined the complete mitochondrial genomes (mitogenomes) of Crested Kingfisher (Ceryle rudis) and Black-capped Kingfisher (Halcyon pileata). The mitogenomes were 17,355 bp (C. rudis) and 17,612 bp (H. pileata) in length, and both of them contained 37 genes (two rRNA genes, 22 tRNA genes and 13 protein-coding genes) and one control region. The gene organizations and characters of two mitogenomes were similar with those of other mitogenomes in Coraciiformes, however the sizes and nucleotide composition of control regions in different mitogenomes were significantly different. Phylogenetic trees were constructed with both Bayesian and Maximum Likelihood methods based on mitogenome sequences from 11 families of six orders. The trees based on two different data sets supported the basal position of Psittacidae (Psittaciformes), the closest relationship between Cuculiformes (Cuculidae) and Trogoniformes (Trogonidae), and the close relationship between Coraciiformes and Piciformes. The phylogenetic placement of the clade including Cuculiformes and Trogoniformes has not been resolved in present study, which need further investigations with more molecular markers and species. The mitogenome sequences presented here provided valuable data for further taxonomic studies on Coraciiformes and other related groups.
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83
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Li YX, Gao YL, He XL, Cao SX. Exploration of mtDNA control region sequences in Chinese Tibetan Mastiffs. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:800-804. [PMID: 28756720 DOI: 10.1080/24701394.2017.1357714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The control region of mitochondrial DNA (mtDNA) was obtained from 40 purebred Chinese Tibetan Mastiffs (TMs). Sequence structure and genetic diversity were analyzed, and a phylogenetic tree was constructed. The TM mtDNA control region was composed of ETAS (extended termination associated sequences), CD (a central domain) and CSBs (conserved sequenced blocks) and sequence length showed some diversity, which was mainly caused by the number of 10 nucleotide repeat units [5'-GTA CAC GT (G/A) C-3'] between CSB I and CSB II, which ranged from 27 to 35 among individuals. Seventy-five polymorphic sites were identified, which defined 37 haplotypes; the haplotype diversity was 0.990, and the nucleotide diversity was 1.201. Based on the control region sequences, Chinese TMs were divided into three categories, which were consistent with the origin and geographical classification of TMs. Phylogenetic analysis of 538-bp HVR-I sequences revealed that TMs were most closely related to Labrador Retrievers.
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Affiliation(s)
- Yin-Xia Li
- a Institute of Animal Science , Jiangsu Academy of Agricultural Sciences , Nanjing , Jiangsu , China.,b Key Laboratory of Animal Breeding and Reproduction , Jiangsu Academy of Agricultural Sciences , Nanjing , Jiangsu , China
| | - Yi-Long Gao
- c Policedog Technology Key Laboratory of the Ministry of Public Security , Nanjing Policedog Research Institute of the Ministry of Public Security , Nanjing , Jiangsu , China
| | - Xing-Liang He
- c Policedog Technology Key Laboratory of the Ministry of Public Security , Nanjing Policedog Research Institute of the Ministry of Public Security , Nanjing , Jiangsu , China
| | - Shao-Xian Cao
- a Institute of Animal Science , Jiangsu Academy of Agricultural Sciences , Nanjing , Jiangsu , China.,b Key Laboratory of Animal Breeding and Reproduction , Jiangsu Academy of Agricultural Sciences , Nanjing , Jiangsu , China
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84
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Characterization of complete mitochondrial genomes of Mastacembelus erythrotaenia and Mastacembelus armatus (Synbranchiformes: Mastacembelidae) and phylogenetic studies of Mastacembelidae. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0807-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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85
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Hernández-Canchola G, León-Paniagua L. Genetic and ecological processes promoting early diversification in the lowland Mesoamerican bat Sturnira parvidens (Chiroptera: Phyllostomidae). Mol Phylogenet Evol 2017. [PMID: 28647618 DOI: 10.1016/j.ympev.2017.06.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
With 22 species, Sturnira is the most speciose genus of frugivorous Neotropical bats. Sturnira parvidens inhabits lowland tropical areas from Mexico to Central America. The elevation of this taxon to species level was recent, and discrepancies with respect to its geographic limits and phylogenetic position continue to exist. In order to identify genetic and ecological processes likely involved in the diversification and current distribution of S. parvidens, we evaluated relationships, researched phylogeographic and demographic history, and tested the divergence/conservatism of the climatic niche of this bat. We used data from mitochondrial loci (cytochrome b and the hypervariable D-loop region I) and the nuclear recombination activating gene 1, in 173 samples of S. parvidens and 77 samples of related species. We performed Bayesian analyses to infer phylogenetic relationships and analyzed phylogeographic structure, genetic diversity, divergence times and historical demography. Sturnira bakeri is the sister group of S. parvidens, and inhabits Western Ecuador. The two species diverged c. 1.84Ma, and their distributions are disjunct and separated by Sturnira luisi. Within S. parvidens there are two haplogroups with nearly allopatric distributions that are limited to the Sierra Madre del Sur, on the Mexican Pacific Slope. The divergence time between haplogroups was c. 0.423Ma and we detected signals of demographic expansion. We also analyzed 526 occurrence data of S. parvidens to test for changes in environmental niche of this species. We detected signals of divergence of climatic niche, mainly in temperature and seasonality variables. Likely, both genetic and ecological processes have shaped the evolutionary history of S. parvidens. Despite many climatic fluctuations during the Pleistocene, only the most intense oscillations had an impact on these bats. In addition, ecological differentiation prevents admixture of genetic lineages that are in contact and lack apparent geographical barriers at the southern Sierra Madre del Sur. We concluded that speciation in Sturnira was promoted by this taxon's ability to colonize new geographical and environmental spaces and form genetically structured groups when populations become isolated.
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Affiliation(s)
- Giovani Hernández-Canchola
- Museo de Zoología - Mastozoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México 04510, Mexico; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México 04510, Mexico.
| | - Livia León-Paniagua
- Museo de Zoología - Mastozoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México 04510, Mexico.
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86
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Khan MF, Khattak MNK, He D, Rehman AU, Chen Y. Mitochondrial genome sequence and gene organization of Kunar Snow trout ( Schizothorax labiatus ) with phylogenetic consideration. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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87
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Zhang B, Zhang Y, Wang X, Zhang H, Lin Q. The mitochondrial genome of a sea anemone Bolocera sp. exhibits novel genetic structures potentially involved in adaptation to the deep-sea environment. Ecol Evol 2017; 7:4951-4962. [PMID: 28690821 PMCID: PMC5496520 DOI: 10.1002/ece3.3067] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/13/2017] [Accepted: 04/24/2017] [Indexed: 01/14/2023] Open
Abstract
The deep sea is one of the most extensive ecosystems on earth. Organisms living there survive in an extremely harsh environment, and their mitochondrial energy metabolism might be a result of evolution. As one of the most important organelles, mitochondria generate energy through energy metabolism and play an important role in almost all biological activities. In this study, the mitogenome of a deep‐sea sea anemone (Bolocera sp.) was sequenced and characterized. Like other metazoans, it contained 13 energy pathway protein‐coding genes and two ribosomal RNAs. However, it also exhibited some unique features: just two transfer RNA genes, two group I introns, two transposon‐like noncanonical open reading frames (ORFs), and a control region‐like (CR‐like) element. All of the mitochondrial genes were coded by the same strand (the H‐strand). The genetic order and orientation were identical to those of most sequenced actiniarians. Phylogenetic analyses showed that this species was closely related to Bolocera tuediae. Positive selection analysis showed that three residues (31 L and 42 N in ATP6, 570 S in ND5) of Bolocera sp. were positively selected sites. By comparing these features with those of shallow sea anemone species, we deduced that these novel gene features may influence the activity of mitochondrial genes. This study may provide some clues regarding the adaptation of Bolocera sp. to the deep‐sea environment.
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Affiliation(s)
- Bo Zhang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yan‐Hong Zhang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Xin Wang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Hui‐Xian Zhang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
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88
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Two mitogenomes in Gruiformes (Amaurornis akool/A. phoenicurus) and the phylogenetic placement of Rallidae. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0562-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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89
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The complete mitochondrial genome of a threatened loach (Sinibotia reevesae) and its phylogeny. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0541-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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90
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Adrian-Kalchhauser I, Svensson O, Kutschera VE, Alm Rosenblad M, Pippel M, Winkler S, Schloissnig S, Blomberg A, Burkhardt-Holm P. The mitochondrial genome sequences of the round goby and the sand goby reveal patterns of recent evolution in gobiid fish. BMC Genomics 2017; 18:177. [PMID: 28209125 PMCID: PMC5314710 DOI: 10.1186/s12864-017-3550-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/02/2017] [Indexed: 11/15/2022] Open
Abstract
Background Vertebrate mitochondrial genomes are optimized for fast replication and low cost of RNA expression. Accordingly, they are devoid of introns, are transcribed as polycistrons and contain very little intergenic sequences. Usually, vertebrate mitochondrial genomes measure between 16.5 and 17 kilobases (kb). Results During genome sequencing projects for two novel vertebrate models, the invasive round goby and the sand goby, we found that the sand goby genome is exceptionally small (16.4 kb), while the mitochondrial genome of the round goby is much larger than expected for a vertebrate. It is 19 kb in size and is thus one of the largest fish and even vertebrate mitochondrial genomes known to date. The expansion is attributable to a sequence insertion downstream of the putative transcriptional start site. This insertion carries traces of repeats from the control region, but is mostly novel. To get more information about this phenomenon, we gathered all available mitochondrial genomes of Gobiidae and of nine gobioid species, performed phylogenetic analyses, analysed gene arrangements, and compared gobiid mitochondrial genome sizes, ecological information and other species characteristics with respect to the mitochondrial phylogeny. This allowed us amongst others to identify a unique arrangement of tRNAs among Ponto-Caspian gobies. Conclusions Our results indicate that the round goby mitochondrial genome may contain novel features. Since mitochondrial genome organisation is tightly linked to energy metabolism, these features may be linked to its invasion success. Also, the unique tRNA arrangement among Ponto-Caspian gobies may be helpful in studying the evolution of this highly adaptive and invasive species group. Finally, we find that the phylogeny of gobiids can be further refined by the use of longer stretches of linked DNA sequence. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3550-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irene Adrian-Kalchhauser
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, Basel, 4051, Switzerland.
| | - Ola Svensson
- Department of Biological and Environmental Sciences, University of Gothenburg, Medicinaregatan 18A, 41390, Göteborg, Sweden.,The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, P.O. Box 460, 40530, Gothenburg, Sweden
| | - Verena E Kutschera
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Magnus Alm Rosenblad
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, P.O. Box 460, 40530, Gothenburg, Sweden.,Department of Marine Sciences, NBIS Bioinformatics Infrastructure for Life Sciences, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden
| | - Martin Pippel
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Siegfried Schloissnig
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
| | - Anders Blomberg
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, P.O. Box 460, 40530, Gothenburg, Sweden.,Department of Marine Sciences, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden
| | - Patricia Burkhardt-Holm
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, Basel, 4051, Switzerland.,Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB, Canada
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91
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Villela LCV, Alves AL, Varela ES, Yamagishi MEB, Giachetto PF, da Silva NMA, Ponzetto JM, Paiva SR, Caetano AR. Complete mitochondrial genome from South American catfish Pseudoplatystoma reticulatum (Eigenmann & Eigenmann) and its impact in Siluriformes phylogenetic tree. Genetica 2017; 145:51-66. [DOI: 10.1007/s10709-016-9945-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 12/22/2016] [Indexed: 01/08/2023]
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92
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Gong L, Liu LQ, Guo BY, Ye YY, Lü ZM. The complete mitochondrial genome characterization of Thunnus obesus (Scombriformes: Scombridae) and phylogenetic analyses of Thunnus. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0688-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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93
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Wang YC, Zou Y, Sun XM, Gong J, Huang L, Jing MD. The complete mitochondrial genome sequence of the little grebe (Tachybaptus ruficollis). Genes Genomics 2017. [DOI: 10.1007/s13258-016-0480-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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94
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Lopez-Oceja A, Gamarra D, Cardoso S, Palencia-Madrid L, Juste RA, De Pancorbo MM. Two ovine mitochondrial DNAs harboring a fifth 75/76 bp repeat motif without altered gene expression in Northern Spain. Electrophoresis 2016; 38:869-875. [PMID: 27990652 DOI: 10.1002/elps.201600308] [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] [Received: 07/01/2016] [Revised: 11/22/2016] [Accepted: 11/29/2016] [Indexed: 11/10/2022]
Abstract
The Basque Country is home to the Latxa sheep breed, which is divided in several varieties such as Latxa Black Face (LBKF) and Latxa Blonde Face (LBLF). Mitochondrial DNA control region analysis of 174 male sheep (97 LBKF and 77 LBLF) was performed with the objective of characterizing the maternal lineages of these two varieties that are the basis to produce the cheese with Idiazabal quality label. The percentage of unique haplotypes was 77.32% in LBKF and 67.53% in LBLF. Most of the individuals were classified into B haplogroup (98.85%), while A haplogroup was much less frequent. Two Latxa individuals (one LBKF and one LBLF), both belonging to B haplogroup, displayed an additional 75/76 bp tandem repeat motif. Only 33 other sequences with this repeat motif were found among 11 061 sheep sequences included in the GenBank database. Gene expression was analyzed in peripheral blood leukocytes since the additional 75/76 bp repeat motif falls within ETAS1, a domain with a possible function in regulation of replication and transcription. The mRNA expression from four mitochondrial genes (COI, cyt b, ND1, and ND2) was analyzed in the two individuals of this study with a fifth repeat motif and in four without it. Although lower transcription was observed when the additional 75/76 bp repeat motif was present, no statistically significant differences were observed. Therefore, the variation in the number of the 75/76 repeat motif does not seem to modify the gene expression rate in mitochondrial genes.
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Affiliation(s)
- A Lopez-Oceja
- BIOMICs Research Group, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - D Gamarra
- BIOMICs Research Group, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - S Cardoso
- BIOMICs Research Group, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - L Palencia-Madrid
- BIOMICs Research Group, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - R A Juste
- Animal Health Department, Instituto Vasco de Investigación y Desarrollo Agrario (NEIKER), Derio, Bizkaia, Spain
| | - M M De Pancorbo
- BIOMICs Research Group, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
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95
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Ding L, Luo G, Li W, Liao J. Characterization and phylogenetic analysis of the complete mitogenome of Allactaga sibirica (Rodentia: Dipodidae). BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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96
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Characterization of the complete mitochondrial genome of Phodopus roborovskii (Rodentia: Cricetidae) and systematic implications for Cricetinae phylogenetics. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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97
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Ding L, Li W, Liao J. Mitochondrial genome of Cricetulus migratorius (Rodentia: Cricetidae): Insights into the characteristics of the mitochondrial genome and the phylogenetic relationships of Cricetulus species. Gene 2016; 595:121-129. [DOI: 10.1016/j.gene.2016.10.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/16/2016] [Accepted: 10/02/2016] [Indexed: 11/29/2022]
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98
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Muangkram Y, Wajjwalku W, Amano A, Sukmak M. The novel primers for mammal species identification-based mitochondrial cytochrome b sequence: implication for reserved wild animals in Thailand and endangered mammal species in Southeast Asia. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 29:62-72. [PMID: 27758125 DOI: 10.1080/24701394.2016.1238902] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We presented the powerful techniques for species identification using the short amplicon of mitochondrial cytochrome b gene sequence. Two faecal samples and one single hair sample of the Asian tapir were tested using the new cytochrome b primers. The results showed a high sequence similarity with the mainland Asian tapir group. The comparative sequence analysis of the reserved wild mammals in Thailand and the other endangered mammal species from Southeast Asia comprehensibly verified the potential of our novel primers. The forward and reverse primers were 94.2 and 93.2%, respectively, by the average value of the sequence identity among 77 species sequences, and the overall mean distance was 35.9%. This development technique could provide rapid, simple, and reliable tools for species confirmation. Especially, it could recognize the problematic biological specimens contained less DNA material from illegal products and assist with wildlife crime investigation of threatened species and related forensic casework.
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Affiliation(s)
- Yuttamol Muangkram
- a Graduate School of Life Sciences , Ritsumeikan University , Kusatsu , Shiga , Japan.,b Faculty of Veterinary Medicine , Kasetsart University , Kamphaeng Saen , Nakhon Pathom , Thailand
| | - Worawidh Wajjwalku
- b Faculty of Veterinary Medicine , Kasetsart University , Kamphaeng Saen , Nakhon Pathom , Thailand
| | - Akira Amano
- a Graduate School of Life Sciences , Ritsumeikan University , Kusatsu , Shiga , Japan
| | - Manakorn Sukmak
- b Faculty of Veterinary Medicine , Kasetsart University , Kamphaeng Saen , Nakhon Pathom , Thailand
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99
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Sequencing and characterization of mitochondrial DNA genome for Brama japonica (Perciformes: Bramidae) with phylogenetic consideration. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.06.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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100
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Lavrov DV, Pett W. Animal Mitochondrial DNA as We Do Not Know It: mt-Genome Organization and Evolution in Nonbilaterian Lineages. Genome Biol Evol 2016; 8:2896-2913. [PMID: 27557826 PMCID: PMC5633667 DOI: 10.1093/gbe/evw195] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2016] [Indexed: 12/11/2022] Open
Abstract
Animal mitochondrial DNA (mtDNA) is commonly described as a small, circular molecule that is conserved in size, gene content, and organization. Data collected in the last decade have challenged this view by revealing considerable diversity in animal mitochondrial genome organization. Much of this diversity has been found in nonbilaterian animals (phyla Cnidaria, Ctenophora, Placozoa, and Porifera), which, from a phylogenetic perspective, form the main branches of the animal tree along with Bilateria. Within these groups, mt-genomes are characterized by varying numbers of both linear and circular chromosomes, extra genes (e.g. atp9, polB, tatC), large variation in the number of encoded mitochondrial transfer RNAs (tRNAs) (0-25), at least seven different genetic codes, presence/absence of introns, tRNA and mRNA editing, fragmented ribosomal RNA genes, translational frameshifting, highly variable substitution rates, and a large range of genome sizes. This newly discovered diversity allows a better understanding of the evolutionary plasticity and conservation of animal mtDNA and provides insights into the molecular and evolutionary mechanisms shaping mitochondrial genomes.
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Affiliation(s)
- Dennis V Lavrov
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
| | - Walker Pett
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, Villeurbanne, France
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