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[PMID]:29381758
[Au] Autor:Song N; Lin A; Zhao X
[Ad] Endereço:College of Plant Protection, Henan Agricultural University, Zhengzhou, China.
[Ti] Título:Insight into higher-level phylogeny of Neuropterida: Evidence from secondary structures of mitochondrial rRNA genes and mitogenomic data.
[So] Source:PLoS One;13(1):e0191826, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:It is well known that the rRNA structure information is important to assist phylogenetic analysis through identifying homologous positions to improve alignment accuracy. In addition, the secondary structure of some conserved motifs is highly stable among distantly related taxa, which can provide potentially informative characters for estimating phylogeny. In this paper, we applied the high-throughput pooled sequencing approach to the determination of neuropteran mitogenomes. Four complete mitogenome sequences were obtained: Micromus angulatus (Hemerobiidae), Chrysoperla nipponensis (Chrysopidae), Rapisma sp. (Ithonidae), and Thaumatosmylus sp. (Osmylidae). This allowed us to sample more complete mitochondrial RNA gene sequences. Secondary structure diagrams for the complete mitochondrial small and large ribosomal subunit RNA genes of eleven neuropterid species were predicted. Comparative analysis of the secondary structures indicated a closer relationship of Megaloptera and Neuroptera. This result was congruent with the resulting phylogeny inferred from sequence alignments of all 37 mitochondrial genes, namely the hypothesis of (Raphidioptera + (Megaloptera + Neuroptera)).
[Mh] Termos MeSH primário: Genoma Mitocondrial
Mitocôndrias/genética
Neópteros/classificação
Filogenia
RNA Ribossômico/genética
[Mh] Termos MeSH secundário: Animais
Genes de Insetos
Neópteros/genética
Conformação de Ácido Nucleico
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (RNA, Ribosomal)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180131
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0191826


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[PMID]:29183283
[Au] Autor:Fraser TA; Shao R; Fountain-Jones NM; Charleston M; Martin A; Whiteley P; Holme R; Carver S; Polkinghorne A
[Ad] Endereço:School of Biological Sciences, University of Tasmania, Sandy Bay, Hobart, TAS, Australia.
[Ti] Título:Mitochondrial genome sequencing reveals potential origins of the scabies mite Sarcoptes scabiei infesting two iconic Australian marsupials.
[So] Source:BMC Evol Biol;17(1):233, 2017 Nov 28.
[Is] ISSN:1471-2148
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Debilitating skin infestations caused by the mite, Sarcoptes scabiei, have a profound impact on human and animal health globally. In Australia, this impact is evident across different segments of Australian society, with a growing recognition that it can contribute to rapid declines of native Australian marsupials. Cross-host transmission has been suggested to play a significant role in the epidemiology and origin of mite infestations in different species but a chronic lack of genetic resources has made further inferences difficult. To investigate the origins and molecular epidemiology of S. scabiei in Australian wildlife, we sequenced the mitochondrial genomes of S. scabiei from diseased wombats (Vombatus ursinus) and koalas (Phascolarctos cinereus) spanning New South Wales, Victoria and Tasmania, and compared them with the recently sequenced mitochondrial genome sequences of S. scabiei from humans. RESULTS: We found unique S. scabiei haplotypes among individual wombat and koala hosts with high sequence similarity (99.1% - 100%). Phylogenetic analysis of near full-length mitochondrial genomes revealed three clades of S. scabiei (one human and two marsupial), with no apparent geographic or host species pattern, suggestive of multiple introductions. The availability of additional mitochondrial gene sequences also enabled a re-evaluation of a range of putative molecular markers of S. scabiei, revealing that cox1 is the most informative gene for molecular epidemiological investigations. Utilising this gene target, we provide additional evidence to support cross-host transmission between different animal hosts. CONCLUSIONS: Our results suggest a history of parasite invasion through colonisation of Australia from hosts across the globe and the potential for cross-host transmission being a common feature of the epidemiology of this neglected pathogen. If this is the case, comparable patterns may exist elsewhere in the 'New World'. This work provides a basis for expanded molecular studies into mange epidemiology in humans and animals in Australia and other geographic regions.
[Mh] Termos MeSH primário: Genoma Mitocondrial
Marsupiais/parasitologia
Sarcoptes scabiei/genética
Escabiose/parasitologia
Análise de Sequência de DNA
[Mh] Termos MeSH secundário: Animais
Animais Selvagens/genética
Austrália/epidemiologia
Composição de Bases/genética
Sequência de Bases
Complexo IV da Cadeia de Transporte de Elétrons/genética
Genes Mitocondriais
Tamanho do Genoma
Haplótipos/genética
Seres Humanos
Anotação de Sequência Molecular
Filogenia
Escabiose/epidemiologia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
EC 1.9.3.1 (Electron Transport Complex IV)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171130
[St] Status:MEDLINE
[do] DOI:10.1186/s12862-017-1086-9


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[PMID]:29178825
[Au] Autor:Abalde S; Tenorio MJ; Afonso CML; Uribe JE; Echeverry AM; Zardoya R
[Ad] Endereço:Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain.
[Ti] Título:Phylogenetic relationships of cone snails endemic to Cabo Verde based on mitochondrial genomes.
[So] Source:BMC Evol Biol;17(1):231, 2017 Nov 25.
[Is] ISSN:1471-2148
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Due to their great species and ecological diversity as well as their capacity to produce hundreds of different toxins, cone snails are of interest to evolutionary biologists, pharmacologists and amateur naturalists alike. Taxonomic identification of cone snails still relies mostly on the shape, color, and banding patterns of the shell. However, these phenotypic traits are prone to homoplasy. Therefore, the consistent use of genetic data for species delimitation and phylogenetic inference in this apparently hyperdiverse group is largely wanting. Here, we reconstruct the phylogeny of the cones endemic to Cabo Verde archipelago, a well-known radiation of the group, using mitochondrial (mt) genomes. RESULTS: The reconstructed phylogeny grouped the analyzed species into two main clades, one including Kalloconus from West Africa sister to Trovaoconus from Cabo Verde and the other with a paraphyletic Lautoconus due to the sister group relationship of Africonus from Cabo Verde and Lautoconus ventricosus from Mediterranean Sea and neighboring Atlantic Ocean to the exclusion of Lautoconus endemic to Senegal (plus Lautoconus guanche from Mauritania, Morocco, and Canary Islands). Within Trovaoconus, up to three main lineages could be distinguished. The clade of Africonus included four main lineages (named I to IV), each further subdivided into two monophyletic groups. The reconstructed phylogeny allowed inferring the evolution of the radula in the studied lineages as well as biogeographic patterns. The number of cone species endemic to Cabo Verde was revised under the light of sequence divergence data and the inferred phylogenetic relationships. CONCLUSIONS: The sequence divergence between continental members of the genus Kalloconus and island endemics ascribed to the genus Trovaoconus is low, prompting for synonymization of the latter. The genus Lautoconus is paraphyletic. Lautoconus ventricosus is the closest living sister group of genus Africonus. Diversification of Africonus was in allopatry due to the direct development nature of their larvae and mainly triggered by eustatic sea level changes during the Miocene-Pliocene. Our study confirms the diversity of cone endemic to Cabo Verde but significantly reduces the number of valid species. Applying a sequence divergence threshold, the number of valid species within the sampled Africonus is reduced to half.
[Mh] Termos MeSH primário: Genoma Mitocondrial
Filogenia
Caramujos/classificação
Caramujos/genética
[Mh] Termos MeSH secundário: Animais
Sequência de Bases
Cabo Verde
DNA Mitocondrial/genética
Variação Genética
Análise de Sequência de DNA
Especificidade da Espécie
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Mitochondrial)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171128
[St] Status:MEDLINE
[do] DOI:10.1186/s12862-017-1069-x


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[PMID]:28456662
[Au] Autor:Kinkar L; Laurimäe T; Sharbatkhori M; Mirhendi H; Kia EB; Ponce-Gordo F; Andresiuk V; Simsek S; Lavikainen A; Irshadullah M; Umhang G; Oudni-M'rad M; Acosta-Jamett G; Rehbein S; Saarma U
[Ad] Endereço:Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 50410 Tartu, Estonia.
[Ti] Título:New mitogenome and nuclear evidence on the phylogeny and taxonomy of the highly zoonotic tapeworm Echinococcus granulosus sensu stricto.
[So] Source:Infect Genet Evol;52:52-58, 2017 Aug.
[Is] ISSN:1567-7257
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Cystic echinococcosis, a zoonotic disease caused by Echinococcus granulosus sensu lato (s. l.), is a significant global public health concern. Echinococcus granulosus s. l. is currently divided into numerous genotypes (G1-G8 and G10) of which G1-G3 are the most frequently implicated genotypes in human infections. Although it has been suggested that G1-G3 could be regarded as a distinct species E. granulosus sensu stricto (s. s.), the evidence to support this is inconclusive. Most importantly, data from nuclear DNA that provide means to investigate the exchange of genetic material between G1-G3 is lacking as none of the published nuclear DNA studies have explicitly included G2 or G3. Moreover, the commonly used relatively short mtDNA sequences, including the complete cox1 gene, have not allowed unequivocal differentiation of genotypes G1-G3. Therefore, significantly longer mtDNA sequences are required to distinguish these genotypes with confidence. The main aim of this study was to evaluate the phylogenetic relations and taxonomy of genotypes G1-G3 using sequences of nearly complete mitogenomes (11,443bp) and three nuclear loci (2984bp). A total of 23 G1-G3 samples were analysed, originating from 5 intermediate host species in 10 countries. The mtDNA data demonstrate that genotypes G1 and G3 are distinct mitochondrial genotypes (separated by 37 mutations), whereas G2 is not a separate genotype or even a monophyletic cluster, but belongs to G3. Nuclear data revealed no genetic separation of G1 and G3, suggesting that these genotypes form a single species due to ongoing gene flow. We conclude that: (a) in the taxonomic sense, genotypes G1 and G3 can be treated as a single species E. granulosus s. s.; (b) genotypes G1 and G3 should be regarded as distinct genotypes only in the context of mitochondrial data; (c) we recommend excluding G2 from the genotype list.
[Mh] Termos MeSH primário: Núcleo Celular/genética
DNA de Helmintos/genética
Echinococcus granulosus/classificação
Mitocôndrias/genética
[Mh] Termos MeSH secundário: África do Norte
Animais
Ásia
Echinococcus granulosus/genética
Echinococcus granulosus/isolamento & purificação
Echinococcus granulosus/metabolismo
Europa (Continente)
Genoma Mitocondrial
Genótipo
Seres Humanos
Filogenia
Filogeografia
América do Sul
Zoonoses/parasitologia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Helminth)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170501
[St] Status:MEDLINE


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[PMID]:28453676
[Au] Autor:Qian Y; Butler TJ; Opsahl-Ong K; Giroux NS; Sidore C; Nagaraja R; Cucca F; Ferrucci L; Abecasis GR; Schlessinger D; Ding J
[Ad] Endereço:Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA.
[Ti] Título:fastMitoCalc: an ultra-fast program to estimate mitochondrial DNA copy number from whole-genome sequences.
[So] Source:Bioinformatics;33(9):1399-1401, 2017 May 01.
[Is] ISSN:1367-4811
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Availability and Implementation: fastMitoCalc is available at https://lgsun.irp.nia.nih.gov/hsgu/software/mitoAnalyzer/index.html. Contact: jun.ding@nih.gov. Supplementary information: Supplementary data are available at Bioinformatics online.
[Mh] Termos MeSH primário: Dosagem de Genes
Genoma Mitocondrial
Genômica/métodos
Análise de Sequência de DNA/métodos
Software
[Mh] Termos MeSH secundário: Genoma Humano
Seres Humanos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE
[do] DOI:10.1093/bioinformatics/btw835


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[PMID]:29181905
[Au] Autor:Li GG; Zhang MX; Swa K; Maung KW; Quan RC
[Ad] Endereço:Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin Nay Pyi Taw 05282, Myanmar.
[Ti] Título:Complete mitochondrial genome of the leaf muntjac ( ) and phylogenetics of the genus .
[So] Source:Zool Res;38(5):310-316, 2017 Sep 18.
[Is] ISSN:2095-8137
[Cp] País de publicação:China
[La] Idioma:eng
[Ab] Resumo:The leaf muntjac ( ) is an endemic deer species found in the east trans-Himalayan region. In recent years, population numbers have decreased due to heavy hunting and habitat loss, and little genetic data exists for this species, thus our knowledge of distribution rangs and population sizes likewise remain limited. We obtained mtDNA genes and the complete mitochondrial genome sequence of using PCR, followed by direct sequencing. The complete mitogenome sequence was determined as a circular 16 349 bp mitochondrial genome, containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region, the gene composition and order of which were similar to most other vertebrates so far reported. Most mitochondrial genes, except for and eight tRNAs, were encoded on the heavy strand. The overall base composition of the heavy strand was 33.1% A, 29.3% T, 24.2% C, and 13.4% G, with a strong AT bias of 62.4%. There were seven regions of gene overlap totaling 95 bp and 11 intergenic spacer regions totaling 74 bp. Phylogenetic analyses (ML and BI) among the genus based on the sequenced of mitogenome and supported as a member of , most closely related to . However, when analyses based on cyt included two more muntjacs, was most closely related to rather than , and together with , likely forming a complex of the species. This study will help in the exploration of the evolutionary history and taxonomic status of the leaf muntjac, as well as its protection as a genetic resource.
[Mh] Termos MeSH primário: DNA Mitocondrial/genética
Genoma Mitocondrial
Cervo Muntjac/genética
Filogenia
[Mh] Termos MeSH secundário: Animais
Especificidade da Espécie
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Mitochondrial)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180305
[Lr] Data última revisão:
180305
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171129
[St] Status:MEDLINE
[do] DOI:10.24272/j.issn.2095-8137.2017.058


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[PMID]:28986237
[Au] Autor:Liu Y; Song F; Jiang P; Wilson JJ; Cai W; Li H
[Ad] Endereço:Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture, Department of Entomology, China Agricultural University, Beijing 100193, China.
[Ti] Título:Compositional heterogeneity in true bug mitochondrial phylogenomics.
[So] Source:Mol Phylogenet Evol;118:135-144, 2018 Jan.
[Is] ISSN:1095-9513
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Mitochondrial phylogenomics is often controversial, in particular for inferring deep relationships. The recent rapid increase of mitochondrial genome data provides opportunities for better phylogenetic estimates and assessment of potential biases resulting from heterogeneity in nucleotide composition and mutation rates. Here, we gathered 76 mitochondrial genome sequences for Heteroptera representing all seven infraorders, including 17 newly sequenced mitochondrial genomes. We found strong heterogeneity in base composition and contrasting evolutionary rates among heteropteran mitochondrial genomes, which affected analyses with various datasets and partitioning schemes under site-homogeneous models and produced false groupings of unrelated taxa exhibiting similar base composition and accelerated evolutionary rates. Bayesian analyses using a site-heterogeneous mixture CAT+GTR model showed high congruence of topologies with the currently accepted phylogeny of Heteroptera. The results confirm the monophyly of the six infraorders within Heteroptera, except for Cimicomorpha which was recovered as two paraphyletic clades. The monophyly of Terheteroptera (Cimicomorpha and Pentatomomorpha) and Panheteroptera (Nepomorpha, Leptopodomorpha and Terheteroptera) was recovered demonstrating a significant improvement over previous studies using mitochondrial genome data. Our study shows the power of the site-heterogeneous mixture models for resolving phylogenetic relationships with Heteroptera and provides one more case showing that model adequacy is critical for accurate tree reconstruction in mitochondrial phylogenomics.
[Mh] Termos MeSH primário: Genoma Mitocondrial
Heterópteros/genética
Mitocôndrias/genética
Filogenia
[Mh] Termos MeSH secundário: Animais
Composição de Bases
Sequência de Bases
Teorema de Bayes
Variação Genética
Funções Verossimilhança
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180302
[Lr] Data última revisão:
180302
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171008
[St] Status:MEDLINE


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[PMID]:29038046
[Au] Autor:Sun S; Li Q; Kong L; Yu H
[Ad] Endereço:Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China.
[Ti] Título:Multiple reversals of strand asymmetry in molluscs mitochondrial genomes, and consequences for phylogenetic inferences.
[So] Source:Mol Phylogenet Evol;118:222-231, 2018 Jan.
[Is] ISSN:1095-9513
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Strand asymmetry in nucleotide composition is a remarkable feature of animal mitochondrial genomes. The strand-specific bias in the nucleotide composition of the mtDNA has been known to be highly problematic for phylogenetic analyses. Here, the strand asymmetry was compared across 140 mollusc species and analyzed for a mtDNA fragment including twelve protein-coding genes. The analyses show that almost all species in Gastropoda (except Heterobranchia) and all species in Bivalvia present reversals of strand bias. The skew values on individual genes for all codon positions (P ), third codon positions (P ), and fourfold redundant third codon positions (P ) indicated that CG skews are the best indicators of strand asymmetry. The differences in the patterns of strand asymmetry significantly influenced the amino acid composition of the encoded proteins. These biases are most striking for the amino acids Valine, Cysteine, Asparagine and Threonines, which appear to have evolved asymmetrical exchanges in response to shifts in nucleotide composition. Molluscs with strong variability of genome architectures (ARs) are usually characterized by a reversal of the usual strand bias. Phylogenetic analyses show that reversals of asymmetric mutational constraints have consequences on the phylogenetic inferences, as taxa characterized by reverse strand bias (Heterobranchia and Bivalvia) tend to group together due to long-branch attraction (LBA) artifacts. Neutral Transitions Excluded (NTE) model did not overcome the problem of heterogeneous biases present in molluscs mt genomes, suggested it may not be appropriate for molluscs mt genome data. Further refinement phylogenetic models may help us better understand internal relationships among these diverse organisms.
[Mh] Termos MeSH primário: Genoma Mitocondrial
Moluscos/classificação
[Mh] Termos MeSH secundário: Aminoácidos/química
Aminoácidos/metabolismo
Animais
Composição de Bases
Bivalves/classificação
Bivalves/genética
Códon
Gastrópodes/classificação
Gastrópodes/genética
Moluscos/genética
Filogenia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Amino Acids); 0 (Codon)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180220
[Lr] Data última revisão:
180220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171018
[St] Status:MEDLINE


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[PMID]:29320542
[Au] Autor:Matisoo-Smith E; Gosling AL; Platt D; Kardailsky O; Prost S; Cameron-Christie S; Collins CJ; Boocock J; Kurumilian Y; Guirguis M; Pla Orquín R; Khalil W; Genz H; Abou Diwan G; Nassar J; Zalloua P
[Ad] Endereço:Department of Anatomy, University of Otago, Dunedin, New Zealand.
[Ti] Título:Ancient mitogenomes of Phoenicians from Sardinia and Lebanon: A story of settlement, integration, and female mobility.
[So] Source:PLoS One;13(1):e0190169, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The Phoenicians emerged in the Northern Levant around 1800 BCE and by the 9th century BCE had spread their culture across the Mediterranean Basin, establishing trading posts, and settlements in various European Mediterranean and North African locations. Despite their widespread influence, what is known of the Phoenicians comes from what was written about them by the Greeks and Egyptians. In this study, we investigate the extent of Phoenician integration with the Sardinian communities they settled. We present 14 new ancient mitogenome sequences from pre-Phoenician (~1800 BCE) and Phoenician (~700-400 BCE) samples from Lebanon (n = 4) and Sardinia (n = 10) and compare these with 87 new complete mitogenomes from modern Lebanese and 21 recently published pre-Phoenician ancient mitogenomes from Sardinia to investigate the population dynamics of the Phoenician (Punic) site of Monte Sirai, in southern Sardinia. Our results indicate evidence of continuity of some lineages from pre-Phoenician populations suggesting integration of indigenous Sardinians in the Monte Sirai Phoenician community. We also find evidence of the arrival of new, unique mitochondrial lineages, indicating the movement of women from sites in the Near East or North Africa to Sardinia, but also possibly from non-Mediterranean populations and the likely movement of women from Europe to Phoenician sites in Lebanon. Combined, this evidence suggests female mobility and genetic diversity in Phoenician communities, reflecting the inclusive and multicultural nature of Phoenician society.
[Mh] Termos MeSH primário: Demografia
Grupos Étnicos/história
Genoma Mitocondrial
Migração Humana/história
Mulheres
[Mh] Termos MeSH secundário: Adolescente
Adulto
Criança
Cultura
DNA Mitocondrial/análise
DNA Mitocondrial/isolamento & purificação
Grupos Étnicos/genética
Feminino
Variação Genética
Haplótipos
História Antiga
Seres Humanos
Itália
Líbano/etnologia
Região do Mediterrâneo
Filogenia
Dinâmica Populacional
Dente
[Pt] Tipo de publicação:HISTORICAL ARTICLE; JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA, Mitochondrial)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180214
[Lr] Data última revisão:
180214
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180111
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190169


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[PMID]:28460352
[Au] Autor:Riman S; Kiesler KM; Borsuk LA; Vallone PM
[Ad] Endereço:U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899-8314, USA. Electronic address: sarah.riman@nist.gov.
[Ti] Título:Characterization of NIST human mitochondrial DNA SRM-2392 and SRM-2392-I standard reference materials by next generation sequencing.
[So] Source:Forensic Sci Int Genet;29:181-192, 2017 07.
[Is] ISSN:1878-0326
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Standard Reference Materials SRM 2392 and 2392-I are intended to provide quality control when amplifying and sequencing human mitochondrial genome sequences. The National Institute of Standards and Technology (NIST) offers these SRMs to laboratories performing DNA-based forensic human identification, molecular diagnosis of mitochondrial diseases, mutation detection, evolutionary anthropology, and genetic genealogy. The entire mtGenome (∼16569bp) of SRM 2392 and 2392-I have previously been characterized at NIST by Sanger sequencing. Herein, we used the sensitivity, specificity, and accuracy offered by next generation sequencing (NGS) to: (1) re-sequence the certified values of the SRM 2392 and 2392-I; (2) confirm Sanger data with a high coverage new sequencing technology; (3) detect lower level heteroplasmies (<20%); and thus (4) support mitochondrial sequencing communities in the adoption of NGS methods. To obtain a consensus sequence for the SRMs as well as identify and control any bias, sequencing was performed using two NGS platforms and data was analyzed using different bioinformatics pipelines. Our results confirm five low level heteroplasmy sites that were not previously observed with Sanger sequencing: three sites in the GM09947A template in SRM 2392 and two sites in the HL-60 template in SRM 2392-I.
[Mh] Termos MeSH primário: DNA Mitocondrial/genética
Sequenciamento de Nucleotídeos em Larga Escala
Análise de Sequência de DNA
[Mh] Termos MeSH secundário: DNA Mitocondrial/normas
Genoma Mitocondrial
Seres Humanos
Padrões de Referência
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
0 (DNA, Mitochondrial)
[Em] Mês de entrada:1707
[Cu] Atualização por classe:180215
[Lr] Data última revisão:
180215
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170502
[St] Status:MEDLINE



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