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1.
Implement Sci ; 14(1): 79, 2019 08 13.
Artigo em Inglês | MEDLINE | ID: mdl-31409417

RESUMO

BACKGROUND: Next-generation sequencing (NGS) is increasingly being translated into routine public health practice, affecting the surveillance and control of many pathogens. The purpose of this scoping review is to identify and characterize the recent literature concerning the application of bacterial pathogen genomics for public health practice and to assess the added value, challenges, and needs related to its implementation from an epidemiologist's perspective. METHODS: In this scoping review, a systematic PubMed search with forward and backward snowballing was performed to identify manuscripts in English published between January 2015 and September 2018. Included studies had to describe the application of NGS on bacterial isolates within a public health setting. The studied pathogen, year of publication, country, number of isolates, sampling fraction, setting, public health application, study aim, level of implementation, time orientation of the NGS analyses, and key findings were extracted from each study. Due to a large heterogeneity of settings, applications, pathogens, and study measurements, a descriptive narrative synthesis of the eligible studies was performed. RESULTS: Out of the 275 included articles, 164 were outbreak investigations, 70 focused on strategy-oriented surveillance, and 41 on control-oriented surveillance. Main applications included the use of whole-genome sequencing (WGS) data for (1) source tracing, (2) early outbreak detection, (3) unraveling transmission dynamics, (4) monitoring drug resistance, (5) detecting cross-border transmission events, (6) identifying the emergence of strains with enhanced virulence or zoonotic potential, and (7) assessing the impact of prevention and control programs. The superior resolution over conventional typing methods to infer transmission routes was reported as an added value, as well as the ability to simultaneously characterize the resistome and virulome of the studied pathogen. However, the full potential of pathogen genomics can only be reached through its integration with high-quality contextual data. CONCLUSIONS: For several pathogens, it is time for a shift from proof-of-concept studies to routine use of WGS during outbreak investigations and surveillance activities. However, some implementation challenges from the epidemiologist's perspective remain, such as data integration, quality of contextual data, sampling strategies, and meaningful interpretations. Interdisciplinary, inter-sectoral, and international collaborations are key for an appropriate genomics-informed surveillance.


Assuntos
Genoma Bacteriano , Genômica/métodos , Prática de Saúde Pública , Humanos , Sequenciamento Completo do Genoma
2.
Gene ; 716: 144016, 2019 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-31377318

RESUMO

Drug resistance of malaria parasites remains a problem affecting antimalarial treatment and control of the disease. We previously synthesized an antimalarial endoperoxide, N-89, having high antimalarial effects in vitro and in vivo. In this study we seek to understand the resistant mechanism against N-89 by establishing a highly N-89-resistant clone, named NRC10H, of the Plasmodium falciparum FCR-3 strain. We describe gene mutations in the parent FCR-3 strain and the NRC10H clone using whole-genome sequencing and subsequently by expression profiling using quantitative real-time PCR. Seven genes related to drug resistance, proteolysis, glycophosphatidylinositol anchor biosynthesis, and phosphatidylethanolamine biosynthesis exhibited a single amino acid substitution in the NRC10H clone. Among these seven genes, the multidrug resistance protein 2 (mdr2) variant A532S was found only in NRC10H. The genetic status of the P. falciparum endoplasmic reticulum-resident calcium binding protein (PfERC), a potential target of N-89, was similar between the NRC10H clone and the parent FCR-3 strain. These findings suggest that the genetic alterations of the identified seven genes, in particular mdr2, in NRC10H could give rise to resistance of the antimalarial endoperoxide N-89.


Assuntos
Antimaláricos/farmacologia , Compostos Heterocíclicos com 2 Anéis/farmacologia , Plasmodium falciparum/efeitos dos fármacos , Compostos de Espiro/farmacologia , Resistência a Medicamentos/genética , Genômica , Plasmodium falciparum/genética , Plasmodium falciparum/metabolismo , Proteínas de Protozoários/genética , Proteínas de Protozoários/metabolismo , RNA Mensageiro/metabolismo , Sequenciamento Completo do Genoma
3.
Lancet ; 394(10197): 533-540, 2019 Aug 10.
Artigo em Inglês | MEDLINE | ID: mdl-31395441

RESUMO

One of the primary goals of genomic medicine is to improve diagnosis through identification of genomic conditions, which could improve clinical management, prevent complications, and promote health. We explore how genomic medicine is being used to obtain molecular diagnoses for patients with previously undiagnosed diseases in prenatal, paediatric, and adult clinical settings. We focus on the role of clinical genomic sequencing (exome and genome) in aiding patients with conditions that are undiagnosed even after extensive clinical evaluation and testing. In particular, we explore the impact of combining genomic and phenotypic data and integrating multiple data types to improve diagnoses for patients with undiagnosed diseases, and we discuss how these genomic sequencing diagnoses could change clinical management.


Assuntos
Doenças Raras/diagnóstico , Análise de Sequência de DNA/métodos , Adulto , Criança , Diagnóstico Precoce , Genômica , Humanos , Fenótipo , Diagnóstico Pré-Natal/métodos , Doenças Raras/genética , Sequenciamento Completo do Exoma , Sequenciamento Completo do Genoma
4.
Genet Sel Evol ; 51(1): 44, 2019 Aug 14.
Artigo em Inglês | MEDLINE | ID: mdl-31412777

RESUMO

BACKGROUND: Experimental intercrosses between outbred founder populations are powerful resources for mapping loci that contribute to complex traits i.e. quantitative trait loci (QTL). Here, we present an approach and its accompanying software for high-resolution reconstruction of founder mosaic genotypes in the intercross offspring from such populations using whole-genome high-coverage sequence data on founder individuals (~ 30×) and very low-coverage sequence data on intercross individuals (< 0.5×). Sets of founder-line informative markers were selected for each full-sib family and used to infer the founder mosaic genotypes of the intercross individuals. The application of this approach and the quality of the estimated genome-wide genotypes are illustrated in a large F2 pedigree between two divergently selected lines of chickens. RESULTS: We describe how we obtained whole-genome genotype data for hundreds of individuals in a cost- and time-efficient manner by using a Tn5-based library preparation protocol and an imputation algorithm that was optimized for this application. In total, 7.6 million markers segregated in this pedigree and, within each full-sib family, between 10.0 and 13.7% of these were fully informative, i.e. fixed for alternative alleles in the founders from the divergent lines, and were used for reconstruction of the offspring mosaic genotypes. The genotypes that were estimated based on the low-coverage sequence data were highly consistent (> 95% agreement) with those obtained using individual single nucleotide polymorphism (SNP) genotyping. The estimated resolution of the inferred recombination breakpoints was relatively high, with 50% of them being defined on regions shorter than 10 kb. CONCLUSIONS: A method and software for inferring founder mosaic genotypes in intercross offspring from low-coverage whole-genome sequencing in pedigrees from heterozygous founders are described. They provide high-quality, high-resolution genotypes in a time- and cost-efficient manner. The software is freely available at https://github.com/CarlborgGenomics/Stripes .


Assuntos
Galinhas/genética , Técnicas de Genotipagem , Sequenciamento Completo do Genoma , Animais , Cruzamento , Custos e Análise de Custo , Cruzamentos Genéticos , Conjuntos de Dados como Assunto , Feminino , Efeito Fundador , Técnicas de Genotipagem/economia , Masculino , Linhagem , Polimorfismo de Nucleotídeo Único , Software , Sequenciamento Completo do Genoma/economia
5.
Medicine (Baltimore) ; 98(33): e16749, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31415371

RESUMO

This study is to analyze the functional genes and metabolic pathways of dexamethasone degradation in Burkholderia through genome sequencing.A new Burkholderia sp. CQQ001 (B. CQ001) with dexamethasone degrading activity was isolated from the hospital wastewater and sequenced using Illumina Hiseq4000 combined with the third-generation sequencing technology. The genomes were assembled, annotated, and genomically mapped. Compared with six Burkholderia strains with typical features and four Burkholderia strains with special metabolic ability, the functional genes and metabolic pathways of dexamethasone degradation were analyzed and confirmed by RT-qPCR.Genome of B. CQ001 was 7,660,596 bp long with 6 ring chromosomes. The genes related to material metabolism accounted for 80.15%. These metabolism related genes could participate in 117 metabolic pathways and cover various microbial metabolic pathways in different environments and decomposition pathways of secondary metabolites, especially the degradation of aromatic compounds. The steroidal metabolic pathway containing 1 ABC transporter and 9 key metabolic enzymes related genes were scattered in the genome. Among them, the ABC transporter, KshA, and KshB increased significantly under the culture conditions of dexamethasone sodium phosphate as carbon source.B. CQ001 is a bacterium with strong metabolic function and rich metabolic pathways. It has the potential to degrade aromatics and other exogenous chemicals and contains genes for steroid metabolism. Our study enriches the genetic information of Burkholderia and provides information for the application of Burkholderia in bioremediation and steroid medicine production.


Assuntos
Anti-Inflamatórios/metabolismo , Burkholderia/metabolismo , Dexametasona/metabolismo , Águas Residuárias , Microbiologia da Água , Burkholderia/genética , Genoma Bacteriano , Humanos , Águas Residuárias/microbiologia , Sequenciamento Completo do Genoma
6.
World J Microbiol Biotechnol ; 35(8): 118, 2019 Jul 22.
Artigo em Inglês | MEDLINE | ID: mdl-31332540

RESUMO

The fungal genus Ustilago consists of intimidating pathogens associated with disease manifestations in plants of agricultural importance and gravity. Rapid progress of genome sequencing has opened the floodgates for biological research. Availability of Ustilago genomes provides a scope to explore complex codon and amino acid usage patterns in the genus. An extensive scrutiny of the factors underlying the complex modalities of codon and amino acid usage in Ustilago has been executed in the present analysis. Multivariate statistical analysis revealed a dominant effect of natural selection pressure, aimed at translational accuracy, to be operative on the codon usage behavior. Subtle impact of GC compositional constraint was also evident on the codon usage patterns. Gene expressivity was inferred to be the most crucial determinant governing observed codon usage variations. Amino acid usage patterns were found to be significantly governed by aromatic and hydrophobic characters of the encoded proteins. GC content and length of protein coding sequences also had considerable influence on the amino acid usage signatures. Extensive analysis of codon context variations revealed that UpA dinucleotides were strictly avoided at the codon-codon junctions (cP3-cA1) which might be attributed to reduce the risk of nonsense mutations and subsequently, improve translational finesse. Identification of the optimal codons, employed preferentially among the genes with high expressivity, and estimation of preferred and avoided codon pairs in Ustilago promises to be useful pertaining to mutational experiments at the codonic level, targeted to thwart the growth of Ustilago and combat associated pathogenesis.


Assuntos
Perfilação da Expressão Gênica , Ustilago/genética , Aminoácidos/metabolismo , Composição de Bases/genética , Códon , Seleção Genética/genética , Ustilago/metabolismo , Sequenciamento Completo do Genoma
7.
Vet Microbiol ; 235: 110-117, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31282368

RESUMO

Bovine Respiratory Disease (BRD) is a major threat to animal health and welfare in the cattle industry. Strains of Mannheimia haemolytica (Mh) that are resistant to multiple classes of antimicrobials are becoming a major concern in the beef industry, as the frequency of isolation of these strains has been increasing. Mobile genetic elements, such as integrative conjugative elements (ICE), are frequently implicated in this rapid increase in multi-drug resistance. The objectives of the current study were to determine the genetic relationship between the isolates collected at arrival before metaphylaxis and at revaccination after metaphylaxis, to identify which resistance genes might be present in these isolates, and to determine if they were carried on an ICE. Twenty calves culture positive for Mh at arrival and revaccination were identified, and a total of 48 isolates with unique susceptibility profiles (26 from arrival, and 22 from revaccination) were submitted for whole-genome sequencing (WGS). A phylogenetic tree was constructed, showing the arrival isolates falling into four clades, and all revaccination isolates within one clade. All revaccination isolates, and one arrival isolate, were positive for the presence of an ICE. Three different ICEs with resistance gene modules were identified. The resistance genes aphA1, strA, strB, sul2, floR, erm42, tetH/R, aadB, aadA25, blaOXA-2, msrE, mphE were all located within an ICE. The gene bla-ROB1 was also present in the isolates, but was not located within an ICE.


Assuntos
Antibacterianos/farmacologia , Bovinos/microbiologia , Farmacorresistência Bacteriana Múltipla/genética , Mannheimia haemolytica/efeitos dos fármacos , Mannheimia haemolytica/genética , Pasteurelose Pneumônica/microbiologia , Animais , Antibacterianos/uso terapêutico , Dissacarídeos/uso terapêutico , Variação Genética , Genoma Bacteriano , Compostos Heterocíclicos/uso terapêutico , Imunização Secundária , Sequências Repetitivas Dispersas , Mannheimia haemolytica/isolamento & purificação , Testes de Sensibilidade Microbiana , Pasteurelose Pneumônica/tratamento farmacológico , Filogenia , Vacinação , Sequenciamento Completo do Genoma
8.
Vet Microbiol ; 235: 118-126, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31282369

RESUMO

The aim of the present study was to investigate the diversity of methicillin-resistant Staphylococcus aureus (MRSA) that originated from Austrian companion animals during the last five-year period. A total of 90 non-repetitive MRSA isolates were obtained during diagnostic activities from autumn 2013 to autumn 2018. They originated from horses (n = 62), cats (n = 13), dogs (n = 10), rabbits (n = 2), a domestic canary, a zoo-kept hammer-headed bat (Hypsignathus monstrosus) and a semi-captive northern bald ibis (Geronticus eremita). Antimicrobial susceptibility testing was performed. All isolates were mecA-positive and mecC-negative. The isolates were genotyped by SCCmec, spa and dru typing, Multiple-Locus Variable number of tandem repeat Analyses (MLVA), S. aureus DNA microarray, and whole-genome sequencing (WGS). Eight sequence types (STs - ST398, ST5275 (new ST), ST225, ST8, ST22, ST152, ST1, and ST45), three SCCmec types (II, IV, and V), sixteen spa types (t003, t008, t011, t015, t032, t034, t1381, t1928, t1985, t223, t334, t355, t430, t6447, t6867, and t7105), fourteen dru types (dt10a, dt10az, dt10q, dt10r, dt11a, dt5e, dt6j, dt9a, dt9ak, dt9g, and four new types dt8as, dt7ak, dt4j, dt14n), and thirty-five MLVA types were detected. WGS-based core genome MLST (cgMLST) displayed five main clusters. Compared to the time period 2004-2013, the results of the present study show not only a higher diversity among the MRSA isolates within the population of Austrian companion animals, but also the introduction of new clones. Although ST398 isolates remained predominant, mainly due to high presence of this lineage among horses, increasing isolation rates of human-associated MRSA clones were observed in cats and dogs.


Assuntos
Variação Genética , Staphylococcus aureus Resistente à Meticilina/classificação , Staphylococcus aureus Resistente à Meticilina/genética , Animais de Estimação/microbiologia , Infecções Estafilocócicas/veterinária , Animais , Antibacterianos/farmacologia , Técnicas de Tipagem Bacteriana , Gatos/microbiologia , Cães/microbiologia , Genótipo , Humanos , Staphylococcus aureus Resistente à Meticilina/isolamento & purificação , Testes de Sensibilidade Microbiana , Tipagem de Sequências Multilocus , Análise de Sequência com Séries de Oligonucleotídeos , Sequenciamento Completo do Genoma
9.
Genome Biol ; 20(1): 136, 2019 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-31300020

RESUMO

BACKGROUND: Bread wheat is one of the most important and broadly studied crops. However, due to the complexity of its genome and incomplete genome collection of wild populations, the bread wheat genome landscape and domestication history remain elusive. RESULTS: By investigating the whole-genome resequencing data of 93 accessions from worldwide populations of bread wheat and its diploid and tetraploid progenitors, together with 90 published exome-capture data, we find that the B subgenome has more variations than A and D subgenomes, including SNPs and deletions. Population genetics analyses support a monophyletic origin of domesticated wheat from wild emmer in northern Levant, with substantial introgressed genomic fragments from southern Levant. Southern Levant contributes more than 676 Mb in AB subgenomes and enriched in the pericentromeric regions. The AB subgenome introgression happens at the early stage of wheat speciation and partially contributes to their greater genetic diversity. Furthermore, we detect massive alien introgressions that originated from distant species through natural and artificial hybridizations, resulting in the reintroduction of ~ 709 Mb and ~ 1577 Mb sequences into bread wheat landraces and varieties, respectively. A large fraction of these intra- and inter-introgression fragments are associated with quantitative trait loci of important traits, and selection events are also identified. CONCLUSION: We reveal the significance of multiple introgressions from distant wild populations and alien species in shaping the genetic components of bread wheat, and provide important resources and new perspectives for future wheat breeding.


Assuntos
Evolução Biológica , Variação Genética , Genoma de Planta , Hibridização Genética , Triticum/genética , Cromossomos de Plantas , Domesticação , Sequenciamento Completo do Genoma
10.
Genet Sel Evol ; 51(1): 34, 2019 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-31262251

RESUMO

BACKGROUND: Milk quality in dairy cattle is routinely assessed via analysis of mid-infrared (MIR) spectra; this approach can also be used to predict the milk's cheese-making properties (CMP) and composition. When this method of high-throughput phenotyping is combined with efficient imputations of whole-genome sequence data from cows' genotyping data, it provides a unique and powerful framework with which to carry out genomic analyses. The goal of this study was to use this approach to identify genes and gene networks associated with milk CMP and composition in the Montbéliarde breed. RESULTS: Milk cheese yields, coagulation traits, milk pH and contents of proteins, fatty acids, minerals, citrate, and lactose were predicted from MIR spectra. Thirty-six phenotypes from primiparous Montbéliarde cows (1,442,371 test-day records from 189,817 cows) were adjusted for non-genetic effects and averaged per cow. 50 K genotypes, which were available for a subset of 19,586 cows, were imputed at the sequence level using Run6 of the 1000 Bull Genomes Project (comprising 2333 animals). The individual effects of 8.5 million variants were evaluated in a genome-wide association study (GWAS) which led to the detection of 59 QTL regions, most of which had highly significant effects on CMP and milk composition. The results of the GWAS were further subjected to an association weight matrix and the partial correlation and information theory approach and we identified a set of 736 co-associated genes. Among these, the well-known caseins, PAEP and DGAT1, together with dozens of other genes such as SLC37A1, ALPL, MGST1, SEL1L3, GPT, BRI3BP, SCD, GPAT4, FASN, and ANKH, explained from 12 to 30% of the phenotypic variance of CMP traits. We were further able to identify metabolic pathways (e.g., phosphate and phospholipid metabolism and inorganic anion transport) and key regulator genes, such as PPARA, ASXL3, and bta-mir-200c that are functionally linked to milk composition. CONCLUSIONS: By using an approach that integrated GWAS with network and pathway analyses at the whole-genome sequence level, we propose candidate variants that explain a substantial proportion of the phenotypic variance of CMP traits and could thus be included in genomic evaluation models to improve milk CMP in Montbéliarde cows.


Assuntos
Bovinos/genética , Queijo , Estudo de Associação Genômica Ampla/veterinária , Leite/química , Animais , Simulação por Computador , Conjuntos de Dados como Assunto , Feminino , Regulação da Expressão Gênica , Redes Reguladoras de Genes , Masculino , Locos de Características Quantitativas , Sequenciamento Completo do Genoma/veterinária
11.
Sci Total Environ ; 691: 80-92, 2019 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-31319261

RESUMO

The emergence and dissemination of infections caused by carbapenem-resistant Klebsiella pneumoniae (CRKP) are of great concern worldwide, as there are limited options for their treatment. Thus, in this study, whole-genome sequencing (WGS) was applied to assess CRKP distribution and dissemination from hospital settings to the aquatic environment in order to identify the extent of the problem. Samples were collected from hospital wastewaters and receiving water bodies. Susceptible K. pneumoniae and CRKP were enumerated and isolated using standard methods. Seventeen CRKP were DNA-sequenced using an Illumina HiSeq X™ platform. De novo assembly and annotation were performed using SPAdes and RAST, respectively. The study analysed antibiotic resistance traits (antibiotic resistant genes, mobile genetic elements, and virulence genes) in CRKP isolates. Although influent of wastewater harboured the highest CRKP, wastewater treatment plants were efficient in reducing the threat. In terms of resistance per matrix, benthic sediment proved to harbour more CRKP (22.88%) versus susceptible K. pneumoniae, as revealed by their resistant quotient analysis, while effluent of wastewaters (4.21%) and water bodies (4.64%) had the lowest CRKP loads. The disseminating CRKP consisted of six sequence types (ST) - ST307 (n = 7), a novel ST3559 (n = 5), ST15 (n = 2), and one isolate of each of ST39, 152 and 298. All CRKP isolates harboured ß-lactams (blaCTX-M-15 and blaOXA-1), quinolone (oqxA and oqxB) and fosfomycin (fosA) resistance genes as well as virulence genes. This study highlights the dissemination of 'high' importance and novel ST CRKP from hospital wastewater to waterbodies. This is concerning, particularly in the African context where a sizable number of people still rely on direct water resources for household use, including drinking. Further research is needed to systematically track the occurrence and distribution of these bacteria so as to mitigate their threat.


Assuntos
Antibacterianos/metabolismo , Carbapenêmicos/metabolismo , Farmacorresistência Bacteriana/genética , Klebsiella pneumoniae/fisiologia , Biodegradação Ambiental , Monitoramento Ambiental , Sequenciamento Completo do Genoma
12.
Int J Syst Evol Microbiol ; 69(8): 2527-2532, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31210629

RESUMO

In this study, the phylogenetic position of Gordonibacter faecihominis and Gordonibacter urolithinfaciens was investigated using phenotypic and molecular (rep-PCR, ARDRA, 16S rRNA gene sequencing and whole-genome sequencing) methods. Our results show that Gordonibacter faecihominis cannot be distinguished from Gordonibacter urolithinfaciens on the basis of the results of this polyphasic approach. Therefore, it is proposed that the two species Gordonibacter faecihominis and Gordonibacter urolithinfaciens belong to the same species.


Assuntos
Actinobacteria/classificação , Filogenia , Técnicas de Tipagem Bacteriana , DNA Bacteriano/genética , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Sequenciamento Completo do Genoma
13.
DNA Res ; 26(3): 261-272, 2019 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-31231762

RESUMO

Adenosine-to-inosine (A-to-I) RNA editing meditated by adenosine deaminases acting on RNA (ADARs) enzymes is a widespread post-transcriptional event in mammals. However, A-to-I editing in skeletal muscle remains poorly understood. By integrating strand-specific RNA-seq, whole genome bisulphite sequencing, and genome sequencing data, we comprehensively profiled the A-to-I editome in developing skeletal muscles across 27 prenatal and postnatal stages in pig, an important farm animal and biomedical model. We detected 198,892 A-to-I editing sites and found that they occurred more frequently at prenatal stages and showed low conservation among pig, human, and mouse. Both the editing level and frequency decreased during development and were positively correlated with ADAR enzymes expression. The hyper-edited genes were functionally related to the cell cycle and cell division. A co-editing module associated with myogenesis was identified. The developmentally differential editing sites were functionally enriched in genes associated with muscle development, their editing levels were highly correlated with expression of their host mRNAs, and they potentially influenced the gain/loss of miRNA binding sites. Finally, we developed a database to visualize the Sus scrofa RNA editome. Our study presents the first profile of the dynamic A-to-I editome in developing animal skeletal muscle and provides evidences that RNA editing is a vital regulator of myogenesis.


Assuntos
Adenosina Desaminase/metabolismo , Músculo Esquelético/crescimento & desenvolvimento , Edição de RNA , RNA Mensageiro/metabolismo , Sus scrofa/crescimento & desenvolvimento , Adenosina Desaminase/genética , Animais , Bases de Dados Genéticas , Regulação da Expressão Gênica no Desenvolvimento , Masculino , Músculo Esquelético/enzimologia , Músculo Esquelético/metabolismo , Análise de Sequência de RNA , Sus scrofa/genética , Sus scrofa/metabolismo , Sequenciamento Completo do Genoma
14.
BMC Bioinformatics ; 20(1): 336, 2019 Jun 17.
Artigo em Inglês | MEDLINE | ID: mdl-31208319

RESUMO

BACKGROUND: Numerical chromosomal variation is a hallmark of populations of malignant cells. Identifying the factors that promote numerical chromosomal variation is important for understanding mechanisms of carcinogenesis. However, the ability to quantify and visualize differences in chromosome number between experimentally-defined groups (e.g. control vs treated) obtained from single-cell experiments is currently limited by the lack of user-friendly software. RESULTS: Aneuvis is a web application that allows users to determine whether numerical chromosomal variation exists between experimental treatment groups. The web interface allows users to upload molecular cytogenetic or processed single cell whole-genome sequencing data in a cell-by-chromosome matrix format and automatically generates visualizations and summary statistics that reflect the degree of numeric chromosomal variability. CONCLUSIONS: Aneuvis is the first user-friendly web application to help researchers identify the genetic and environmental perturbations that promote numerical chromosomal variation. Aneuvis is freely available as a web application at https://dpique.shinyapps.io/aneuvis/ and the source code for the application is available at https://github.com/dpique/aneuvis .


Assuntos
Cromossomos/genética , Internet , Análise de Célula Única , Software , Linhagem Celular , Variações do Número de Cópias de DNA/genética , Humanos , Interface Usuário-Computador , Sequenciamento Completo do Genoma
15.
Genome Biol ; 20(1): 117, 2019 06 03.
Artigo em Inglês | MEDLINE | ID: mdl-31159850

RESUMO

BACKGROUND: Structural variations (SVs) or copy number variations (CNVs) greatly impact the functions of the genes encoded in the genome and are responsible for diverse human diseases. Although a number of existing SV detection algorithms can detect many types of SVs using whole genome sequencing (WGS) data, no single algorithm can call every type of SVs with high precision and high recall. RESULTS: We comprehensively evaluate the performance of 69 existing SV detection algorithms using multiple simulated and real WGS datasets. The results highlight a subset of algorithms that accurately call SVs depending on specific types and size ranges of the SVs and that accurately determine breakpoints, sizes, and genotypes of the SVs. We enumerate potential good algorithms for each SV category, among which GRIDSS, Lumpy, SVseq2, SoftSV, Manta, and Wham are better algorithms in deletion or duplication categories. To improve the accuracy of SV calling, we systematically evaluate the accuracy of overlapping calls between possible combinations of algorithms for every type and size range of SVs. The results demonstrate that both the precision and recall for overlapping calls vary depending on the combinations of specific algorithms rather than the combinations of methods used in the algorithms. CONCLUSION: These results suggest that careful selection of the algorithms for each type and size range of SVs is required for accurate calling of SVs. The selection of specific pairs of algorithms for overlapping calls promises to effectively improve the SV detection accuracy.


Assuntos
Variação Estrutural do Genoma , Genômica/métodos , Sequenciamento Completo do Genoma , Algoritmos , Humanos
16.
Forensic Sci Int ; 301: 107-117, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31153988

RESUMO

In the last year direct-to-consumer (DTC) genetic genealogy databases have been used to identify suspects and missing persons in over fifty cold cases, many of which have been unsolved for decades. Genealogists worked on these cases in collaboration with law enforcement agencies. Raw DNA data files were uploaded to the genealogy websites GEDmatch and FamilyTreeDNA, and identification was made by tracing the family trees of relatives who were predicted to be close genetic matches in the database. Such searches have far-reaching consequences because they affect not just those who have consented to upload their DNA results to these databases but also all of their relatives, regardless of whether or not they have taken a DNA test. This article provides an overview of the methods used, the potential privacy and security issues, and the wider implications for society. There is an urgent need for forensic scientists, bioethicists, law enforcement agencies, genetic genealogists and other interested parties to work together to produce international guidelines and policies to ensure that the techniques are used responsibly and effectively.


Assuntos
Crime , Impressões Digitais de DNA , Bases de Dados de Ácidos Nucleicos , Aplicação da Lei , Linhagem , Cromossomos Humanos Y , Privacidade Genética , Humanos , Consentimento Livre e Esclarecido , Repetições de Microssatélites , Sequenciamento Completo do Genoma
17.
Genet Sel Evol ; 51(1): 32, 2019 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-31242855

RESUMO

BACKGROUND: This study aimed at (1) comparing the accuracies of genomic prediction for parasite resistance in sheep based on whole-genome sequence (WGS) data to those based on 50k and high-density (HD) single nucleotide polymorphism (SNP) panels; (2) investigating whether the use of variants within quantitative trait loci (QTL) regions that were selected from regional heritability mapping (RHM) in an independent dataset improved the accuracy more than variants selected from genome-wide association studies (GWAS); and (3) comparing the prediction accuracies between variants selected from WGS data to variants selected from the HD SNP panel. RESULTS: The accuracy of genomic prediction improved marginally from 0.16 ± 0.02 and 0.18 ± 0.01 when using all the variants from 50k and HD genotypes, respectively, to 0.19 ± 0.01 when using all the variants from WGS data. Fitting a GRM from the selected variants alongside a GRM from the 50k SNP genotypes improved the prediction accuracy substantially compared to fitting the 50k SNP genotypes alone. The gain in prediction accuracy was slightly more pronounced when variants were selected from WGS data compared to when variants were selected from the HD panel. When sequence variants that passed the GWAS [Formula: see text] threshold of 3 across the entire genome were selected, the prediction accuracy improved by 5% (up to 0.21 ± 0.01), whereas when selection was limited to sequence variants that passed the same GWAS [Formula: see text] threshold of 3 in regions identified by RHM, the accuracy improved by 9% (up to 0.25 ± 0.01). CONCLUSIONS: Our results show that through careful selection of sequence variants from the QTL regions, the accuracy of genomic prediction for parasite resistance in sheep can be improved. These findings have important implications for genomic prediction in sheep.


Assuntos
Doenças dos Ovinos/genética , Doenças dos Ovinos/parasitologia , Sequenciamento Completo do Genoma/veterinária , Animais , Austrália , Resistência à Doença/genética , Feminino , Marcadores Genéticos , Testes Genéticos/veterinária , Variação Genética , Estudo de Associação Genômica Ampla/veterinária , Masculino , Contagem de Ovos de Parasitas/veterinária , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Ovinos
18.
Arch Virol ; 164(9): 2371-2374, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31165927

RESUMO

A previously undescribed badnavirus was identified in plants of Polyscias fruticosa (Ming aralia) showing symptoms of mild mosaic and leaf senescence. Characteristic bacilliform virions of the Polyscias badnavirus averaging 30 × 120 nm in size were observed by transmission electron microscopy in partially purified leaf tissue extracts from symptomatic but not asymptomatic plants collected in the USA and Nigeria. The isolate from the USA was complete sequenced. The genome is 7592 bp in length and contains three open reading frames with an arrangement similar to that of other members of the genus Badnavirus. The largest open reading frame (ORF3) encodes a putative polyprotein, with predicted domains including zinc finger, aspartic protease, reverse transcriptase (RT) and RNase H, in that order. The USA and Nigeria isolates of the virus had a high level (98%) of nucleotide sequence identity in the RT+RNase H region. Within the genus Badnavirus, these viruses were most closely related to schefflera ringspot virus (SRV), sharing 63% identity at the nucleotide level. Based on the ICTV species demarcation criteria for the genus Badnavirus (more than 20% nucleotide sequence divergence in the RT+RNase H region), the Polyscias virus is proposed to be a new member of the genus, and the name polyscias mosaic virus (PoMV) is proposed. The complete genome sequence was deposited in the NCBI GenBank database under accession no. MH475918.


Assuntos
Araliaceae/virologia , Badnavirus/isolamento & purificação , Genoma Viral , Doenças das Plantas/virologia , Badnavirus/classificação , Badnavirus/genética , Sequência de Bases , Dados de Sequência Molecular , Nigéria , Fases de Leitura Aberta , Filogenia , Folhas de Planta/virologia , Sequenciamento Completo do Genoma
19.
Arch Virol ; 164(9): 2375-2378, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31183555

RESUMO

The complete genomic RNA sequence of a tentative new umbravirus from Patrinia scabiosaefolia, tentatively named "patrinia mild mottle virus" (PatMMoV), was determined. The genome of PatMMoV consists of 4,214 nucleotides and has a typical umbravirus genome organization with four open reading frames. BLAST searches showed that the complete nucleotide sequence of PatMMoV had the highest identity (72%; 50% query coverage) to Ixeridium yellow mottle-associated virus 2 (IxYMaV-2; an unclassified umbravirus). In addition, phylogenetic analysis and pairwise comparisons showed that PatMMoV and IxYMaV-2 were the most closely related and placed in the same clade within a group of umbraviruses. These results suggest that PatMMoV is a putative new member of the genus Umbravirus in the family Tombusviridae.


Assuntos
Genoma Viral , Patrinia/virologia , Doenças das Plantas/virologia , Tombusviridae/genética , Tombusviridae/isolamento & purificação , Sequência de Bases , Dados de Sequência Molecular , Fases de Leitura Aberta , Filogenia , Tombusviridae/classificação , Sequenciamento Completo do Genoma
20.
J Microbiol ; 57(8): 655-660, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31187415

RESUMO

A Gram-negative, aerobic, short-rod-shaped, motile (with a terminal flagellum), non-spore-forming bacterium, designated strain 85T, was isolated from a surface-sterilized bark of Sonneratia caseolaris collected from Qinzhou in Guangxi, China and was analyzed using a polyphasic approach to determine its taxonomic position. Strain 85T grew optimally in the presence of 1-2% (w/v) NaCl at 30°C and pH 6.0-7.0. Phylogenetic analysis based on 16S rRNA gene sequence suggested that strain 85T belonged to the genus Fulvimarina and shared the highest 16S rRNA gene sequence similarity with Fulvimarina pelagi HTCC2506T (96.16%). The cell-wall peptidoglycan contained meso-diaminopimelic acid and ubiquinone Q-10 was the predominant respiratory lipoquinone. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified amino lipid, three unidentified phospholipids and six unidentified lipids. The major fatty acid was C18:1ω7c. The DNA G+C content of strain 85T was 65.4 mol%, and the average nucleotide identity and estimated DDH values between strain 85T and the type strain of Fulvimarina pelagi HTCC2506T were 77.3% and 21.7%, respectively. Based on the phylogenetic, phenotypic, and chemotaxonomic analyses, strain 85T should be considered as a novel species of the genus Fulvimarina with the proposed name Fulvimarina endophytica sp. nov., and its type strain is 85T (= KCTC 62717T = CGMCC 1.13665T).


Assuntos
Alphaproteobacteria/classificação , Endófitos/classificação , Lythraceae/microbiologia , Casca de Planta/microbiologia , Alphaproteobacteria/genética , Alphaproteobacteria/crescimento & desenvolvimento , Alphaproteobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana/métodos , Composição de Bases , China , DNA Bacteriano/genética , Endófitos/genética , Endófitos/crescimento & desenvolvimento , Endófitos/isolamento & purificação , RNA Ribossômico 16S/genética , Sequenciamento Completo do Genoma/métodos
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