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A novel putative member of the family Benyviridae is associated with soilborne wheat mosaic disease in Brazil. Repositório Alice
VALENTE, J. B.; PEREIRA, F. S.; STEMPKOWSKI, L. A.; FARIAS, M.; KUHNEM, P.; LAU, D.; FAJARDO, T. V. M.; NHANI JUNIOR, A.; CASA, R. T.; BOGO, A.; SILVA, F. N. da.
Soilborne wheat mosaic disease (SBWMD), originally attributed to infections by Soilborne wheat mosaic virus (SBWMV) and Wheat spindle streak mosaic virus (WSSMV), is one of the most frequent virus diseases and causes economic losses in wheat in southern Brazil. This study aimed to characterize molecularly the viral species associated with wheat plants showing mosaic symptoms in Brazil. Wheat leaves and stems displaying mosaic symptoms were collected from different wheat cultivars in Passo Fundo municipality, Rio Grande do Sul State, southern Brazil. Double-stranded RNA was extracted and submitted to cDNA library synthesis and next-generation sequencing. No sequences of SBWMV and WSSMV were detected but the complete genome sequence of a putative new member...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Benyviridae; Mosaic symptoms; Next-generation sequencing; Wheat stripe mosaic virus; Polymyxa Graminis; Triticum Aestivum.
Ano: 2018 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1102942
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Applying genotyping by sequencing to peach breeding Germplasm from Embrapa. Repositório Alice
THUROW, L. B.; GASIC, K.; RASEIRA, M. do C. B.; BONOW, S.; CASTRO, C. M..
2015
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Prunus persica; GBS; Next-generation sequencing; SNP diversity.
Ano: 2015 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1022898
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Complete sequence and comparative analysis of the chloroplast genome of Plinia trunciflora Genet. Mol. Biol.
Eguiluz,Maria; Yuyama,Priscila Mary; Guzman,Frank; Rodrigues,Nureyev Ferreira; Margis,Rogerio.
Abstract Plinia trunciflora is a Brazilian native fruit tree from the Myrtaceae family, also known as jaboticaba. This species has great potential by its fruit production. Due to the high content of essential oils in their leaves and of anthocyanins in the fruits, there is also an increasing interest by the pharmaceutical industry. Nevertheless, there are few studies focusing on its molecular biology and genetic characterization. We herein report the complete chloroplast (cp) genome of P. trunciflora using high-throughput sequencing and compare it to other previously sequenced Myrtaceae genomes. The cp genome of P. trunciflora is 159,512 bp in size, comprising inverted repeats of 26,414 bp and single-copy regions of 88,097 bp (LSC) and 18,587 bp (SSC). The...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Jaboticaba; Myrtaceae; Chloroplast genome; Next-generation sequencing.
Ano: 2017 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572017000500871
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Development of a comprehensive noninvasive prenatal test Genet. Mol. Biol.
Malcher,Carolina; Yamamoto,Guilherme L.; Burnham,Philip; Ezquina,Suzana A.M.; Lourenço,Naila C.V.; Balkassmi,Sahilla; Antonio,David S. Marco; Hsia,Gabriella S.P.; Gollop,Thomaz; Pavanello,Rita C.; Lopes,Marco Antonio; Bakker,Egbert; Zatz,Mayana; Bertola,Débora; Vlaminck,Iwijn De; Passos-Bueno,Maria Rita.
Abstract Our aim was to develop and apply a comprehensive noninvasive prenatal test (NIPT) by using high-coverage targeted next-generation sequencing to estimate fetal fraction, determine fetal sex, and detect trisomy and monogenic disease without parental genotype information. We analyzed 45 pregnancies, 40 mock samples, and eight mother-child pairs to generate 35 simulated datasets. Fetal fraction (FF) was estimated based on analysis of the single nucleotide polymorphism (SNP) allele fraction distribution. A Z-score was calculated for trisomy of chromosome 21 (T21), and fetal sex detection. Monogenic disease detection was performed through variant analysis. Model validation was performed using the simulated datasets. The novel model to estimate FF was...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Cell-free DNA; Next-generation sequencing; Trisomy; Noninvasive prenatal test; Fetal fraction.
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572018000400545
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Evaluation of MC1R high-throughput nucleotide sequencing data generated by the 1000 Genomes Project Genet. Mol. Biol.
Marano,Leonardo Arduino; Marcorin,Letícia; Castelli,Erick da Cruz; Mendes-Junior,Celso Teixeira.
Abstract The advent of next-generation sequencing allows simultaneous processing of several genomic regions/individuals, increasing the availability and accuracy of whole-genome data. However, these new approaches may present some errors and bias due to alignment, genotype calling, and imputation methods. Despite these flaws, data obtained by next-generation sequencing can be valuable for population and evolutionary studies of specific genes, such as genes related to how pigmentation evolved among populations, one of the main topics in human evolutionary biology. Melanocortin-1 receptor (MC1R) is one of the most studied genes involved in pigmentation variation. As MC1R has already been suggested to affect melanogenesis and increase risk of developing...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Melanocortin-1 Receptor; The 1000 Genomes Project; Next-generation sequencing.
Ano: 2017 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572017000300530
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Full genome sequencing of the bluetongue virus-1 isolate MKD20/08/Ind from goat in India BJM
Chand,Karam; Biswas,Sanchay Kumar; Sharma,Gaurav; Saxena,Arpit; Tewari,Neha; Mahajan,Sonalika; Pandey,Awadh Bihari.
ABSTRACT This communication reports full genome sequencing of the bluetongue virus-1 (BTV-1) isolate MKD20/08/Ind from goat in northern India. The total BTV-1 genome size was found to be 19,190 bp. A comparison study between the Indian isolate and other global isolates revealed that it belongs to the 'Eastern' BTV topotype. The full genome sequence of BTV-1 will provide vital information on its geographical origin and it will also be proved useful for comparing the Indian isolate with global isolates from other host species.
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bluetongue virus-1; Goat; Eastern BTV topotype; Next-generation sequencing.
Ano: 2016 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822016000300527
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Genomic Approaches in Marine Biodiversity and Aquaculture Biol. Res.
Huete-Pérez,Jorge A; Quezada,Fernando.
Recent advances in genomic and post-genomic technologies have now established the new standard in medical and biotechnological research. The introduction of next-generation sequencing, NGS,has resulted in the generation of thousands of genomes from all domains of life, including the genomes of complex uncultured microbial communities revealed through metagenomics. Although the application of genomics to marine biodiversity remains poorly developed overall, some noteworthy progress has been made in recent years. The genomes of various model marine organisms have been published and a few more are underway. In addition, the recent large-scale analysis of marine microbes, along with transcriptomic and proteomic approaches to the study of teleost fishes,...
Tipo: Journal article Palavras-chave: Aquaculture; Genomics; Marine biodiversity; Next-generation sequencing; Proteomics.
Ano: 2013 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602013000400007
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Grapevine virus diseases: economic impact and current advances in viral prospection and management. Repositório Alice
BASSO, M. F.; FAJARDO, T. V. M.; SALDARELLI, P..
A videira (Vitis spp.) é propagada vegetativamente e considerada uma das principais culturas frutíferas por sua importância socioeconômica mundial. Ela é suscetível a vários agentes transmitidos por meio da enxertia, os quais causam diversas doenças e significativas perdas na produtividade e produção, redução na qualidade dos frutos, no vigor da planta e na longevidade dos vinhedos. A propagação vegetativa e o frequente intercâmbio de material propagativo entre países contribuem para a disseminação destes patógenos, favorecendo a emergência de doenças complexas. Seu ciclo de vida perene acelera ainda mais a mistura e a introdução de vários agentes virais em uma mesma planta. Atualmente, aproximadamente 65 vírus pertencentes a diferentes famílias foram...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Vírus de planta; Redução da produtividade; Redução da produção; Qualidade das bagas; Sequenciamento de nova geração; Crop losses; Berry quality; Next-generation sequencing; Propagação vegetativa; Vírus; Vegetative propagation; Plant viruses.
Ano: 2017 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1069060
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GRAPEVINE VIRUS DISEASES:ECONOMIC IMPACT AND CURRENT ADVANCES IN VIRAL PROSPECTION AND MANAGEMENT Rev. Bras. Frutic.
BASSO,MARCOS FERNANDO; FAJARDO,THOR VINÍCIUS MARTINS; SALDARELLI,PASQUALE.
ABSTRACT Grapevine (Vitis spp.) is a major vegetative propagated fruit crop with high socioeconomic importance worldwide. It is susceptible to several graft-transmitted agents that cause several diseases and substantial crop losses, reducing fruit quality and plant vigor, and shorten the longevity of vines. The vegetative propagation and frequent exchanges of propagative material among countries contribute to spread these pathogens, favoring the emergence of complex diseases. Its perennial life cycle further accelerates the mixing and introduction of several viral agents into a single plant. Currently, approximately 65 viruses belonging to different families have been reported infecting grapevines, but not all cause economically relevant diseases. The...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Vegetative propagation; Plant viruses; Crop losses; Berry quality; Next-generation sequencing.
Ano: 2017 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-29452017000104001
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Hereditary cancer risk assessment: insights and perspectives for the Next-Generation Sequencing era Genet. Mol. Biol.
Gomy,Israel; Diz,Maria Del Pilar Estevez.
Abstract Hereditary cancer risk assessment is a multidisciplinary and dynamic process, with the purpose of estimating probabilities of germline mutations in cancer susceptibility genes and assessing empiric risks of cancer based on personal and family histories, in order to offer clinical and molecular diagnoses and clinical management based on these risks. Genetic tests are available and most of them are reimbursed by insurance companies, although they are generally not covered by the public health systems of developing countries. More recently, molecular diagnosis of hereditary cancer is feasible through next-generation sequencing (NGS) panels. Here we review the benefits and limitations of NGS technologies in the clinical practice.
Tipo: Info:eu-repo/semantics/article Palavras-chave: Next-generation sequencing; Hereditary cancer; Genetic counseling; Risk assessment.
Ano: 2016 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572016000200184
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High-throughput sequencing applied for the identification of viruses infecting grapevines in Brazil and genetic variability analysis. Repositório Alice
FAJARDO, T. V. M.; SILVA, F. N.; EIRAS, M.; NICKEL, O..
The application of high-throughput sequencing technologies (HTS) enables the recovery of many nucleotide sequence fragments from diseased plants and may help in pathogen identification. This study was designed to identify viruses infecting 15 grapevine (Vitis spp.) samples collected from experimental fields and vine collections and assess the genetic variability of the identified viruses. The virus-enriched dsRNAs were extracted from bark scrapings and sequenced using an Illumina platform. The paired-end reads were analyzed, assembled contigs were generated and identified as related to viruses. Contigs of 14 viruses have been identified, some of them covering large extensions of viral genomes or resulting in assembly of near-complete or complete genomes....
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Diagnosis; HTS; Next-generation sequencing; NGS; Vitis; Variability.
Ano: 2017 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1077833
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Identification of candidate genes for lung cancer somatic mutation test kits Genet. Mol. Biol.
Chen,Yong; Shi,Jian-Xin; Pan,Xu-Feng; Feng,Jian; Zhao,Heng.
Over the past three decades, mortality from lung cancer has sharply and continuously increased in China, ascending to the first cause of death among all types of cancer. The ability to identify the actual sequence of gene mutations may help doctors determine which mutations lead to precancerous lesions and which produce invasive carcinomas, especially using next-generation sequencing (NGS) technology. In this study, we analyzed the latest lung cancer data in the COSMIC database, in order to find genomic "hotspots" that are frequently mutated in human lung cancer genomes. The results revealed that the most frequently mutated lung cancer genes are EGFR, KRAS and TP53.In recent years, EGFR and KRAS lung cancer test kits have been utilized for detecting lung...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Lung cancer; Next-generation sequencing; Somatic mutation kit; COSMIC.
Ano: 2013 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572013000300022
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Illumina sequencing and assessment of new cost-efficient protocol for metagenomic-DNA extraction from environmental water samples BJM
Hassan,Mariam; Essam,Tamer; Megahed,Salwa.
Abstract In this study, the development and assessment of a modified, efficient, and cost-efficient protocol for mDNA (metagenomic DNA) extraction from contaminated water samples was attempted. The efficiency of the developed protocol was investigated in comparison to a well-established commercial kit (Epicentre, Metagenomic DNA Isolation Kit for Water). The comparison was in terms of degree of shearing, yield, purity, duration, suitability for polymerase chain reaction and next-generation sequencing in addition to the quality of next-generation sequencing data. The DNA yield obtained from the developed protocol was 2.6 folds higher than that of the commercial kit. No significant difference in the alpha (Observed species, Chao1, Simpson and PD whole tree)...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bioinformatics; Method; Microbiome; Next-generation sequencing; QIIME.
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822018000500001
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Microsatellite loci development for three catfish species from northwestern South America Neotropical Ichthyology
Restrepo-Escobar,Natalia; Márquez,Edna J..
ABSTRACT The Neotropical catfish species Ageneiosus pardalis, Pimelodus grosskopfii, and Sorubim cuspicaudus are important fishery resources in Colombia that show historical declines in their capture. This study used next-generation sequencing with 454 FLX technology (Roche Applied Science) and bioinformatics analysis to develop between 18 and 24 microsatellite loci for these species. The novel microsatellite loci showed high values of polymorphic information content -PIC (A. pardalis: 0.601-0.903, P. grosskopfii: 0.748-0.946 and S. cuspicaudus: 0.383-0.876), and the average number of alleles/locus ranged from 7-15 for A. pardalis, 9-30 for P. grosskopfii and 5-14 for S. cuspicaudus. The average observed and expected heterozygosities were respectively,...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Freshwater fish; Molecular markers; Next-generation sequencing; Siluriformes.
Ano: 2020 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1679-62252020000100210
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Next-generation sequencing analysis reveals high bacterial diversity in wild venomous and non-venomous snakes from India J. Venom. Anim. Toxins incl. Trop. Dis.
Krishnankutty,Sajesh Puthenpurackal; Muraleedharan,Megha; Perumal,Rajadurai Chinnasamy; Michael,Saju; Benny,Jubina; Balan,Bipin; Kumar,Pramod; Manazhi,Jishnu; Kumar,Bangaruswamy Dhinoth; Santhosh,Sam; Thomas,George; Gupta,Ravi; Zachariah,Arun.
Abstract Background: The oral cavities of snakes are replete with various types of bacterial flora. Culture-dependent studies suggest that some of the bacterial species are responsible for secondary bacterial infection associated with snakebite. A complete profile of the ophidian oral bacterial community has been unreported until now. Therefore, in the present study, we determined the complete bacterial compositions in the oral cavity of some snakes from India. Methods: Total DNA was isolated from oral swabs collected from three wild snake species (Indian Cobra, King Cobra and Indian Python). Next, the DNA was subjected to PCR amplification of microbial 16S rRNA gene using V3-region-specific primers. The amplicons were used for preparation of DNA...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Microbial community; Next-generation sequencing; Venomous snake; Hypervariable region.
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1678-91992018000100331
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Next-generation sequencing virulome analysis of a Yersinia enterocolitica subsp. palearctica bioserotype 4/O:3 ST18 isolated from human blood in Brazil BJID
Rusak,Leonardo Alves; Junqueira,Ricardo Magrani; Hofer,Ernesto; Vallim,Deyse Christina; Asensi,Marise Dutra.
Abstract Yersinia enterocolitica is a widespread Gram-negative bacterium that causes gastrointestinal disease and other clinical manifestations in humans. Potentially pathogenic Y. enterocolitica has been isolated in Brazil, from human, environmental, food, and animal sources. Herein we report a genome sequence of Y. enterocolitica subsp. palearctica strain YE 19, serotype O:3, biotype 4, sequence type 18, with virulence determinants isolated from human blood in Rio de Janeiro in 2005. The results corroborate other findings that this strain harbors a set of virulence determinants that could play a role in host pathoadaptation and may also justify the successful dissemination of bioserotype 4/O:3 in Brazil. The presence of strains harboring all of these...
Tipo: Info:eu-repo/semantics/other Palavras-chave: Yersinia enterocolitica; Virulence; Brazil; Next-generation sequencing.
Ano: 2017 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1413-86702017000500550
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Quality assessment and quality control of next-generation sequencing for Leishmania infantum MV&Z
Guerra, Juliana Mariotti; Fernandes, Natália Coelho Couto de Azevedo; Barbosa, José Eduardo de Raeffray; Taniguchi, Helena Hilomi; Hiramoto, Roberto Mitsuyoshi; Tolezano, José Eduardo; Cogliati, Bruno.
Next-generation sequencing (NGS) technologies are becoming widely used, and although a massive number of sequences can be generated in a single experiment, it is still important to characterize the reads. Characterizing reads may prevent undesirable outcomes in the assembly or mapping processes. Discarding low-quality reads, controlling for contamination, and trimming adaptor sequences are examples of preliminary quality control procedures that can be applied to raw reads before further analysis. Here it was applied the FastQ Quality Control Software (FastQC) in order to assess the quality of the data of next-generation sequecing for Leishmania infatum.
Tipo: Info:eu-repo/semantics/article Palavras-chave: Leishmania infatum; Next-generation sequencing Leishmania infatum; Next-generation sequencing.
Ano: 2016 URL: http://www.revistamvez-crmvsp.com.br/index.php/recmvz/article/view/31056
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Sensitivity, advantages, limitations, and clinical utility of targeted next-generation sequencing panels for the diagnosis of selected lysosomal storage disorders Genet. Mol. Biol.
Málaga,Diana Rojas; Brusius-Facchin,Ana Carolina; Siebert,Marina; Pasqualim,Gabriela; Saraiva-Pereira,Maria Luiza; Souza,Carolina F.M de; Schwartz,Ida V.D.; Matte,Ursula; Giugliani,Roberto.
Abstract Lysosomal storage disorders (LSDs) constitute a heterogeneous group of approximately 50 genetic disorders. LSDs diagnosis is challenging due to variability in phenotype penetrance, similar clinical manifestations, and a high allelic heterogeneity. A powerful tool for the diagnosis of the disease could reduce the “diagnostic odyssey” for affected families, leading to an appropriate genetic counseling and a better outcome for current therapies, since enzyme replacement therapies have been approved in Brazil for Gaucher, Fabry, and Pompe diseases, and are under development for Niemann-Pick Type B. However, application of next-generation sequencing (NGS) technology in the clinical diagnostic setting requires a previous validation phase. Here, we...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Ion Torrent; Molecular diagnostics; Next-generation sequencing; Lysosomal storage disorders; Validation.
Ano: 2019 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572019000200197
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The chloroplast genome of the desiccation-tolerant moss Pseudocrossidium replicatum (Taylor) R.H. Zander Genet. Mol. Biol.
Cevallos,Miguel A.; Guerrero,Gabriela; Ríos,Selma; Arroyo,Analilia; Villalobos,Miguel Angel; Porta,Helena.
Abstract Mosses in conjunction with hornworts and liverworts are collectively referred to as bryophytes. These seedless, nonvascular plants are the closest extant relatives of early terrestrial plants and their study is essential to understand the evolutionary first steps of land plants. Here we report the complete chloroplast (cp) genome sequence of Pseudocrossidium replicatum, a moss belonging to the Pottiaceae family that is common in the central highlands of Mexico, in South America, in southern USA, and in Kenia. The cp genome (plastome) of P. replicatum is 123,512 bp in size, comprising inverted repeats of 9,886 bp and single-copy regions of 85,146 bp (LSC) and 18,594 bp (SSC). The plastome encodes 82 different proteins, 31 different tRNAs, and 4...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bryophytes; Pottiaceae; Chloroplast; Next-generation sequencing.
Ano: 2019 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572019000300488
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Transcriptome analysis of wheat under drought. Repositório Alice
POERSCH-BORTOLON, L. B.; PEREIRA, J. F.; NHANI JUNIOR, A.; SOTO GONZÁLES, H. H. S.; PATRICIO, D. I.; TORRES, G. A. M.; CONSOLI, L.; MARGIS-PINHEIRO, M.; BODANESE-ZANETTINI, M. H..
2013
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Trigo; Sequenciamento de nova geração; Tolerância à seca; Transcriptoma; Wheat; Next-generation sequencing; Drought tolerance; Transcriptome.
Ano: 2013 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1051342
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