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Registros recuperados: 31
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A new BLAST-based Gbrowse plugin. Repositório Alice
VELLOZO, A.; LOBO, F. P.; YAMAGISHI, M..
In this work, we present a new plugin to search sequences against the genome using the BLAST tool.
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Bioinformática; Genoma; Sequência genética; Bioinformatics; Genome; Sequence analysis.
Ano: 2012 URL: http://www.alice.cnptia.embrapa.br/handle/doc/946664
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Aluminum-induced genes in grass species. Repositório Alice
NODA, R. W.; GUIMARAES, C. T.; GOMES, E. A.; CARNEIRO, N. P.; LANA, U. G. de P.; MAGALHAES, J. V. de; COSTA, M. M. do C.; SILVA, F. R. D.; BRAMMER, S. P.; LÂNGARO, N. C.; CARVALHO, L. J. C. B.; BEVITORI, R.; PURCINO, A. A. C..
bitstream/item/25479/1/Aluminum-induced.pdf
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Tolerância a alumínio; Sequence analysis; Genetics; Aluminum; Genes.
Ano: 2010 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/873120
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Analysis and sequencing of h6hmRNA, last enzyme in the tropane alkaloids pathway from anthers and hairy root cultures of Brugmansia candida (Solanaceae) Electron. J. Biotechnol.
Cardillo,Alejandra B.; Giulietti,Ana M.; Marconi,Patricia L..
Brugmansia candida (Solanaceae) is a native tree distributed across South-American and produces the pharmacologically- important group of tropane alkaloids including scopolamine. This biocompound is synthesised from hyoscyamine by action of Hyoscyamine 6-β hydroxylase (H6H, EC 1.14.11.11) at the end of the tropane alkaloid pathway. Here are reported the tissue and organ-specific expression of h6hmRNA by RT-PCR analyses and the isolation, cloning and sequencing of the cDNA obtained from B. candida anthers and hairy root transformed cultures. Bioinformatic analysis of the nucleotide sequence revealed an uninterrupted ORF of 1038 bp and the predicted aminoacid sequence could be 344 aminoacid long. A database search showed that this sequence has high...
Tipo: Journal article Palavras-chave: H6H; Hairy roots; Hyoscyamine; Scopolamine; Sequence analysis; Transformation.
Ano: 2006 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582006000300004
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Avaliação e aplicação de métodos de genotipagem para estudo da síndrome da musculatura dupla em bovinos da raça Senepol. Repositório Alice
URQUIZA, A. da S. C..
Em várias raças de bovinos de corte é observada a síndrome da musculatura dupla, caracterizada pela presença do fenótipo de hipertrofia muscular, sendo esta uma condição hereditária e controlada pelo gene GDF-8 (Growth Differentiation Factor-8). Em bovinos da raça Senepol, a mutação nt821, localizada no exon III deste gene, é responsável por esta síndrome. Neste contexto, os objetivos deste trabalho foram avaliar três metodologias de genotipagem desta mutação, com o intuito de verificar qual a mais adequada em relação a custo/benefício e verificar a associação do alelo mutado com características de interesse econômico em touros jovens da raça Senepol. Foram extraídos DNA genômico de amostras biológicas de 17 bezerros, sendo sete com o fenótipo da...
Tipo: Tese/dissertação (ALICE) Palavras-chave: Gene GDF-8; Sequenciamento; Selection; Hipertrofia muscular; Mutação; Seleção; Gado de corte; Fenotipo; Mutation; Sequence analysis.
Ano: 2017 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1082405
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Characterization and expression of two cDNA encoding 3-hydroxy-3-methylglutaryl coenzyme A reductase isoforms in coffee (Coffea arabica L.). Repositório Alice
TISKI, I.; MARRACCINI, P.; POT, D.; VIEIRA, L. G.; PEREIRA, L. F. P..
In higher plants there are two independent pathways for isoprenoid biosynthesis, located in the cytosol (mevalonic acid or MVA pathway) or in the plastids (methylerythritol phosphate ? MEP pathway). The 3-hydroxy-3-methyglutaryl-CoA reductase (HMGR) is the first committed step in the MVA pathway. Using the information available from the Brazilian Coffee Genome Project, we found 13 ESTs that originated two isoforms, CaHMGR1 and CaHMGR2, for the enzyme HMGR of Coffea arabica. A complementary DNA encoding the isoform CaHMGR1 was cloned, and its complete nucleotide sequence determined. The full-length cDNA of CaHMGR1 was 2242 bp containing a 1812-bp ORF encoding 604 amino acids. Bioinformatic analyses revealed that the deduced CaHMGR1 had extensive homology...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Gene expression; Sequence analysis; Expressed sequence tag (EST); Molecular characterization; Coffee; Ydroxy; Methyglutaryl-CoA reductase; Isoprenoids.
Ano: 2011 URL: http://www.alice.cnptia.embrapa.br/handle/doc/902481
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Confirmation and Sequence analysis of N gene of PPRV in South Xinjiang, China Arq. Bras. Med. Vet. Zootec.
Liu,YongHong; Yang,Bo; Li,XianQiang; Wang,XueFeng; Zhang,LuYao; Li,Fei; Zhao,Li.
ABSTRACT In China, Peste des petits ruminants (PPR) was officially first reported in 2007. From 2010 until the outbreak of 2013, PPRV infection was not reported. In November 2013, PPRV re-emerged in Xinjiang and rapidly spread to 22 P/A/M (provinces, autonomous regions and municipalities) of China. In the study, suspected PPRV-infected sheep in a breeding farm of South Xinjiang in 2014 were diagnosed and the characteristics of complete sequence of N protein gene of PPRV was analyzed. The sheep showed PPRV-infected signs, such as fever, orinasal secretions increase, dyspnea and diarrhea, with 60% of morbidity and 21.1% of fatality rate. The macroscopic lesions after autopsy and histopathological changes were observed under light microscope including...
Tipo: Info:eu-repo/semantics/article Palavras-chave: PPR; Diagnosis; N gene; Sequence analysis.
Ano: 2017 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0102-09352017000501105
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de novo genome assembly of the South American freshwater fish Tambaqui (Colossoma macropomum). Repositório Alice
LOBO, F. P.; CINTRA, L. C.; VARELA, E. S.; ALVES, A. L.; VILLELA, L. C. V.; SILVA, N. M. A. da; PAIVA, S. R.; CAETANO, A. R..
The Tambaqui (Colossoma macropomum) is a freshwater fish species naturally found in the Amazon river basin which has historically been widely exploited by community and commercial fishing. Recent efforts to domesticate, breed and raise the species in aquaculture systems has led to significant increases in production (>10-fold) over the last ten years. Current production is above 120,000 metric tons per year with a strong growth trend, making it the most important native aquaculture species in Brazil. Data for generating the draft assembly were produced from shotgun libraries with two different insert sizes and mate-paired libraries with four different sizes sequenced (2x150bps) with Illumina HiSeq2000 technology. A total of 124.8Gbp quality-filtered...
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Sequência genômica; Tambaqui; Genome assembly; Sequence analysis; Colossoma macropomum.
Ano: 2015 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1013201
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De novo RNA sequencing and analysis of the transcriptome of signalgrass (Urochloa decumbens) roots exposed to aluminum. Repositório Alice
SALGADO, L. R.; LIMA, R.; SANTOS, B. F. dos; SHIRAKAWA, K. T.; VILELA, M. de A.; ALMEIDA, N. F.; PEREIRA. R. M.; NEPOMUCENO, A. L.; CHIARI, L..
bitstream/item/166628/1/Nepomuceno-plant-2017.pdf
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Marcador molecular; Brachiaria decumbens; Graminea forrageira; Sequence analysis; Genetic markers; Urochloa decumbens.
Ano: 2017 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1079563
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Draft genome sequencing of the Yeast Spathaspora arborariae sp. Repositório Alice
SANTOS, E. de M.; FRANCO, G. R.; STAMBUK, B. J. C. U.; ROSA, C. A.; LOBO, F. P..
This work provides the description of a draft genome of S. arborariae.
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Sequência de genoma; Yeast Spathaspora arborariae sp.; Sequence analysis; Yeasts; Genomics.
Ano: 2012 URL: http://www.alice.cnptia.embrapa.br/handle/doc/946642
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Efficient gap-closure of eukaryotic genome sequence assemblies by third-generation sequencing. Repositório Alice
CRUZ, I. R. da C.; GERALDO, J. A.; LEITE, L. R.; ZERLOTINI, A.; ARAÚJO, F.; SILVA, M. V. G. B.; COIMBRA, R. S.; CARVALHO, M. R. S.; OLIVEIRA, G..
Recently, we produced the first draft assemblies of Guzerá and Gir genomes. Two Zebu (Bos indicus) breeds adapted to tropical climate and under genetic evaluation to milk purposes in Brazil.
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Sequenciamento de genoma de zebu; Plataforma SOLiD; Genome; Zebu; Sequence analysis.
Ano: 2012 URL: http://www.alice.cnptia.embrapa.br/handle/doc/946528
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Factor 9 de crecimiento y diferenciación asociado al índice de prolificidad en la oveja pelibuey. Colegio de Postgraduados
Pérez Ruíz, Elizabeth.
El Factor 9 de Crecimiento y Diferenciación (GDF9) es miembro de la súperfamilia β de factores de crecimiento (TGFβ) y su expresión en el ovocito es esencial para el desarrollo y crecimiento folicular. Diferentes mutaciones en el gen GDF9 han sido asociadas con el incremento de tasa de ovulación y/o prolificidad en algunas razas de ovejas, por lo que el objetivo de este estudio fue la búsqueda de polimorfismos de una sola base (SNPs) en el gen GDF9, así como la asociación entre polimorfismos del gen GDF9 y el índice de prolificidad en ovejas de la raza Pelibuey. Se tomaron muestras sanguíneas de la vena yugular de 16 ovejas y fueron conservadas en papel FTA® (Whatman Mini Card). El exón dos del gen fue amplificado mediante la técnica de Polimerase Chain...
Palavras-chave: Análisis de secuencias; GDF9; Mutación; Polimorfismo; PCR; SNP; Sequence analysis; Mutation; Polymorphism; Maestría; Ganadería.
Ano: 2012 URL: http://hdl.handle.net/10521/1712
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First detection of canine parvovirus type 2c in Brazil BJM
Streck,André Felipe; Souza,Carine Kunzler de; Gonçalves,Karla Rathje; Zang,Luciana; Pinto,Luciane Dubina; Canal,Cláudio Wageck.
The presence of canine parvovirus type 2 (CPV-2), 2a and 2b has been described in Brazil, however, the type 2c had not been reported until now. In the current study, seven out of nine samples from dogs with diarrhea were characterized as CPV-2c, indicating that this virus is already circulating in the Brazilian canine population.
Tipo: Info:eu-repo/semantics/article Palavras-chave: Canine parvovirus type 2c; Sequence analysis; Brazil.
Ano: 2009 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822009000300008
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Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds. Repositório Alice
VOORT, M. van der; MEIJER, H. J. G.; SCHMIDT, Y.; WATROUS, J; DEKKERS, E.; MENDES, R.; DORRESTEIN, P.C; GROSS, H.; RAAIJMAKERS, J. M..
Abstract: The plant microbiome represents an enormous untapped resource for discovering novel genes and bioactive compounds. Previously, we isolated Pseudomonas sp. SH-C52 from the rhizosphere of sugar beet plants grown in a soil suppressive to the fungal pathogen Rhizoctonia solani and showed that its antifungal activity is, in part, attributed to the production of the chlorinated 9-amino-acid lipopeptide thanamycin (Mendes et al., 2011). To get more insight into its biosynthetic repertoire, the genome of Pseudomonas sp. SH-C52 was sequenced and subjected to in silico, mutational and functional analyses. The sequencing revealed a genome size of 6.3 Mb and 5579 predicted ORFs. Phylogenetic analysis placed strain SH-C52 within the Pseudomonas corrugata...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Pseudomonads; Genomes sequencing; Biocontrol; Rizosfera; Bactéria; Pseudomonas sp; Peptídeo; Beterraba; Controle biológico; Beneficial microorganisms; Rhizosphere bacteria; Antimicrobial peptides; Sequence analysis; Mass spectrometry; Biological control.
Ano: 2015 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1032807
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Genome Sequencing and de novo assembly of the South American Tiger Catfish (Pseudoplatystoma punctifer). Repositório Alice
LOBO, F. P.; CINTRA, L. C.; VARELA, E. S.; ALVES, A. L.; SILVA, N. M. A. da; IANELLA, P.; PAIVA, S. R.; CAETANO, A. R..
The South American Tiger Catfish (Pseudoplatystoma punctifer) is a freshwater fish species naturally found in the Amazon river basin with an important role in local community and commercial fishing. Recent efforts to domesticate and raise the species in aquaculture systems has led to >10-fold production increases in the last decade. Current production levels are >15,000mt/year. Recently stablished initiatives to structure genetic improvement programs for increasing productivity-associated traits could greatly benefit from using genomic tools for broodstock management and assisted genetic evaluations and breeding. Multiple shotgun libraries with two different insert sizes and multiple Nextera mate pair libraries with three different sizes were...
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Bioinformática; Genômica; Sequenciamento de genoma; Bioinformatics; Genomics; Genome assembly; Sequence analysis.
Ano: 2016 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1038884
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Genomic variants revealed by invariably missing genotypes in nelore cattle. Repositório Alice
SILVA, J. M. da; GIACHETTO, P. F.; SILVA, L. O. C. da; CINTRA, L. C.; PAIVA, S. R.; CAETANO, A. R.; YAMAGISHI, M. E. B..
High density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Polimorfismo de nucleotídeo único; Sequenciamento de DNA; Gado de corte; Single nucleotide polymorphism; Bos indicus; Sequence analysis; Cattle.
Ano: 2015 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1033982
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Identification of a novel COL1A1 frameshift mutation, c.700delG, in a Chinese osteogenesis imperfecta family Genet. Mol. Biol.
Wang,Xiran; Pei,Yu; Dou,Jingtao; Lu,Juming; Li,Jian; Lv,Zhaohui.
Osteogenesis imperfecta (OI) is a family of genetic disorders associated with bone loss and fragility. Mutations associated with OI have been found in genes encoding the type I collagen chains. People with OI type I often produce insufficient α1-chain type I collagen because of frameshift, nonsense, or splice site mutations in COL1A1 or COL1A2. This report is of a Chinese daughter and mother who had both experienced two bone fractures. Because skeletal fragility is predominantly inherited, we focused on identifying mutations in COL1A1 and COL1A2 genes. A novel mutation in COL1A1, c.700delG, was detected by genomic DNA sequencing in the mother and daughter, but not in their relatives. The identification of this mutation led to the conclusion that they were...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Osteogenesis imperfecta; Chinese OI type 1 family; Type I collagen; Sequence analysis; Frameshift mutation.
Ano: 2015 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572015000100001
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Isolation and sequencing of seven Sox genes from the lacertid lizard Eremias breuchleyi Genet. Mol. Biol.
Jie,Li; Zheng,Ping-Ping; Song,Jiao-Lian; Rui,Jin-Long; Nie,Liu-Wang.
The Sox family of genes shares a high sequence similarity with the HMG box region of the human Y chromosomal gene, SRY. We used highly degenerate primers to clone and sequence seven Eremias breuchleyi Sox genes (EbSox2, EbSox3, EbSox4, EbSox11, EbSox12, EbSox14 and EbSox21). A database search for the cloned sequences revealed the following percentage identity with the homologous human SOX genes: EbSox2 = 96%, EbSox3 = 88%, EbSox4 = 94%, EbSox11 = 99%, EbSox12 = 96%, EbSox14 = 98%, EbSox21 = 97%. Cluster analysis indicates that they seem to belong to group B and group C of Sox gene family, respectively.
Tipo: Info:eu-repo/semantics/article Palavras-chave: Eremias breuchleyi; PCR; Sequence analysis; Sox genes; SSCP.
Ano: 2006 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572006000300031
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Marker-assisted elimination of drought-susceptible accessions in upland rice breeding. Repositório Alice
VIEIRA, A. F.; PANTALIÃO, G. F.; ABREU, F. M.; SILVEIRA, R. D.; GARCIA, A. L. B.; NEVES, L. G.; VIANELLO, R. P.; CASTRO, A. P. de; BRONDANI, C..
Breeding for water-deficit tolerance is fundamental to guarantee the sustainability of upland rice production, mainly due to the possibility of an increased frequency of drought episodes due to climate change. This work aimed to identify single nucleotide polymorphism (SNP) markers, derived from RNA sequencing (RNA-Seq), genome-wide association study (GWAS) and candidate genes from Arabidopsis, with potential for use in marker-assisted selection (MAS) for drought tolerance. RNA-Seq and GWAS were efficient in identifying useful SNP markers from the data obtained from three years of field experiments for 175 upland rice accessions, which were sequenced using 32 genes by Capture-Seq. Three genes were equally able to generate SNP markers that discriminated 95%...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Arroz; Melhoramento genético vegetal; Resistência a seca; Rice; Genotyping by sequencing; Plant breeding; Genetic techniques and protocols; Single nucleotide polymorphism; Nucleotide sequences; Sequence analysis; Drought tolerance.
Ano: 2018 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1088846
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Mitochondrial control region genetic diversity and maternal ancestry of a Brangus-Ibage cattle populations Genet. Mol. Biol.
Henkes,Luiz Ernani; Silva Jr,Wilson Araújo; Moraes,José Carlos Ferrugem; Weimer,Tania Azevedo.
The genetic diversity of 277 nucleotides in the mitochondrial DNA control region (nt 15,964 to 16,240 in reference sequence) was analyzed in crossbreed beef cattle (Brangus-Ibage, 5/8 Bos primigenius taurus x 3/8 Bos primigenius indicus) as well as in some Nellore samples (B. p. indicus). Fifty-seven mutations were found in Brangus-Ibage comprising 18 haplotypes (haplotype diversity, h = 0.851 ± 0.041 and nucleotide diversity, ntd = 0.009 ± 0.006) and 66 in Nellore (h = 1.00 ± 0.27, ntd = 0.014 ± 0.012). These data indicated sequence identities of 99.6 and 92.1% between the B. p. taurus' reference sequence and Brangus-Ibage and Nellore, respectively. The comparison of our data with sequence data for 612 individuals recovered from GenBank showed a total of...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bovine mtDNA; Maternal lineage; Sequence analysis; Beef cattle; Genetic diversity.
Ano: 2005 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572005000100011
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Molecular systematics of Barbatosphaeria (Sordariomycetes): multigene phylogeny and secondary ITS structure Naturalis
Réblová, M.; Réblová, K.; Štěpánek, V..
Thirteen morphologically similar strains of barbatosphaeria- and tectonidula-like fungi were studied based on the comparison of cultural and morphological features of sexual and asexual morphs and phylogenetic analyses of five nuclear loci, i.e. internal transcribed spacer rDNA operon (ITS), large and small subunit nuclear ribosomal DNA, β-tubulin, and second largest subunit of RNA polymerase II. Phylogenetic results were supported by in-depth comparative analyses of common core secondary structure of ITS1 and ITS2 in all strains and the identification of non-conserved, co-evolving nucleotides that maintain base pairing in the RNA transcript. Barbatosphaeria is defined as a well-supported monophyletic clade comprising several lineages and is placed in the...
Tipo: Article / Letter to the editor Palavras-chave: Phylogenetics; Ramichloridium; Sequence analysis; Spacer regions; Sporothrix; Tectonidula.
Ano: 2015 URL: http://www.repository.naturalis.nl/record/588698
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