SABIIA - Sistema Aberto e Integrado de Informação em Agricultura (Sabiia)

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.

Aluminum-induced genes in grass species.

Palavras-chave: Bioinformática; Sequência genética.; Genoma.; Bioinformatics; Genome; Sequence analysis.

Ano: 2012

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/946664

Analysis and sequencing of h6hmRNA, last enzyme in the tropane alkaloids pathway from anthers and hairy root cultures of Brugmansia candida (Solanaceae)

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..

AB3C X-meeting 2010.

Tipo: Parte de livro

Palavras-chave: Tolerância a alumínio; Sequence analysis; Genetics; Aluminum; Genes.

Ano: 2010

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/873120

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

Avaliação e aplicação de métodos de genotipagem para estudo da síndrome da musculatura dupla em bovinos da raça Senepol.

Caracterização de bibliotecas de RNA-Seq de amendoim forrageiro para o desenvolvimento de novos microssatélites.

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: Teses

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

Characterization and expression of two cDNA encoding 3-hydroxy-3-methylglutaryl coenzyme A reductase isoforms in coffee (Coffea arabica L.).

OLIVEIRA, J. C. de; SILVA, A. L. D. da; SILVA, C. C. da; SOUZA, A. P. de; FORMIGHIERI, E. F.; CAMPOS, T. de.

O uso do amendoim forrageiro (Arachis pintoi) em pastagens consorciadas com gramíneas tem importância econômica e ambiental. Avanços no programa de melhoramento da espécie podem ser obtidos com a ampla informação gerada pelo sequenciamento de segunda geração. A tecnologia de RNA-Seq permite obter extensa cobertura dos genes existentes no genoma com custo consideravelmente baixo. Os dados gerados possibilitam identificar novos marcadores, validar genes e rotas metabólicas. Atualmente existem poucos microssatélites disponíveis para o amendoim forrageiro. Assim, o objetivo deste trabalho foi desenvolver novos marcadores microssatélites a partir de bibliotecas de RNA-Seq de amendoim forrageiro. O RNA de duas cultivares (Belomonte e Amarillo MG-100) foi...

Tipo: Parte de livro

Palavras-chave: Pastos forrajeros; Forage peanut; Cacahuetes forrajeros; RNA-Seq; RNA sequencing; Belomonte; Amarillo MG-100; Genoma funcional; Cultivo mixto; Leguminosas forrajeras; Repeticiones de microsatélite; Análisis de secuencia; Embrapa Acre; Rio Branco (AC); Acre; Amazônia Ocidental; Western Amazon; Amazonia Occidental.; Amendoim forrageiro; Pastagem Consorciada; Marcador Genético; Banco de Germoplasma.; Leguminosa Forrageira; Gramínea Forrageira; Sequence analysis; Germplasm conservation.; Forage legumes; Arachis pintoi; Microsatellite repeats; Mixed cropping; Forage grasses.

Ano: 2020

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1125415

Confirmation and Sequence analysis of N gene of PPRV in South Xinjiang, China

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 de periódico

Palavras-chave: Ydroxy.; Molecular characterization; Expressed sequence tag (EST); Methyglutaryl-CoA reductase; Coffee; Gene expression; Sequence analysis; Isoprenoids..

Ano: 2011

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/902481

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...

Draft genome sequencing of the Yeast Spathaspora arborariae sp.

Palavras-chave: PPR; Diagnosis; N gene; Sequence analysis.

Ano: 2017

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0102-09352017000501105

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.

Efficient gap-closure of eukaryotic genome sequence assemblies by third-generation sequencing.

Palavras-chave: Sequência de genoma; Yeast Spathaspora arborariae sp.; Sequence analysis; Yeasts; Genomics.

Ano: 2012

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/946642

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.

Factor 9 de crecimiento y diferenciación asociado al índice de prolificidad en la oveja pelibuey.

Palavras-chave: Sequenciamento de genoma de zebu; Plataforma SOLiD; Genome; Zebu; Sequence analysis.

Ano: 2012

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/946528

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

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.

Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds.

Palavras-chave: Canine parvovirus type 2c; Sequence analysis; Brazil.

Ano: 2009

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822009000300008

Genome Sequencing and de novo assembly of the South American Tiger Catfish (Pseudoplatystoma punctifer).

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: Separatas

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/alice/handle/doc/1032807

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...

Genomic variants revealed by invariably missing genotypes in nelore cattle.

Palavras-chave: Bioinformática; Genômica; Sequenciamento de genoma; Bioinformatics; Genomics; Genome assembly; Sequence analysis.

Ano: 2016

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1038884

Identification of a novel COL1A1 frameshift mutation, c.700delG, in a Chinese osteogenesis imperfecta family

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 de periódico

Palavras-chave: Polimorfismo de nucleotídeo único; Sequenciamento de DNA.; Gado de corte; Bos Indicus.; Single nucleotide polymorphism; Sequence analysis; Cattle..

Ano: 2015

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1033982

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...

Isolation and sequencing of seven Sox genes from the lacertid lizard Eremias breuchleyi

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

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.

Marker-assisted elimination of drought-susceptible accessions in upland rice breeding.

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

Mitochondrial control region genetic diversity and maternal ancestry of a Brangus-Ibage cattle populations

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 de periódico

Palavras-chave: Genotyping by sequencing.; Arroz; Melhoramento genético vegetal; Resistência a seca; Rice; 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

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...