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

A high-throughput data mining of single nucleotide polymorphisms in Coffea species expresed sequence tags suggests differential homeologous gene expression in the allotetrapoloid Coffea arabica.

NASCIMENTO, L. C.; COSTA, G. G. L.; MEYER, L.; BINNECK, E.; RODRIGUES, F.; KULCHESKI, F. R.; MARGIS, R.; KIDO, E. A.; MARCELINO, F. C.; NEPOMUCENO, A. L.; ABDELNOOR, R. V.; PEREIRA, G. A. G.; CARAZZOLLE, M. F..

Soybean is a legume with large economic importance in the international market, with a world production of almost two hundred and ten million tons in the 2008/2009 harvest. Brazil appears as the second largest producer, with about twenty-five percent of the world production. In 2007, the Brazilian Soybean Genome Consortium (GENOSOJA) was established with the goal of integrating several institutions currently working with soybean genomics in Brazil. The project has an initiative to search for new treats to improve the soybean production process, emphasizing in stresses that affect the national production, like the occurrence of droughts, pests attacks and the Asian Rust disease. Among the objectives of GENOSOJA is the creation of a relational database,...

Tipo: Resumo em anais de congresso (ALICE)

Palavras-chave: Soybean.

Ano: 2010

URL: http://www.alice.cnptia.embrapa.br/handle/doc/874417

VIDAL, R. O.; MONDEGO, J. M. C.; POT, D.; AMBRÓSIO, A. B.; ANDRADE, A. C.; PEREIRA, L. F. P.; COLOMBO, C. A.; VIEIRA, L. G. E.; CARAZZOLLE, M. F.; PEREIRA, G. A. G..

Polyploidization constitutes a common mode of evolution in flowering plants. This event provides the raw material for the divergence of function in homeologous genes, leading to phenotypic novelty that can contribute to the success of polyploids in nature or their selection for use in agriculture. Mounting evidence underlined the existence of homeologous expression biases in polyploid genomes; however, strategies to analyze such transcriptome regulation remained scarce. Important factors regarding homeologous expression biases remain to be explored, such as whether this phenomenon influences specific genes, how paralogs are affected by genome doubling, and what is the importance of the variability of homeologous expression bias to genotype differences....

A web-based bioinformatics interface applied to the GENOSOJA Project: databases and pipelines.

Palavras-chave: Coffea arabica.

Ano: 2010

URL: http://www.alice.cnptia.embrapa.br/handle/doc/880492

NASCIMENTO, L. C. do; COSTA, G. G. L.; BINNECK, E.; PEREIRA, G. A. G.; CARAZZOLLE, M. F..

The Genosoja consortium is an initiative to integrate different omics research approaches carried out in Brazil. Basically, the aim of the project is to improve the plant by identifying genes involved in responses against stresses that affect domestic production, like drought stress and Asian Rust fungal disease. To do so, the project generated several types of sequence data using different methodologies, most of them sequenced by next generation sequencers. The initial stage of the project is highly dependent on bioinformatics analysis, providing suitable tools and integrated databases. In this work, we describe the main features of the Genosoja web database, including the pipelines to analyze some kinds of data (ESTs, SuperSAGE, microRNAs, subtractive...

Análise da composição e organização do genoma de Eucalyptus grandis com base em sequenciamento "shotgun" por amostragem ("sample sequencing").

Palavras-chave: Bioinformática; Expressão genética; Soja; Gene; Soybeans; Genes; Bioinformatics; Gene expression.

Ano: 2012

URL: http://www.alice.cnptia.embrapa.br/handle/doc/926586

LOURENÇO, R. T.; CUNHA, A. F.; TSUKUMO, F.; PEREIRA, G. A. G.; GRATTAPAGLIA, D..

2002

Bioinformatics analysis applied to genosoja project.

Palavras-chave: Genoma; Eucalyptus grandis; Sequenciamento "shotgun"; Amostragem.

Ano: 2002

URL: http://www.alice.cnptia.embrapa.br/handle/doc/184624

Boto, a class II transposon in Moniliophthora perniciosa, is the first representative of the PIF/Harbinger superfamily in a phytopathogenic fungus.

NASCIMENTO, L. C.; COSTA, G. G. L.; VIDAL, R. O.; MEYER, L.; BINNECK, E.; KIDO, E. A.; RODRIGUES, F.; KULCHESKI, F. R.; NEPOMUCENO, A. L.; ABDELNOOR, R. V.; PEREIRA, G. A. G.; CARAZZOLLE, M. F..

Soybean is the legume of most economic importance in the international market, with world production of almost two hundred and thirty million tons in the 2007/2008 harvest. The Brazil appears as the largest exporter of the product in the world, with about twenty-five percent of the world production. In 2007 the brazilian government started the GENOSOJA project with the main objective of discover new treats to improve the plant production process, emphasizing in stresses that affect the national production like the occurrence of droughts, pests attacks and the Asian rust disease. This work is inserted in the GENOSOJA scope and aims to generate bioinformatics tools to integrate the public soybean data like ESTS and genomic sequences, with all data generated...

Tipo: Resumo em anais de congresso (ALICE)

Palavras-chave: Bioinformática.

Ano: 2009

URL: http://www.alice.cnptia.embrapa.br/handle/doc/894410

PEREIRA, J. F.; ALMEIDA, A. P. M. M.; COTA, J.; PAMPHILE, J. A.; SILVA, G. F. da; ARAUJO, E. F. de; GRAMACHO, K. P.; BROMMONSCHENKEL, S. H.; PEREIRA, G. A. G.; QUEIROZ, M. V. de.

2013

Boto, a class II transposon in Moniliophthora perniciosa, is the first representative of the PIF/Harbinger superfamily in a phytopathogenic fungus.

Palavras-chave: Genética; Fungo; Planta; Doença.

Ano: 2013

URL: http://www.alice.cnptia.embrapa.br/handle/doc/976811

PEREIRA, J. F.; ALMEIDA, A. P. M. M.; COTA, J.; PAMPHILE, J. A.; SILVA, G. F. da; ARAÚJO, E. F. de; GRAMACHO, K. P.; BROMMONSCHENKEL, S. H.; PEREIRA, G. A. G.; QUEIROZ, M. V. de.

Boto, a class II transposable element, was characterized in the Moniliophthora perniciosa genome. The Boto transposase is highly similar to plant PIF-like transposases that belong to the newest class II superfamily known as PIF/Harbinger. Although Boto shares characteristics with PIF-like elements, other characteristics, such as the transposase intron position, the position and direction of the second ORF, and the footprint, indicate that Boto belongs to a novel family of the PIF/Harbinger superfamily. Southern blot analyses detected 6?12 copies of Boto in C-biotype isolates and a ubiquitous presence among the C- and S-biotypes, as well as a separation in the C-biotype isolates from Bahia State in Brazil in at least two genotypic groups, and a new...

Brazilian coffee genome project: an EST-based genomic resource.

Palavras-chave: Moniliophthora perniciosa.

Ano: 2013

URL: http://www.alice.cnptia.embrapa.br/handle/doc/946075

VIEIRA, L. G. E.; ANDRADE, A. C.; COLOMBO, C. A.; MORAES, A. H. de A.; METHA, A.; OLIVEIRA, A. C. de; LABATE, C. A.; MARINO, C. L.; MONTEIRO-VITORELLO, C. de B.; MONTE, D. C.; GIGLIOTI, E.; KIMURA, E. T.; ROMANO, E.; KURAMAE, E. E.; LEMOS, E. G. M.; ALMEIDA, E. R. P. de; JORGE, E. C.; ALBUQUERQUE, E. V. S.; SILVA, F. R. da; VINECKY, F.; SAWAZAKI, H. E.; DORRY, H. F. A.; CARRER, H.; ABREU, I. N.; BATISTA, J. A. N.; TEIXEIRA, J. B.; KITAJIMA, J. P.; XAVIER, K. G.; LIMA, L. M. de; CAMARGO, L. E. A. de; PEREIRA, L. F. P.; COUTINHO, L. L.; LEMOS, M. V. F.; ROMANO, M. R.; MACHADO, M. A.; COSTA, M. M. do C.; SÁ, M. F. G. de; GOLDMAN, M. H. S.; FERRO, M. I. T.; TINOCO, M. L. P.; OLIVEIRA, M. C.; VAN SLUYS, M-A.; SHIMIZU, M. M.; MALUF, M. P.; EIRA, M. T. S. da; GUERREIRO FILHO, O.; ARRUDA, P.; MAZZAFERA, P.; MARIANI, P. D. S. C.; OLIVEIRA, R. L. B. C. de; HARAKAVA, R.; BALBAO, S. F.; TSAI, S. M.; MAURO, S. M. Z. di; SANTOS, S. N.; SIQUEIRA, W. J.; COSTA, G. G. L.; FORMIGHIERI, E. F.; CARAZZOLLE, M. F.; PEREIRA, G. A. G..

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Estrutura genômica de três megabases de dna genômico "shotgun" de eucalyptus: conteúdo nucleotídico, seouências repetitivas e genes.

Palavras-chave: Projeto genoma; Brasil; Café.

Ano: 2006

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/187149

LOURENÇO, R.T.; PAPPAS, G. J.; CUNHA, A. F.; PEREIRA, G. A. G.; GRATTAPAGLIA, D..

2003

Genotipagem de cultivares brasileiros de soja através da detecção de SNPs.

Ano: 2003

URL: http://www.alice.cnptia.embrapa.br/handle/doc/188171

NASCIMENTO, L. C.; VIDAL R. O.; MONDEGO, J. M. C.; COSTA, G. G. L.; JUNIOR, O. R.; RODRIGUES, F.; NEPOMUCENO, A. L.; MARCELINO-GUIMARÃES, F. C.; ABDELNOOR, R. V.; PEREIRA, G. A. G.; CARAZZOLLE, M. F..

A soja é um dos principais produtos da balança comercial brasileira, respondendo por mais de 10% do total das exportações do país. No ano de 2007, o governo brasileiro estabeleceu um consórcio de pesquisas em soja ? denominado GENOSOJA ? com o objetivo de identificar características genéticas que possam facilitar o processo produtivo da planta, com foco nos diversos estresses que acometem a produção nacional, como a ocorrência de secas, o ataque de pragas e a doença da ferrugem asiática. Entre os objetivos do consórcio está a geração de sequências de DNA e mRNA de cultivares brasileiros selecionados em programas de melhoramento. Polimorfismos de nucleotídeo único (SNPs; single nucleotide polymorphisms) são diferenças de uma base entre as sequências de DNA...

Identification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars.

Palavras-chave: Biotecnologia.

Ano: 2012

URL: http://www.alice.cnptia.embrapa.br/handle/doc/928160

MOFATTO, L. S.; CARNEIRO, F. de A.; VIEIRA, N. G.; DUARTE, K. E.; VIDAL, R. O.; ALEKCEVETCH, J. C.; COTTA, M. G.; VERDEIL, J-L.; LAPEYRE-MONTES, F.; LARTAUD, M.; LEROY, T.; DE BELLIS, F.; POT, D; RODRIGUES, G. C.; ALSARELLA CARAZZOLLE, M.; PEREIRA, G. A. G.; ANDRADE, A. C.; MARRACCINI, P..

BACKGROUND: Drought is a widespread limiting factor in coffee plants. It affects plant development, fruit production, bean development and consequently beverage quality. Genetic diversity for drought tolerance exists within the coffee genus. However, the molecular mechanisms underlying the adaptation of coffee plants to drought are largely unknown. In this study, we compared the molecular responses to drought in two commercial cultivars (IAPAR59, drought-tolerant and Rubi, drought-susceptible) of Coffea arabica grown in the field under control (irrigation) and drought conditions using the pyrosequencing of RNA extracted from shoot apices and analysing the expression of 38 candidate genes. RESULTS: Pyrosequencing from shoot apices generated a total of 34.7...

Identification of defence-related genes expressed in coffee and citrus during infection by Xylella fastidiosa.

Palavras-chave: Candidate gene; Coffee; Differential gene expression; RNA-Seq; Real-time PCR (RT-qPCR); Drought; Coffea arabica.

Ano: 2016

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1043710

CARAZZOLLE, M. F.; RABELLO, F. R.; MARTINS, N. F.; SOUZA, A. A. de; AMARAL, A. M. do; FREITAS-ASTUA, J.; PEREIRA, G. A. G.; MACHADO, M. A.; MEHTA, A..

One of the phytosanitary problems of coffee cultivation in Brazil is Coffee Leaf Scorch (CLS) disease, caused by the phytopathogenic bacterium Xylella fastidiosa. Due to the economic importance of coffee to Brazil and the losses caused by X. fastidiosa, a cDNA library (RX1) was constructed using infected coffee stems. This library is one of the 37 coffee EST libraries constructed using different organs and tissues and biological conditions (Coffee Genome Project-CafEST). The objective of this study was to identify genes potentially involved in defence processes in response to X. fastidiosa infection by in silico analysis of the transcripts from the RX1 library as well as compare the coffee ESTs to citrus Xylella-infected ESTs. Clustering analysis of the...

Identification of novel soybean microRNAs involved in abiotic and biotic stresses.

Palavras-chave: Doença de planta; Xylella fastidiosa; Plant disease.

Ano: 2011

URL: http://www.alice.cnptia.embrapa.br/handle/doc/896465

KULCHESKI, F. R.; OLIVEIRA, L. F. V.; MOLINA, L. G.; ALMERAO, M. P.; RODRIGUES, F. A.; MARCOLINO, J.; BARBOSA, J. F.; STOLF-MOREIRA, R.; NEPOMUCENO, A. L.; MARCELINO-GUIMARÃES, F. C.; ABDELNOOR, R. V.; NASCIMENTO, L. C.; CARAZZOLLE, M. F.; PEREIRA, G. A. G.; MARGIS, R..

Background: Small RNAs (19-24 nt) are key regulators of gene expression that guide both transcriptional and posttranscriptional silencing mechanisms in eukaryotes. Current studies have demonstrated that microRNAs (miRNAs) act in several plant pathways associated with tissue proliferation, differentiation, and development and in response to abiotic and biotic stresses. In order to identify new miRNAs in soybean and to verify those that are possibly water deficit and rust-stress regulated, eight libraries of small RNAs were constructed and submitted to Solexa sequencing. Results: The libraries were developed from drought-sensitive and tolerant seedlings and rust-susceptible and resistant soybeans with or without stressors. Sequencing the library and...

Microarray analysis of eucalyptus gene expression.

Palavras-chave: Soja; Deficiência hídrica; Gene marcador; Soybeans; Gene expression; Soil water deficit.

Ano: 2011

URL: http://www.alice.cnptia.embrapa.br/handle/doc/911802

PASQUALI, G.; PAPPAS JUNIOR, G. J.; BASTOLLA, F. M.; VOM ENDT, D.; BRONDANI, R. V.; COELHO, A. S. G.; BROMMONSCHENKEL, S. H.; PEREIRA, G. A. G.; CASCARDO, J. C. M.; GRATTAPAGLIA, D..

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Novos microssatélltes para eucalyptus a partir de clones "shotgun".

Palavras-chave: Eucalyptus genome; Eucalipto; Genoma.

Ano: 2006

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/187590

BATISTA, A. R. S.; LOURENÇO, R. T.; PEREIRA, G. A. G.; GRATTAPAGLIA, D..

2003

Overall picture of expressed Heat Shock Factors in Glycine max, Lotus japonicus and Medicago truncatula.

Ano: 2003

URL: http://www.alice.cnptia.embrapa.br/handle/doc/188139

SOARES-CAVALCANTI, N. M.; BELARMINO, L. C.; KIDO, E. A.; PANDOLFI, V.; MARCELINO-GUIMARÃES, F. C.; RODRIGUES, F. A.; PEREIRA, G. A. G.; BENKO-ISEPPON, A. M..

Heat shock (HS) leads to the activation of molecular mechanisms, known as HS-response, that prevent damage and enhance survival under stress. Plants have a flexible and specialized network of Heat Shock Factors (HSFs), which are transcription factors that induce the expression of heat shock proteins. The present work aimed to identify and characterize the Glycine max HSF repertory in the Soybean Genome Project (GENOSOJA platform), comparing them with other legumes (Medicago truncatula and Lotus japonicus) in view of current knowledge of Arabidopsis thaliana. The HSF characterization in leguminous plants led to the identification of 25, 19 and 21 candidate ESTs in soybean, Lotus and Medicago, respectively. A search in the SuperSAGE libraries revealed 68...

The genome projects of the closely related cacao pathogens Moniliophthora roreri and Moniliophthora perniciosa.

Palavras-chave: Bioinformática; Soja; Gene; Genoma; Bioinformatics; Soybeans; Genome; Genes; Abiotic stress; Transcription factors.

Ano: 2012

URL: http://www.alice.cnptia.embrapa.br/handle/doc/926601

Transcriptional activity, chromosomal distribution and expression effects of transposable elements in Coffea genomes.

CARAZZOLLE, M. F.; COSTA, G. G. L.; HERAI, R. H.; R. JÚNIOR, O.; NASCIMENTO, L. C.; TEIXEIRA, P. J.; TIBURCIO, R. A.; MONDEGO, J. M. C.; PEREIRA, G. A. G..

The basidiomycetes Moniliophthora roreri and Moniliophthora perniciosa are the etiologic agents of the two most devastating diseases in cacao (Theobroma cacao ): frosty pod rot and the witches? broom, respectively. The species are very closely related and even hybrid cells have been previously obtained. In cacao, both species infect pods, causing necrosis, and M. perniciosa is also able to invade other tissues causing changes in plant metabolisms, such as hyperplasia and hypertrophy. In order to understand the molecular basis of these organisms, we sequenced the genome of these two species. We also obtained transcriptomic data (RNA-seq) in several different conditions including the interaction between cacao and both pathogens. This work reports a pipeline...

Tipo: Resumo em anais de congresso (ALICE)

Palavras-chave: Patógenos do cacau; Genoma; Moniliophthora roreri; Moniliophthora perniciosa; Theobroma cacao; Genome.

Ano: 2010

URL: http://www.alice.cnptia.embrapa.br/handle/doc/868507

LOPES, F. R.; JJINGO, D.; SILVA C. R. M. da; ANDRADE, A. C.; MARRACCINI, P.; TEIXEIRA, J. B.; CARAZZOLLE, M. F.; PEREIRA, G. A. G.; PEREIRA, L. F. P.; VANZELA, A. L. L.; WANG, L.; JORDAN, I. K.; CARARETO, C. M. A..

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