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Registro Completo |
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Biblioteca(s): |
Embrapa Soja. |
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Data corrente: |
18/06/2012 |
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Data da última atualização: |
13/07/2017 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
NASCIMENTO, L. C. do; COSTA, G. G. L.; BINNECK, E.; PEREIRA, G. A. G.; CARAZZOLLE, M. F. |
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Afiliação: |
LEANDRO COSTA DO NASCIMENTO, UNICAMP; GUSTAVO GILSON LACERDA COSTA, UNICAMP; ELISEU BINNECK, CNPSO; GONÇALO AMARANTE GUIMARÃES PEREIRA, UNICAMP; MARCELO FALSARELLA CARAZZOLLE, UNICAMP. |
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Título: |
A web-based bioinformatics interface applied to the GENOSOJA Project: databases and pipelines. |
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Ano de publicação: |
2012 |
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Fonte/Imprenta: |
Genetics and Molecular Biology, Ribeirão Preto, v. 35, n. 1, suppl., p. 203-211, May 2012. |
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Idioma: |
Inglês |
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Conteúdo: |
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 cDNA libraries), as well as web interfaces to access information about soybean gene annotation and expression. |
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Palavras-Chave: |
Bioinformática; Expressão genética. |
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Thesagro: |
Gene; Soja. |
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Thesaurus Nal: |
Bioinformatics; Gene expression; Genes; Soybeans. |
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Categoria do assunto: |
S Ciências Biológicas |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/61065/1/gmb.web-based.v35n1s.203-211.2012.pdf
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Marc: |
LEADER 01639naa a2200265 a 4500
001 1926586
005 2017-07-13
008 2012 bl uuuu u00u1 u #d
100 1 $aNASCIMENTO, L. C. do
245 $aA web-based bioinformatics interface applied to the GENOSOJA Project$bdatabases and pipelines.
260 $c2012
520 $aThe 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 cDNA libraries), as well as web interfaces to access information about soybean gene annotation and expression.
650 $aBioinformatics
650 $aGene expression
650 $aGenes
650 $aSoybeans
650 $aGene
650 $aSoja
653 $aBioinformática
653 $aExpressão genética
700 1 $aCOSTA, G. G. L.
700 1 $aBINNECK, E.
700 1 $aPEREIRA, G. A. G.
700 1 $aCARAZZOLLE, M. F.
773 $tGenetics and Molecular Biology, Ribeirão Preto$gv. 35, n. 1, suppl., p. 203-211, May 2012.
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Registro original: |
Embrapa Soja (CNPSO) |
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Registro Completo
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Biblioteca(s): |
Embrapa Mandioca e Fruticultura; Embrapa Recursos Genéticos e Biotecnologia. |
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Data corrente: |
18/06/2013 |
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Data da última atualização: |
08/03/2023 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Circulação/Nível: |
A - 1 |
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Autoria: |
PASSOS, M. A. N.; CRUZ, V. O. de; EMEDIATO, F. L.; TEIXEIRA, C. C. de; AZEVEDO, V. C. R.; BRASILEIRO, A. C. M.; AMORIM, E. P.; FERREIRA, C. F.; MARTINS, N. F.; TOGAWA, R. C.; PAPPAS JÚNIOR, G. J.; SILVA JUNIOR, O. B. da; MILLER, R. T N. G. |
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Afiliação: |
MARCO A N PASSOS, UNB; VIVIANE OLIVEIRA DE CRUZ, UNB; FLAVIA L EMEDIATO, UNB; CRISTIANE CAMARGO DE TEIXEIRA, UCB; VANIA CRISTINA RENNO AZEVEDO, CENARGEN; ANA CRISTINA MIRANDA BRASILEIRO, CENARGEN; EDSON PERITO AMORIM, CNPMF; CLAUDIA FORTES FERREIRA, CNPMF; NATALIA FLORENCIO MARTINS, CENARGEN; ROBERTO COITI TOGAWA, CENARGEN; GEORGIOS J PAPPAS JÚNIOR, UNB; ORZENIL BONFIM DA SILVA JUNIOR, CENARGEN; ROBERT N. G. MILLER, UNB. |
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Título: |
Analysis of the leaf transcriptome of Musa acuminata during interaction with Mycosphaerella musicola: gene assembly, annotation and marker development. |
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Ano de publicação: |
2013 |
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Fonte/Imprenta: |
BMC Genomics, v.14, n.78, 2013. |
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Idioma: |
Inglês |
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Conteúdo: |
Background: Although banana (Musa sp.) is an important edible crop, contributing towards poverty alleviation and food security, limited transcriptome datasets are available for use in accelerated molecular-based breeding in this genus. 454 GS-FLX Titanium technology was employed to determine the sequence of gene transcripts in genotypes of Musa acuminata ssp. burmannicoides Calcutta 4 and M. acuminata subgroup Cavendish cv. Grande Naine, contrasting in resistance to the fungal pathogen Mycosphaerella musicola, causal organism of Sigatoka leaf spot disease. To enrich for transcripts under biotic stress responses, full length-enriched cDNA libraries were prepared from whole plant leaf materials, both uninfected and artificially challenged with pathogen conidiospores. Results: The study generated 846,762 high quality sequence reads, with an average length of 334 bp and totaling 283 Mbp. De novo assembly generated 36,384 and 35,269 unigene sequences for M. acuminata Calcutta 4 and Cavendish Grande Naine, respectively. A total of 64.4% of the unigenes were annotated through Basic Local Alignment Search Tool (BLAST) similarity analyses against public databases. Assembled sequences were functionally mapped to Gene Ontology (GO) terms, with unigene functions covering a diverse range of molecular functions, biological processes and cellular components. Genes from a number of defense-related pathways were observed in transcripts from each cDNA library. Over 99% of contig unigenes mapped to exon regions in the reference M. acuminata DH Pahang whole genome sequence. A total of 4068 genic-SSR loci were identified in Calcutta 4 and 4095 in Cavendish Grande Naine. A subset of 95 potential defense-related gene-derived simple sequence repeat (SSR) loci were validated for specific amplification and polymorphism across M. acuminata accessions. Fourteen loci were polymorphic, with alleles per polymorphic locus ranging from 3 to 8 and polymorphism information content ranging from 0.34 to 0.82. Conclusions: A large set of unigenes were characterized in this study for both M. acuminata Calcutta 4 and Cavendish Grande Naine, increasing the number of public domain Musa ESTs. This transcriptome is an invaluable resource for furthering our understanding of biological processes elicited during biotic stresses in Musa. Gene-based markers will facilitate molecular breeding strategies, forming the basis of genetic linkage mapping and analysis of quantitative trait loci. MenosBackground: Although banana (Musa sp.) is an important edible crop, contributing towards poverty alleviation and food security, limited transcriptome datasets are available for use in accelerated molecular-based breeding in this genus. 454 GS-FLX Titanium technology was employed to determine the sequence of gene transcripts in genotypes of Musa acuminata ssp. burmannicoides Calcutta 4 and M. acuminata subgroup Cavendish cv. Grande Naine, contrasting in resistance to the fungal pathogen Mycosphaerella musicola, causal organism of Sigatoka leaf spot disease. To enrich for transcripts under biotic stress responses, full length-enriched cDNA libraries were prepared from whole plant leaf materials, both uninfected and artificially challenged with pathogen conidiospores. Results: The study generated 846,762 high quality sequence reads, with an average length of 334 bp and totaling 283 Mbp. De novo assembly generated 36,384 and 35,269 unigene sequences for M. acuminata Calcutta 4 and Cavendish Grande Naine, respectively. A total of 64.4% of the unigenes were annotated through Basic Local Alignment Search Tool (BLAST) similarity analyses against public databases. Assembled sequences were functionally mapped to Gene Ontology (GO) terms, with unigene functions covering a diverse range of molecular functions, biological processes and cellular components. Genes from a number of defense-related pathways were observed in transcripts from each cDNA library. Over 99% of contig unigenes mapp... Mostrar Tudo |
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Thesagro: |
Banana; Fungo; Musa Acuminata; Mycosphaerella Musicola. |
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Thesaurus NAL: |
Microsatellite repeats; Transcriptome. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/156239/1/1471-2164-14-78.pdf
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Marc: |
LEADER 03504naa a2200337 a 4500
001 1964212
005 2023-03-08
008 2013 bl uuuu u00u1 u #d
100 1 $aPASSOS, M. A. N.
245 $aAnalysis of the leaf transcriptome of Musa acuminata during interaction with Mycosphaerella musicola$bgene assembly, annotation and marker development.$h[electronic resource]
260 $c2013
520 $aBackground: Although banana (Musa sp.) is an important edible crop, contributing towards poverty alleviation and food security, limited transcriptome datasets are available for use in accelerated molecular-based breeding in this genus. 454 GS-FLX Titanium technology was employed to determine the sequence of gene transcripts in genotypes of Musa acuminata ssp. burmannicoides Calcutta 4 and M. acuminata subgroup Cavendish cv. Grande Naine, contrasting in resistance to the fungal pathogen Mycosphaerella musicola, causal organism of Sigatoka leaf spot disease. To enrich for transcripts under biotic stress responses, full length-enriched cDNA libraries were prepared from whole plant leaf materials, both uninfected and artificially challenged with pathogen conidiospores. Results: The study generated 846,762 high quality sequence reads, with an average length of 334 bp and totaling 283 Mbp. De novo assembly generated 36,384 and 35,269 unigene sequences for M. acuminata Calcutta 4 and Cavendish Grande Naine, respectively. A total of 64.4% of the unigenes were annotated through Basic Local Alignment Search Tool (BLAST) similarity analyses against public databases. Assembled sequences were functionally mapped to Gene Ontology (GO) terms, with unigene functions covering a diverse range of molecular functions, biological processes and cellular components. Genes from a number of defense-related pathways were observed in transcripts from each cDNA library. Over 99% of contig unigenes mapped to exon regions in the reference M. acuminata DH Pahang whole genome sequence. A total of 4068 genic-SSR loci were identified in Calcutta 4 and 4095 in Cavendish Grande Naine. A subset of 95 potential defense-related gene-derived simple sequence repeat (SSR) loci were validated for specific amplification and polymorphism across M. acuminata accessions. Fourteen loci were polymorphic, with alleles per polymorphic locus ranging from 3 to 8 and polymorphism information content ranging from 0.34 to 0.82. Conclusions: A large set of unigenes were characterized in this study for both M. acuminata Calcutta 4 and Cavendish Grande Naine, increasing the number of public domain Musa ESTs. This transcriptome is an invaluable resource for furthering our understanding of biological processes elicited during biotic stresses in Musa. Gene-based markers will facilitate molecular breeding strategies, forming the basis of genetic linkage mapping and analysis of quantitative trait loci.
650 $aMicrosatellite repeats
650 $aTranscriptome
650 $aBanana
650 $aFungo
650 $aMusa Acuminata
650 $aMycosphaerella Musicola
700 1 $aCRUZ, V. O. de
700 1 $aEMEDIATO, F. L.
700 1 $aTEIXEIRA, C. C. de
700 1 $aAZEVEDO, V. C. R.
700 1 $aBRASILEIRO, A. C. M.
700 1 $aAMORIM, E. P.
700 1 $aFERREIRA, C. F.
700 1 $aMARTINS, N. F.
700 1 $aTOGAWA, R. C.
700 1 $aPAPPAS JÚNIOR, G. J.
700 1 $aSILVA JUNIOR, O. B. da
700 1 $aMILLER, R. T N. G.
773 $tBMC Genomics$gv.14, n.78, 2013.
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Embrapa Recursos Genéticos e Biotecnologia (CENARGEN) |
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