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 | Acesso ao texto completo restrito à biblioteca da Embrapa Agricultura Digital. Para informações adicionais entre em contato com cnptia.biblioteca@embrapa.br. |
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Registro Completo |
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Biblioteca(s): |
Embrapa Agricultura Digital. |
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Data corrente: |
20/01/2015 |
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Data da última atualização: |
08/01/2020 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
CRATIVOL, C.; REGULSKI, M.; BERTALAN, M.; MCCOMBIE, W. R.; SILVA, F. R. da; ZERLOTINI NETO, A.; VICENTINI, R.; FARINELLI, L.; HEMERLY, A. S.; MARTIENSSEN, R. A.; FERREIRA, P. C. G. |
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Afiliação: |
CLÍCIA GRATIVOL, UFRJ; MICHAEL REGULSKI, Cold Spring Harbor Laboratory; MARCELO BERTALAN, Institute of Biological Psychiatry, Mental Health Center; W. RICHARD MCCOMBIE, Cold Spring Harbor Laboratory; FELIPE RODRIGUES DA SILVA, CNPTIA; ADHEMAR ZERLOTINI NETO, CNPTIA; RENATO VICENTINI, CBMEG/Unicamp; LAURENT FARINELLI, Fasteris SA; ADRIANA SILVA HEMERLY, UFRJ; ROBERT A. MARTIENSSEN, Cold Spring Harbor Laboratory; PAULO CAVALCANTI GOMES FERREIRA, UFRJ. |
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Título: |
Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum. |
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Ano de publicação: |
2014 |
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Fonte/Imprenta: |
The Plant Journal, Oxford, v. 79, n. 1, p. 162-172, 2014. |
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DOI: |
10.1111/tpj.12539 |
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Idioma: |
Inglês |
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Conteúdo: |
Many economically important crops have large and complex genomes that hamper their sequencing by standard methods such as whole genome shotgun (WGS). Large tracts of methylated repeats occur in plant genomes that are interspersed by hypomethylated gene-rich regions. Gene-enrichment strategies based on methylation profiles offer an alternative to sequencing repetitive genomes. Here, we have applied methyl filtration with McrBC endonuclease digestion to enrich for euchromatic regions in the sugarcane genome. To verify the efficiency of methylation filtration and the assembly quality of sequences submitted to gene-enrichment strategy, we have compared assemblies using methyl-filtered (MF) and unfiltered (UF) libraries. The use of methy filtration allowed a better assembly by filtering out 35% of the sugarcane genome and by producing 1.53 more scaffolds and 1.73 more assembled Mb in length compared with unfiltered dataset. The coverage of sorghum coding sequences (CDS) by MF scaffolds was at least 36% higher than by the use of UF scaffolds. Using MF technology, we increased by 1343 the coverage of gene regions of the monoploid sugarcane genome. The MF reads assembled into scaffolds that covered all genes of the sugarcane bacterial artificial chromosomes (BACs), 97.2% of sugarcane expressed sequence tags (ESTs), 92.7% of sugarcane RNA-seq reads and 98.4% of sorghum protein sequences. Analysis of MF scaffolds from encoded enzymes of the sucrose/starch pathway discovered 291 single-nucleotide polymorphisms (SNPs) in the wild sugarcane species, S. spontaneum and S. officinarum. A large number of microRNA genes was also identified in the MF scaffolds. The information achieved by the MF dataset provides a valuable tool for genomic research in the genus Saccharum and for improvement of sugarcane as a biofuel crop. MenosMany economically important crops have large and complex genomes that hamper their sequencing by standard methods such as whole genome shotgun (WGS). Large tracts of methylated repeats occur in plant genomes that are interspersed by hypomethylated gene-rich regions. Gene-enrichment strategies based on methylation profiles offer an alternative to sequencing repetitive genomes. Here, we have applied methyl filtration with McrBC endonuclease digestion to enrich for euchromatic regions in the sugarcane genome. To verify the efficiency of methylation filtration and the assembly quality of sequences submitted to gene-enrichment strategy, we have compared assemblies using methyl-filtered (MF) and unfiltered (UF) libraries. The use of methy filtration allowed a better assembly by filtering out 35% of the sugarcane genome and by producing 1.53 more scaffolds and 1.73 more assembled Mb in length compared with unfiltered dataset. The coverage of sorghum coding sequences (CDS) by MF scaffolds was at least 36% higher than by the use of UF scaffolds. Using MF technology, we increased by 1343 the coverage of gene regions of the monoploid sugarcane genome. The MF reads assembled into scaffolds that covered all genes of the sugarcane bacterial artificial chromosomes (BACs), 97.2% of sugarcane expressed sequence tags (ESTs), 92.7% of sugarcane RNA-seq reads and 98.4% of sorghum protein sequences. Analysis of MF scaffolds from encoded enzymes of the sucrose/starch pathway discovered 291 single... Mostrar Tudo |
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Palavras-Chave: |
Cana-de-açúcar; De novo assembly; Gene-rich regions. |
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Thesagro: |
Metilação. |
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Thesaurus Nal: |
Methylation; Saccharum; Sugarcane. |
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Categoria do assunto: |
-- |
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Marc: |
LEADER 02815naa a2200337 a 4500
001 2006128
005 2020-01-08
008 2014 bl uuuu u00u1 u #d
024 7 $a10.1111/tpj.12539$2DOI
100 1 $aCRATIVOL, C.
245 $aSugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum.$h[electronic resource]
260 $c2014
520 $aMany economically important crops have large and complex genomes that hamper their sequencing by standard methods such as whole genome shotgun (WGS). Large tracts of methylated repeats occur in plant genomes that are interspersed by hypomethylated gene-rich regions. Gene-enrichment strategies based on methylation profiles offer an alternative to sequencing repetitive genomes. Here, we have applied methyl filtration with McrBC endonuclease digestion to enrich for euchromatic regions in the sugarcane genome. To verify the efficiency of methylation filtration and the assembly quality of sequences submitted to gene-enrichment strategy, we have compared assemblies using methyl-filtered (MF) and unfiltered (UF) libraries. The use of methy filtration allowed a better assembly by filtering out 35% of the sugarcane genome and by producing 1.53 more scaffolds and 1.73 more assembled Mb in length compared with unfiltered dataset. The coverage of sorghum coding sequences (CDS) by MF scaffolds was at least 36% higher than by the use of UF scaffolds. Using MF technology, we increased by 1343 the coverage of gene regions of the monoploid sugarcane genome. The MF reads assembled into scaffolds that covered all genes of the sugarcane bacterial artificial chromosomes (BACs), 97.2% of sugarcane expressed sequence tags (ESTs), 92.7% of sugarcane RNA-seq reads and 98.4% of sorghum protein sequences. Analysis of MF scaffolds from encoded enzymes of the sucrose/starch pathway discovered 291 single-nucleotide polymorphisms (SNPs) in the wild sugarcane species, S. spontaneum and S. officinarum. A large number of microRNA genes was also identified in the MF scaffolds. The information achieved by the MF dataset provides a valuable tool for genomic research in the genus Saccharum and for improvement of sugarcane as a biofuel crop.
650 $aMethylation
650 $aSaccharum
650 $aSugarcane
650 $aMetilação
653 $aCana-de-açúcar
653 $aDe novo assembly
653 $aGene-rich regions
700 1 $aREGULSKI, M.
700 1 $aBERTALAN, M.
700 1 $aMCCOMBIE, W. R.
700 1 $aSILVA, F. R. da
700 1 $aZERLOTINI NETO, A.
700 1 $aVICENTINI, R.
700 1 $aFARINELLI, L.
700 1 $aHEMERLY, A. S.
700 1 $aMARTIENSSEN, R. A.
700 1 $aFERREIRA, P. C. G.
773 $tThe Plant Journal, Oxford$gv. 79, n. 1, p. 162-172, 2014.
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Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
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| Registros recuperados : 15 | |
| 4. |  | ALVES, L. W. R.; SILVA, J. B. da; SOUZA, I. F. Efeitos da deriva simulada, através de aplicações de subdoses dos herbicidas Glyphosate e Oxyfluorfen, sobre a cultura do milho (Zea mays L.). In: CONGRESSO BRASILEIRO DA CIÊNCIA DAS PLANTAS DANINHAS, 21., 1997, Caxambu. Resumos. Viçosa, MG: SBCPD, 1997. p. 456.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Milho e Sorgo. |
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| 6. | | ANTUNES, W. R.; SILVA, S. D. dos A. e; TATTO, F. R.; CAMPOS, A. D. S. de; EICHOLZ, M. D. Avaliação de brotação e posição de plantio de mini-toletes na produção de mudas de cana-de-açúcar (Saccharum SPP.) no sistema de mudas pré-brotadas, em Pelotas-RS, safra 2012/13. In: SIMPÓSIO ESTADUAL DE AGROENERGIA; REUNIÃO TÉCNICA DE AGROENERGIA - RS, 5.; ENCONTRO DE ENERGIAS RENOVÁVEIS NA AGRICULTURA FAMILIAR, 2., Pelotas, 2014. Anais... Pelotas: Embrapa Clima Temperado, 2014. 1 pen card.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Clima Temperado. |
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| 7. | | OLIVEIRA, R. J. P. de; EICHOLZ, M. D.; TATTO, F. R.; ANTUNES, W. R.; SILVA, S. D. dos A. e; EICHOLZ, E. D. Avaliação do desempenho dos genótipos elite de pinhão-manso na safra de 2011/12 no município de Pelotas/RS. In: SIMPÓSIO ESTADUAL DE AGROENERGIA, 4.; REUNIÃO TÉCNICA DE AGROENERGIA, 4., 2012, AMRIGS: Porto Alegre. Anais... Pelotas: Embrapa Clima Temperado, 2012. Organizado por Sérgio Delmar dos Anjos e Silva Ivan Rodrigues de Almeida.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Clima Temperado. |
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| 8. | | ZAIDEM, A. L. de M.; FERREIRA, A. L.; RIBEIRO, W. R.; SILVA, A. Y. P. e; SILVA, J. F. A. e; RAGNI, M.; PINHEIRO, P. V. Atração de adultos da mosca branca, Bemisia tabaci, à luz LED em instrumento para o monitoramento automatizado de pragas. In: SEMINÁRIO JOVENS TALENTOS, 16., 2022, Santo Antônio de Goiás. Resumos... Brasília, DF: Embrapa; Santo Antônio de Goiás: Embrapa Arroz e Feijão, 2022. p. 31.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Arroz e Feijão. |
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| 9. | | MELO, I. S. de; SOUZA, W. R.; SILVA, L. J.; SANTOS, S. N.; ASSALIN, M. R.; ZUCCHI, T. D.; QUEIROZ, S. C. do N. de. Antifungal activity of Pseudomonas frederiksbergensis CMAA 1323 isolated from the Antarctic hair grass Deschampsia antarctica. British Microbiology Research Journal, London, v. 14, n. 3, p. 1-11, 2016. Article n. BMRJ.25314.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 5 |
| Biblioteca(s): Embrapa Meio Ambiente. |
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| 10. | | EICHOLZ, M. D.; ANTUNES, W. R.; SILVA, P. S. da; OLIVEIRA, R. J. P. de; SILVA, S. D. dos A. e. Caracterização do potencial produtivo de genótipos de tungue em Pelotas/RS. In: SIMPÓSIO ESTADUAL DE AGROENERGIA, 4.; REUNIÃO TÉCNICA DE AGROENERGIA, 4., 2012, AMRIGS: Porto Alegre. Anais... Pelotas: Embrapa Clima Temperado, 2012. Organizado por Sérgio Delmar dos Anjos e Silva Ivan Rodrigues de Almeida.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Clima Temperado. |
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| 11. | | ALMEIDA, A. de S.; RIBEIRO, W. R.; SILVA, R. M.; BARBOSA, E. T.; GERALDINE, A. M.; ALVES, T. M.; PINHEIRO, P. V.; LOBO JUNIOR, M. Diagnóstico de podridões radiculares do feijoeiro comum com sensor hiperespectral. In: CONGRESSO BRASILEIRO DE FITOPATOLOGIA, 53., 2023, Brasília, DF. Anais... Brasília, DF: Sociedade Brasileira de Fitopatologia, 2023. p. 137.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Arroz e Feijão. |
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| 12. | | MELO, I. S. de; SOUZA, W. R.; SILVA, L. da; SANTOS, S. N.; ASSALIN, M. R.; ZUCCHI, T. D.; QUEIROZ, S. C. do N. de. Isolation and characterization of a novel Pseudomonas sp. strain from Deschampsia antarctica as a potential biocontrol agent. In: INTERNATIONAL SYMPOSIUM ON MICROBIAL ECOLOGY, 15., 2014, Seoul. Proceedings... Wageningen: The International Society for Microbial Ecology (ISME), 2014. p. 139.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Meio Ambiente. |
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| 13. | | CHAVES, S. S. de F.; FERNANDES, P. C. C.; FREITAS, D. R. de; ALVES, L. W. R.; SILVA, A. V.; SILVEIRA FILHO, A.; VELOSO, C. A. C. Sistemas de integração lavoura-pecuária-floresta: meta-análise dos resultados no Brasil. In: CONGRESSO BRASILEIRO DE AGRONOMIA, 26., 2009, Gramado. Agricultura forte: alimento, energia e meio ambiente. Gramado: CONFAEAB: SARGS, 2009.| Tipo: Artigo em Anais de Congresso / Nota Técnica |
| Biblioteca(s): Embrapa Amazônia Oriental. |
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| 14. | | MACHACA-CALSIN, C. P.; W. R. SILVA; MÁRQUEZ, L. A. Y.; HELLER, E.; MATOSO, E. S.; TATTO, F. R.; MOCCELLIN, R.; SILVA, S. D. dos A. e; GOMES, C. B. Promoção de crescimento e biocontrole do nematoide das galhas (meloidogyne javanica) e das lesões (pratylenchus brachyurus) em cana-de-açúcar por rizobacterias. In: CONGRESSO BRASILEIRO DE NEMATOLOGIA, 36, 2019, Caldas Novas. Nematoides: da Ciência ao Campo. [Anais, palestras e resumos]. Campinas: Infobibos, 2019. Promotion growth and biocontrol of root-knot and root-lesion nematodes in sugarcane by rhizobacteria.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Clima Temperado. |
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| 15. | | CRATIVOL, C.; REGULSKI, M.; BERTALAN, M.; MCCOMBIE, W. R.; SILVA, F. R. da; ZERLOTINI NETO, A.; VICENTINI, R.; FARINELLI, L.; HEMERLY, A. S.; MARTIENSSEN, R. A.; FERREIRA, P. C. G. Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum. The Plant Journal, Oxford, v. 79, n. 1, p. 162-172, 2014.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| Registros recuperados : 15 | |
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