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| 9. | | LEITE, J. A.; DRUMOND, B. P.; TRINDADE, G. de S.; BONJARDIM, C. A.; FERREIRA, P. C. P.; KROON, E. G. Brazilian vaccinia virus strains show genetic polymorphism at the ati gene. Virus Genes, v. 35, n. 3, p. 531-539, 2007.| Biblioteca(s): Embrapa Gado de Leite. |
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| 10. | | BUSTAMANTE, P. G.; PÁDUA, V. L. M.; MAIA, V. H.; FRANÇA, L. M.; FERREIRA, P. C. G. Maize (Zea mays L.) dispersion and human migration in the South America: linking biological and archaeological foccus. In: SIMPOSIO DE RECURSOS GENÉTICOS PARA AMÉRICA LATINA Y EL CARIBE, SIRGEALC, 5., 2005, Montevideo, Uruguay. Resúmenes... Montevideo: Instituto Nacional de Investigación Agropecuaria: Universidad de la República, Facultad de Agronomía, 2005. p. 44.| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 11. | | MAIA, V. H.; MEGA, L. F.; PÁDUA, V. L. M.; BUSTAMANTE, P. G.; FERREIRA, P. C. G. A rota pré-colombiana de Peabiru e o estudo genético-evolutivo do milho (Zea mays mays l.): conciliando biologia e arqueologia. In: CONGRESSO BRASILEIRO DE GENÉTICA, 51., 2005, Águas de Lindóia, SP. A era da genômica: da bioestatística à bioinformática: anais. Ribeirão Preto, SP: Sociedade Brasileira de Genética, 2005. p. 645.| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 12. | | PACHECO, G.; CARDOSO, S. R. S.; GAGLIARDI, R. F.; VALLS, J. F. M.; FERREIRA, P. C. G.; CARDOSO, M. A.; MANSUR, E. Avaliação da estabilidade genética e epigenética de plantas in vitro de Arachis villosulicarpa Hoehne (leguminosae) obtidas por diferentes sistemas de regeneração. In: CONGRESSO BRASILEIRO DE FISIOLOGIA VEGETAL, 11., 2007, Gramado, RS. Fotossíntese: a essência da vida: [Resumos...]. Pelotas, RS: SBFV, 2007. Publicado também em: Brazilian Journal of Plant Physiology, v. 19, supl., 2007.| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 13. | | CAVALCANTE, J. J. V.; VARGAS, C.; NOGUEIRA, E. M.; VINAGRE, F.; SCHWARCZ, K.; BALDANI, J. I.; FERREIRA, P. C. G.; HEMERLY, A. S. Members of the ethylene signalling pathway are regulated in sugarcane during the association with nitrogen-fixing endophytic bacteria. Journal of Experimental Botany, Oxford, v. 58, n. 3, p. 673-686, feb. 2007.| Biblioteca(s): Embrapa Agrobiologia. |
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| 14. | | BASSO, M. F.; FERREIRA, P. C. G.; KOBAYASHI, A. K.; HARMON, F. G.; NEPOMUCENO, A. L.; MOLINARI, H. B. C.; GROSSI-DE-SA, M. F. MicroRNAs and new biotechnological tools for its modulation and improving stress tolerance in plants. Plant Biotechnology Journal, v. 17, p. 1482-1500, 2019.| Biblioteca(s): Embrapa Agroenergia; Embrapa Recursos Genéticos e Biotecnologia; Embrapa Soja. |
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| 15. | | VILAR, C. V.; COSTA LIMA, M. A.; REIS, V. M.; OLIVARES, F. L.; BALDANI, J. I.; FERREIRA, P. C. G.; HEMERLY, A. S. Molecular analysis of a sugarcane (Saccharum officinarum L.) gene induced by endophytic nitrogen-fixing bacteria. In: REUNIAO ANUAL DA SOCIEDADE BRASILEIRA DE BIOQUIMICA E BIOLOGIA MOLECULAR, 25., maio 1996, Caxambu. Resumos... Caxambu: Sociedade Brasileira de Bioquimica e Biologia Molecular, 1996. p.42. Resumo E-75.| Biblioteca(s): Embrapa Agrobiologia. |
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| 17. | | MARCARENHAS, M. H. T.; LARA, J. F. R.; KARAM, D.; ARAUJO, S. G. A.; FERREIRA, P. C.; FREIRE, F. M.; VIANA, M. C. M.; PEDROSA, M. W. Nabo forrageiro: seletividade de herbicidas para produção de agroenergia. In: CONGRESSO BRASILEIRO DA CIÊNCIA DAS PLANTAS DANINHAS, 27., 2010, Ribeirão Preto. Responsabilidade social e ambiental no manejo de plantas daninhas: [anais]. Ribeirão Preto: SBCPD, 2010. 1 CD-ROM.| Biblioteca(s): Embrapa Milho e Sorgo. |
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| 18. | | CURSINO, A. E.; VILELA, A. P. P.; OLIVEIRA, D. B.; FERREIRA, P. C. P.; LIMA, M. F. N. T. de; LIMA, J. P. A.; KROON, E. G. Detecção e caracterização molecular do Equine Infectious Anemia virus em amostras de cavalos provenientes do pantanal brasileiro. In: SIMPÓSIO DE MICROBIOLOGIA DA UFMS, 2., 2015, Belo horizonte. Caderno de resumos... Belo Horizonte: [s.n.], 2015. p. 36.| Biblioteca(s): Embrapa Pantanal. |
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| 19. | | COSTA LIMA, M. A.; VILAR, C. V.; REIS, V. M.; OLIVARES, F. L.; BALDANI, J. I.; FERREIRA, P. C. G.; HEMERLY, A. S. Detection of sugarcane (Saccharum officinarum L.) genes induced by endophytic nitrogen-fixing bacteria. In: REUNIAO ANUAL DA SOCIEDADE BRASILEIRA DE BIOQUIMICA E BIOLOGIA MOLECULAR, 25., maio 1996, Caxambu. Resumos... Caxambu: Sociedade Brasileira de Bioquimica e Biologia Molecular, 1996. p.42. Resumo E-74.| Biblioteca(s): Embrapa Agrobiologia. |
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| Registros recuperados : 41 | |
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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. |
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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Circulação/Nível: |
A - 1 |
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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
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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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