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Registro Completo |
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Biblioteca(s): |
Embrapa Agricultura Digital; Embrapa Gado de Corte. |
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Data corrente: |
02/01/2014 |
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Data da última atualização: |
22/01/2020 |
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Tipo da produção científica: |
Resumo em Anais de Congresso |
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Autoria: |
CINTRA, L. C.; ZERLOTINI, A.; LOBO, F. P.; SILVA, F. R. da; GIACHETTO, P. F.; KUSER-FALCÃO, P. R.; SILVA, L. O. C. da; EGITO, A. A. do; SIQUEIRA, F.; SILVA, N. M. A. da; PAIVA, S. R.; YAMAGISHI, M. E. B.; CAETANO, A. R. |
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Afiliação: |
LEANDRO CARRIJO CINTRA, CNPTIA; ADHEMAR ZERLOTINI NETO, CNPTIA; FRANCISCO PEREIRA LOBO, CNPTIA; FELIPE RODRIGUES DA SILVA, CNPTIA; POLIANA FERNANDA GIACHETTO, CNPTIA; PAULA REGINA KUSER FALCAO, CNPTIA; LUIZ OTAVIO CAMPOS DA SILVA, CNPGC; ANDREA ALVES DO EGITO, CNPGC; FABIANE SIQUEIRA, CNPGC; NAIARA MILAGRES AUGUSTO DA SILVA, CENARGEN; SAMUEL REZENDE PAIVA, Cenargen; MICHEL EDUARDO BELEZA YAMAGISHI, CNPTIA; ALEXANDRE RODRIGUES CAETANO, CENARGEN. |
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Título: |
Sequencing and de novo genome assembly of a nelore (Bos indicus) bull. |
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Ano de publicação: |
2013 |
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Fonte/Imprenta: |
In: INTERNATIONAL PLANT & ANIMAL GENOME, 21., 2013, San Diego. [Abstracts...]. [S.l.: s.n.], 2013. |
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Páginas: |
Não paginado. |
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Idioma: |
Inglês
Português |
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Notas: |
Pôster 0522. |
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Conteúdo: |
Bos indicus cattle breeds have been extensively used for dairy and beef production in tropical climates and present several natural adaptations to biotic and abiotic stresses found in these regions of the world. As breeder associations stride towards incorporating genomic tools into ongoing genetic evaluations and breeding programs to improve productivity and beef and milk quality traits, a (B. indicus) genome assembly represents an essential tool which will be vital to help identify and understand the underlying genetic variations that distinguish taurine and indicine cattle, which have diverged >250,000 years ago. DNA obtained from semen from a Nelore bull born in 1987, with an estimated cumulative inbreeding coefficient of 29.4%, and that can be traced to animals imported from India, was used to produce 100bp paired-end sequences from short (300 and 700bp) and long insert (3, 5 and 10 kbp) libraries, with an Illumina HiSeq platform. A total of 120Gbp were sequenced, corresponding to 45x raw coverage of the genome. The SOAP de novo assembler was used to build contigs and scaffolding. Several parameters sets were evaluated to obtain the best assembly based on the number of scaffolds, number of bases in scaffolds, N50, and total gap length. The best assembly obtained so far contains 2.7Gbp, 15,103 scaffolds with N50 of 649Kbp, and 756Mbp of gaps. Current results are being used to target additional sequencing of specific libraries to improve scaffold assembly. In addition, different sequencing technologies are also under evaluation for generating additional data to improve sequence assembly quality before comparisons with the reference (B. taurus) sequence are performed. MenosBos indicus cattle breeds have been extensively used for dairy and beef production in tropical climates and present several natural adaptations to biotic and abiotic stresses found in these regions of the world. As breeder associations stride towards incorporating genomic tools into ongoing genetic evaluations and breeding programs to improve productivity and beef and milk quality traits, a (B. indicus) genome assembly represents an essential tool which will be vital to help identify and understand the underlying genetic variations that distinguish taurine and indicine cattle, which have diverged >250,000 years ago. DNA obtained from semen from a Nelore bull born in 1987, with an estimated cumulative inbreeding coefficient of 29.4%, and that can be traced to animals imported from India, was used to produce 100bp paired-end sequences from short (300 and 700bp) and long insert (3, 5 and 10 kbp) libraries, with an Illumina HiSeq platform. A total of 120Gbp were sequenced, corresponding to 45x raw coverage of the genome. The SOAP de novo assembler was used to build contigs and scaffolding. Several parameters sets were evaluated to obtain the best assembly based on the number of scaffolds, number of bases in scaffolds, N50, and total gap length. The best assembly obtained so far contains 2.7Gbp, 15,103 scaffolds with N50 of 649Kbp, and 756Mbp of gaps. Current results are being used to target additional sequencing of specific libraries to improve scaffold assembly. In addition, di... Mostrar Tudo |
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Palavras-Chave: |
Bioinformática; Sequenciamento de genoma. |
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Thesagro: |
Bos indicus. |
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Thesaurus Nal: |
bioinformatics; genome assembly; Nellore. |
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Categoria do assunto: |
--
X Pesquisa, Tecnologia e Engenharia |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/94595/1/P0522.odt
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Marc: |
LEADER 02729nam a2200349 a 4500
001 1974758
005 2020-01-22
008 2013 bl uuuu u00u1 u #d
100 1 $aCINTRA, L. C.
245 $aSequencing and de novo genome assembly of a nelore (Bos indicus) bull.$h[electronic resource]
260 $aIn: INTERNATIONAL PLANT & ANIMAL GENOME, 21., 2013, San Diego. [Abstracts...]. [S.l.: s.n.]$c2013
300 $aNão paginado.
500 $aPôster 0522.
520 $aBos indicus cattle breeds have been extensively used for dairy and beef production in tropical climates and present several natural adaptations to biotic and abiotic stresses found in these regions of the world. As breeder associations stride towards incorporating genomic tools into ongoing genetic evaluations and breeding programs to improve productivity and beef and milk quality traits, a (B. indicus) genome assembly represents an essential tool which will be vital to help identify and understand the underlying genetic variations that distinguish taurine and indicine cattle, which have diverged >250,000 years ago. DNA obtained from semen from a Nelore bull born in 1987, with an estimated cumulative inbreeding coefficient of 29.4%, and that can be traced to animals imported from India, was used to produce 100bp paired-end sequences from short (300 and 700bp) and long insert (3, 5 and 10 kbp) libraries, with an Illumina HiSeq platform. A total of 120Gbp were sequenced, corresponding to 45x raw coverage of the genome. The SOAP de novo assembler was used to build contigs and scaffolding. Several parameters sets were evaluated to obtain the best assembly based on the number of scaffolds, number of bases in scaffolds, N50, and total gap length. The best assembly obtained so far contains 2.7Gbp, 15,103 scaffolds with N50 of 649Kbp, and 756Mbp of gaps. Current results are being used to target additional sequencing of specific libraries to improve scaffold assembly. In addition, different sequencing technologies are also under evaluation for generating additional data to improve sequence assembly quality before comparisons with the reference (B. taurus) sequence are performed.
650 $abioinformatics
650 $agenome assembly
650 $aNellore
650 $aBos indicus
653 $aBioinformática
653 $aSequenciamento de genoma
700 1 $aZERLOTINI, A.
700 1 $aLOBO, F. P.
700 1 $aSILVA, F. R. da
700 1 $aGIACHETTO, P. F.
700 1 $aKUSER-FALCÃO, P. R.
700 1 $aSILVA, L. O. C. da
700 1 $aEGITO, A. A. do
700 1 $aSIQUEIRA, F.
700 1 $aSILVA, N. M. A. da
700 1 $aPAIVA, S. R.
700 1 $aYAMAGISHI, M. E. B.
700 1 $aCAETANO, A. R.
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Esconder MarcMostrar Marc Completo |
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Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
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Biblioteca |
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| Registros recuperados : 41 | |
| 1. |  | CINTRA, L. C. Computational investigations in eukaryotes genome de novo assembly using short reads. In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 7.; INTERNATIONAL CONFERENCE OF THE IBEROAMERICAN SOCIETY FOR BIOINFORMATICS, 3., 2011, Florianópolis. Proceedings... Florianópolis: Associação Brasileira de Bioinformática e Biologia Computacional, 2011. Não paginado. X-MEETING 2011.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 9. | | CINTRA, L. C.; NAKAI, A. M.; CORREA, J. L. Métodos, procedimentos e técnicas utilizadas na construção de AgroTIC. In: MASSRUHÁ, S. M. F. S.; LEITE, M. A. de A.; LUCHIARI JUNIOR, A.; ROMANI, L. A. S. (Ed.). Tecnologias da informação e comunicação e suas relações com a agricultura. Brasília, DF: Embrapa, 2014. Cap. 15. p. 293-301.| Tipo: Capítulo em Livro Técnico-Científico |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 10. | | CINTRA, L. C.; NAKAI, A. M.; CORREA, J. L. Methods, procedures and techniques used in constructing AgroICT. In: MASSRUHÁ, S. M. F. S.; LEITE, M. A. de A.; LUCHIARI JUNIOR, A.; ROMANI, L. A. S. (Ed.). Information and communication technologies and their relations with agriculture. Brasília, DF: Embrapa, 2016. ch. 15, p. 287-294.| Tipo: Capítulo em Livro Técnico-Científico |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 12. | | HONGO, J. A.; CASTRO, G. M. de; CINTRA, L. C.; ZERLOTINI, A.; LOBO, F. P. POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes. BMC Genomics, London, v. 16, n. 1, 567, Aug. 2015.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 14. | | FELTRIM, D.; GUPTA, B.; GUNDIMEDA, S.; KIYOTA, E.; DOMINGUES JÚNIOR, A. P.; CINTRA, L. C.; MAZZAFERA, P. Exposure of Eucalyptus to varied temperature and CO2 has a profound effect on the physiology and expression of genes related to cell wall formation and remodeling. Tree Genetics & Genomes v. 18, n. 1, 3, Feb. 2022.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Agricultura Digital. |
|  |
| 16. | | ZERLOTINI NETO, A.; NHANI JÚNIOR, A.; VIEIRA, F. D.; CINTRA, L. C.; MUDADU, M. de A.; FALCÃO, P. R. K.; GIACHETTO, P. F. Aplicações da bioinformática na agricultura. In: MASSRUHÁ, S. M. F. S.; LEITE, M. A. de A.; OLIVEIRA, S. R. de M.; MEIRA, C. A. A.; LUCHIARI JUNIOR, A.; BOLFE, E. L. (Ed.). Agricultura digital: pesquisa, desenvolvimento e inovação nas cadeias produtivas. Brasília, DF: Embrapa, 2020. cap. 10, p. 234-257.| Tipo: Capítulo em Livro Técnico-Científico |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 17. | | ZERLOTINI NETO, A.; NHANI JÚNIOR, A.; VIEIRA, F. D.; CINTRA, L. C.; MUDADU, M. de A.; FALCÃO, P. R. K.; GIACHETTO, P. F. Applications of bioinformatics in agriculture. In: MASSRUHÁ, S. M. F. S.; LEITE, M. A. de A.; OLIVEIRA, S. R. de M.; MEIRA, C. A. A.; LUCHIARI JUNIOR, A.; BOLFE, E. L. (ed.). Digital agriculture: research, development and innovation in production chains. Brasília, DF: Embrapa, 2023. cap. 10, p. 179-194.| Tipo: Capítulo em Livro Técnico-Científico |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 18. | | GUIMARÃES, P. S.; SCHENK, J. C. M.; CINTRA, L. C.; GIACHETTO, P. F.; SILVAROLLA, M. B.; PADILHA, L.; MALUF, M. P. Large-scale prospection of genes on caffeine-free Coffea arabica plants - discovery of novel markers associated with development and secondary metabolism. Plant Gene, v. 27, p. 1-9, Sept. 2021. Article 100314.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 3 |
| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Café. |
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| 19. | | 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. Genome Sequencing and de novo assembly of the South American Tiger Catfish (Pseudoplatystoma punctifer). In: PLANT & ANIMAL GENOME CONFERENCE, 24., 2016, San Diego, CA. [Abstracts...]. San Diego: [s. n.], 2016. Não paginado. PAG 2016. Pôster P0481.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 20. | | 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. Genome sequencing and de novo assembly of the South American Tiger Catfish (Pseudoplatystoma punctifer). In: PLANT & ANIMAL GENOME CONFERENCE, 24., 2016, San Diego, CA. [Abstracts...]. San Diego: [s. n.], 2016. Não paginado. PAG 2016. Pôster P0481.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Pesca e Aquicultura. |
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| Registros recuperados : 41 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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