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Registro Completo |
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Biblioteca(s): |
Embrapa Agricultura Digital. |
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Data corrente: |
09/01/2020 |
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Data da última atualização: |
09/01/2020 |
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Tipo da produção científica: |
Resumo em Anais de Congresso |
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Autoria: |
CAETANO, A. R.; IANELLA, P.; VARELA, E. S.; PAIVA, S. R.; LOBO, F. P.; CINTRA, L. C.; ZERLOTINI NETO, A.; YAMAGISHI, M. E. B. |
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Afiliação: |
ALEXANDRE RODRIGUES CAETANO, Cenargen; PATRICIA IANELLA, Cenargen; EDUARDO SOUSA VARELA, CNPASA; SAMUEL REZENDE PAIVA, Cenargen; FRANCISCO PEREIRA LOBO; LEANDRO CARRIJO CINTRA, CNPTIA; ADHEMAR ZERLOTINI NETO, CNPTIA; MICHEL EDUARDO BELEZA YAMAGISHI, CNPTIA. |
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Título: |
Genome sequencing and de novo assembly of tambaqui (Colossoma macropomum). |
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Ano de publicação: |
2019 |
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Fonte/Imprenta: |
In: AQUACULTURE, 2019, New Orleans. Aquaculture: the big choice! abstracts. [S.l.: s.n.], 2019. |
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Páginas: |
p. 182. |
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Idioma: |
Inglês |
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Conteúdo: |
The South American freshwater fish Tambaqui (Colossoma macropomum) is the most important native aquaculture species in Brazil. Current production levels are above 150,000 mt per year. Recent efforts to domesticate, breed and raise the species in aquaculture systems has led to significant increases in production (>10-fold) over the last decade, and development of new technologies based on genomic tools and information could help further increase productivity and production growth rates. A Tambaqui genome assembly was generated with data produced from shotgun libraries from two different insert sizes and matepair libraries with four different sizes sequenced (2x150bps) with a HiSeq2000 platform. A total of 124.8Gbp quality-filtered nucleotides were sequenced which amount to 85x mean genome coverage, considering previously published information (C-value = 1.5pg = 1.467Gbp). Initial sequence assembly was performed with SOAPdenovo and generated 8.920 scaffolds spanning 1.54 Gbps (N50 scaffold length: 2,041kb, L50 scaffold count: 162). Gene model predictions with MAKER2 using as extrinsic evidence protein and EST data from phylogenetically related taxa found 23,632 genes, ~20,000 shared with A. mexicanus. CEGMA analysis (prior to gap filling) detected 85% core genes completely assembled and 9% partially assembled. Tambaqui assembly scaffolds ordering and orientation was carried out using ALLMAPS software based on the available linkage map (LM) (Nunes et al. 2017). A total of 1440 scaffolds were placed in the map with 27 linkage groups (n=x=27), totaling 1,508,696,562bp and 94% (6,788) of all mapped markers, with an average of 4.7 markers per megabase. Of the 6,788 mapped markers, ~93% were anchored, 84.9% in concordance with marker orientation, and 7.1% markers were unplaced. Obtained results reveal a high-quality NGS de novo Tambaqui genome assemble, providing a valuable tool for future genomic studies and the use of genomic tools for broodstock management and assisted genetic evaluations and breeding. MenosThe South American freshwater fish Tambaqui (Colossoma macropomum) is the most important native aquaculture species in Brazil. Current production levels are above 150,000 mt per year. Recent efforts to domesticate, breed and raise the species in aquaculture systems has led to significant increases in production (>10-fold) over the last decade, and development of new technologies based on genomic tools and information could help further increase productivity and production growth rates. A Tambaqui genome assembly was generated with data produced from shotgun libraries from two different insert sizes and matepair libraries with four different sizes sequenced (2x150bps) with a HiSeq2000 platform. A total of 124.8Gbp quality-filtered nucleotides were sequenced which amount to 85x mean genome coverage, considering previously published information (C-value = 1.5pg = 1.467Gbp). Initial sequence assembly was performed with SOAPdenovo and generated 8.920 scaffolds spanning 1.54 Gbps (N50 scaffold length: 2,041kb, L50 scaffold count: 162). Gene model predictions with MAKER2 using as extrinsic evidence protein and EST data from phylogenetically related taxa found 23,632 genes, ~20,000 shared with A. mexicanus. CEGMA analysis (prior to gap filling) detected 85% core genes completely assembled and 9% partially assembled. Tambaqui assembly scaffolds ordering and orientation was carried out using ALLMAPS software based on the available linkage map (LM) (Nunes et al. 2017). A total of 1440 ... Mostrar Tudo |
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Palavras-Chave: |
Bioinformática. |
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Thesagro: |
Colossoma Macropomum; Tambaqui. |
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Thesaurus Nal: |
Bioinformatics; Genome assembly. |
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Categoria do assunto: |
-- |
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Marc: |
LEADER 02826nam a2200265 a 4500
001 2118464
005 2020-01-09
008 2019 bl uuuu u01u1 u #d
100 1 $aCAETANO, A. R.
245 $aGenome sequencing and de novo assembly of tambaqui (Colossoma macropomum).$h[electronic resource]
260 $aIn: AQUACULTURE, 2019, New Orleans. Aquaculture: the big choice! abstracts. [S.l.: s.n.]$c2019
300 $ap. 182.
520 $aThe South American freshwater fish Tambaqui (Colossoma macropomum) is the most important native aquaculture species in Brazil. Current production levels are above 150,000 mt per year. Recent efforts to domesticate, breed and raise the species in aquaculture systems has led to significant increases in production (>10-fold) over the last decade, and development of new technologies based on genomic tools and information could help further increase productivity and production growth rates. A Tambaqui genome assembly was generated with data produced from shotgun libraries from two different insert sizes and matepair libraries with four different sizes sequenced (2x150bps) with a HiSeq2000 platform. A total of 124.8Gbp quality-filtered nucleotides were sequenced which amount to 85x mean genome coverage, considering previously published information (C-value = 1.5pg = 1.467Gbp). Initial sequence assembly was performed with SOAPdenovo and generated 8.920 scaffolds spanning 1.54 Gbps (N50 scaffold length: 2,041kb, L50 scaffold count: 162). Gene model predictions with MAKER2 using as extrinsic evidence protein and EST data from phylogenetically related taxa found 23,632 genes, ~20,000 shared with A. mexicanus. CEGMA analysis (prior to gap filling) detected 85% core genes completely assembled and 9% partially assembled. Tambaqui assembly scaffolds ordering and orientation was carried out using ALLMAPS software based on the available linkage map (LM) (Nunes et al. 2017). A total of 1440 scaffolds were placed in the map with 27 linkage groups (n=x=27), totaling 1,508,696,562bp and 94% (6,788) of all mapped markers, with an average of 4.7 markers per megabase. Of the 6,788 mapped markers, ~93% were anchored, 84.9% in concordance with marker orientation, and 7.1% markers were unplaced. Obtained results reveal a high-quality NGS de novo Tambaqui genome assemble, providing a valuable tool for future genomic studies and the use of genomic tools for broodstock management and assisted genetic evaluations and breeding.
650 $aBioinformatics
650 $aGenome assembly
650 $aColossoma Macropomum
650 $aTambaqui
653 $aBioinformática
700 1 $aIANELLA, P.
700 1 $aVARELA, E. S.
700 1 $aPAIVA, S. R.
700 1 $aLOBO, F. P.
700 1 $aCINTRA, L. C.
700 1 $aZERLOTINI NETO, A.
700 1 $aYAMAGISHI, M. E. B.
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Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
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| Registros recuperados : 17 | |
| 3. |  | BORGHI, E.; INAMASU, R. Y.; AVANZI, J. C.; LUCHIARI JUNIOR, A.; BORTOLON, L.; BORTOLON, E. S. O. Avaliação do padrão tecnológico e tendências da Agricultura de Precisão - Safra 2011/12. In: BERNARDI, A. C. de C.; NAIME, J. de M.; RESENDE, A. V. de; BASSOI, L. H.; INAMASU, R. Y. (Ed.). Agricultura de precisão: resultados de um novo olhar. Brasília, DF: Embrapa, 2014. p. 578-584.| Tipo: Capítulo em Livro Técnico-Científico |
| Biblioteca(s): Embrapa Instrumentação. |
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| 6. | | MELO, P. R. de; ROSINHA, G. M. S.; SANCHES, S. C.; GOMES, J. S; GALVÃO, C. E.; SOARES, C. O. Caracterização de amostras de Corynebacterium pseudotuberculosis isoladas de ovinos e caprinos. In: JORNADA CIENTÍFICA EMBRAPA GADO DE CORTE, 8., 2012, Campo Grande, MS. [Anais da..]. Campo Grande, MS: Embrapa Gado de Corte, 2012. 2 p. (Embrapa Gado de Corte. Documentos, 198).| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Gado de Corte. |
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| 9. | | BARROS, M. E. S.; LIMA, A. C.; ROCHA, L. S.; QUEIROGA, V. de P.; GIRAO, E. G.; VASCONCELOS, H. E. M.; ALMEIDA, F. DE A. C.; ARAUJO, I. M. da S. Extração do óleo de pequi e aproveitamento agroindustrial e energético. In: QUEIROGA, V. de P. (Org.). Pequizeiro: extrativismo na Chapada do Araripe. Campina Grande: AREPB, 2016. Cap. 2, p. 143-180.| Tipo: Capítulo em Livro Técnico-Científico |
| Biblioteca(s): Embrapa Agroindústria Tropical. |
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| 17. | | OLIVEIRA, R. O.; CHAGAS, P. C.; MOURA, E. A.; ALVES, J. M. A.; COUTINHO, O. L.; GRIGIO, M. L.; CHAGAS, E. A. Maturação e caracterização física e físico-química de frutos de Ata nas condições de Cerrado de Roraima. In: CONGRESSO BRASILEIRO DE PROCESSAMENTO MÍNIMO E PÓS COLHEITA DE FRUTAS, FLORES E HORTALIÇAS, 1.; SIMPÓSIO BRASILEIRO DE PÓS-COLHEITA, FRUTAS, HORTALIÇAS E FLORES, 5.; ENCONTRO NACIONAL SOBRE PROCESSAMENTO MÍNIMO DE FRUTAS E HORTALIÇAS, 8., 2015, Sergipe. Avanço na conservação e qualidade de frutas, flores e hortaliças: [anais]. Aracaju : Universidade Federal de Sergipe, 2015.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Roraima. |
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| Registros recuperados : 17 | |
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