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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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 | Acesso ao texto completo restrito à biblioteca da Embrapa Pantanal. Para informações adicionais entre em contato com cpap.biblioteca@embrapa.br. |
Registro Completo
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Biblioteca(s): |
Embrapa Pantanal. |
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Data corrente: |
06/12/2021 |
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Data da última atualização: |
06/12/2021 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
DAMASCENO JUNIOR, G. A.; ROQUE, F. de O.; GARCIA, L. C.; RIBEIRO, D. B.; TOMAS, W. M.; DIAS, E. S.; DIAS, F. A.; LIBONATI, R.; RODRIGUES, J. A.; SANTOS, F. L. M.; PEREIRA, A. de M. M.; SOUZA, E. B. de; REIS, L. K.; OLIVEIRA, M. da R.; SOUZA, A. H. de A.; PINEDA, D. A. M.; FERREIRA, B. H. dos S.; BORTOLOTTO, I. M.; POTT, A. |
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Afiliação: |
GERALDO ALVES DAMASCENO JUNIOR, Universidade Federal de Mato Grosso do Sul; FABIO DE OLIVEIRA ROQUE, Universidade Federal de Mato Grosso do Sul; LETÍCIA COUTO GARCIA, Universidade Federal de Mato Grosso do Sul; DANILO BANDINI RIBEIRO, Universidade Federal de Mato Grosso do Sul; WALFRIDO MORAES TOMAS, CPAP; EDNA SCREMIN DIAS, Universidade Federal de Mato Grosso do Sul; FELIPE AUGUSTO DIAS, SOS Pantanal; RENATA LIBONATI, Laboratory for Environmental Satellite Applications - LASA; JULIA ABRANTES RODRIGUES, Universidade Federal do Rio de Janeiro; FILLIPE LEMOS MAIA SANTOS, Laboratory for Environmental Satellite Applications - LASA; ALEXANDRE DE MATOS MARTINS PEREIRA, Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis - IBAMA; EVALDO BENEDITO DE SOUZA, Universidade Federal de Mato Grosso do Sul; LETÍCIA KOUTCHIN REIS, Universidade Federal de Mato Grosso do Sul; MAXWELL DA ROSA OLIVEIRA, Universidade Federal de Mato Grosso do Sul; ALLAN HENRIQUE DE ALMEIDA SOUZA, Universidade Federal de Mato Grosso do Sul; DANIEL ARMANDO MANRIQUE PINEDA, Universidade Federal de Mato Grosso do Sul; BRUNO HENRIQUE DOS SANTOS FERREIRA, Universidade Federal de Mato Grosso do Sul; IEDA MARIA BORTOLOTTO, Universidade Federal de Mato Grosso do Sul; ARNILDO POTT, Universidade Federal de Mato Grosso do Sul. |
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Título: |
Lessons to be learned from the wildfire catastrophe of 2020 in the Pantanal wetland. |
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Ano de publicação: |
2021 |
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Fonte/Imprenta: |
Wetland Science & Practice, v. 38, n. 2, p. 107-115, april 2021. |
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Idioma: |
Português |
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Conteúdo: |
ABSTRACT: South America's Pantanal is recognized as one of the largest wetlands in the world and a UNESCO World Heritage Site for its ecological significance (high biodiversity). The region experiences both seasonal wet/dry periods and pluriannual cycles of wet and dry years. Vegetation changes throughout the year as well as over the long-term with fires and floods being the major factors affecting vegetation patterns. In 2020 the Pantanal experienced an extraordinary high numbers of wildfires. An overview of the region's fire history is presented along with information on the 2020 wildfires, society's response, lessons learned, and suggestions on where to go from here. |
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Thesagro: |
Fogo Selvagem; Incêndio Florestal. |
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Thesaurus NAL: |
Fire ecology; Wildfires. |
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Categoria do assunto: |
P Recursos Naturais, Ciências Ambientais e da Terra |
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Marc: |
LEADER 01775naa a2200385 a 4500
001 2137149
005 2021-12-06
008 2021 bl uuuu u00u1 u #d
100 1 $aDAMASCENO JUNIOR, G. A.
245 $aLessons to be learned from the wildfire catastrophe of 2020 in the Pantanal wetland.$h[electronic resource]
260 $c2021
520 $aABSTRACT: South America's Pantanal is recognized as one of the largest wetlands in the world and a UNESCO World Heritage Site for its ecological significance (high biodiversity). The region experiences both seasonal wet/dry periods and pluriannual cycles of wet and dry years. Vegetation changes throughout the year as well as over the long-term with fires and floods being the major factors affecting vegetation patterns. In 2020 the Pantanal experienced an extraordinary high numbers of wildfires. An overview of the region's fire history is presented along with information on the 2020 wildfires, society's response, lessons learned, and suggestions on where to go from here.
650 $aFire ecology
650 $aWildfires
650 $aFogo Selvagem
650 $aIncêndio Florestal
700 1 $aROQUE, F. de O.
700 1 $aGARCIA, L. C.
700 1 $aRIBEIRO, D. B.
700 1 $aTOMAS, W. M.
700 1 $aDIAS, E. S.
700 1 $aDIAS, F. A.
700 1 $aLIBONATI, R.
700 1 $aRODRIGUES, J. A.
700 1 $aSANTOS, F. L. M.
700 1 $aPEREIRA, A. de M. M.
700 1 $aSOUZA, E. B. de
700 1 $aREIS, L. K.
700 1 $aOLIVEIRA, M. da R.
700 1 $aSOUZA, A. H. de A.
700 1 $aPINEDA, D. A. M.
700 1 $aFERREIRA, B. H. dos S.
700 1 $aBORTOLOTTO, I. M.
700 1 $aPOTT, A.
773 $tWetland Science & Practice$gv. 38, n. 2, p. 107-115, april 2021.
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Embrapa Pantanal (CPAP) |
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