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Registro Completo |
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Biblioteca(s): |
Embrapa Recursos Genéticos e Biotecnologia. |
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Data corrente: |
13/12/2018 |
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Data da última atualização: |
23/06/2022 |
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Tipo da produção científica: |
Resumo em Anais de Congresso |
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Autoria: |
PESSOA FILHO, M. A. C. de P.; SOUZA SOBRINHO, F. de; FRAGOSO, R. da R.; SILVA JUNIOR, O. B. da; FERREIRA, M. E. |
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Afiliação: |
MARCO AURELIO CALDAS DE PINHO PESSO, CPAC; FAUSTO DE SOUZA SOBRINHO, CNPGL; RODRIGO DA ROCHA FRAGOSO, CPAC; ORZENIL BONFIM DA SILVA JUNIOR, Cenargen; MARCIO ELIAS FERREIRA, SIRE. |
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Título: |
A draft genome assembly for the forage grass Urochloa ruziziensis based on single-molecule real-time sequencing. |
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Ano de publicação: |
2018 |
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Fonte/Imprenta: |
In: BRAZILIAN BIOTECHNOLOGY CONGRESS, 7.; BIOTECHNOLOGY IBERO-AMERICAN CONGRESS, 2., 2018, Brasília, DF. Proceedings... Brasília, DF: SBBiotec, 2018. |
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Idioma: |
Inglês |
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Conteúdo: |
ABSTRACT: Ruzigrass (Urochloa ruziziensis) is a diploid, tropical forage grass native to Africa, widely planted in Brazil, and known for its high nutritional quality. It is closely related to other important forage species of Urochloa, playing a crucial role in the breeding program of brachiaria grasses, which is mostly focused on inter-specific hybrids. Previous studies from our group based on shallow Illumina sequencing resulted in the development of the first molecular markers for the species, as well as in assessments of germplasm diversity and structure. Assembly and analysis of complete plastid genomes for four Urochloa species allowed the characterization of their phylogenetic divergence. Here, we strengthen the set of genomic tools for tropical forage grasses by assembling long reads into a first draft for the nuclear genome of the heterozygous clone C69. We used PacBio Sequel to generate over 13.3 million raw reads (mean size 6.5 kbp), adding up to 87.5 Gbp of raw data (~142x coverage). The current assembly using FALCON contains ~1.02 Gbp in 7,628 primary contigs, with NG50 of 412 kbp. It covers almost twice the size of the estimated haploid genome size of 615 Mbp for ruzigrass, indicating that haplotypes were assembled separately. In addition, RNA-seq data was obtained, totaling 258 million reads and 26 Gbp of raw data. These will allow transcriptome characterization for different tissues and aid gene prediction and annotation. Ongoing research includes haplotype phasing, polishing, assembly curation and Hi-C scaffolding. A high-quality genome assembly for ruzigrass will aid research groups in the development and application of genomic tools in breeding and genetics of brachiaria grasses. MenosABSTRACT: Ruzigrass (Urochloa ruziziensis) is a diploid, tropical forage grass native to Africa, widely planted in Brazil, and known for its high nutritional quality. It is closely related to other important forage species of Urochloa, playing a crucial role in the breeding program of brachiaria grasses, which is mostly focused on inter-specific hybrids. Previous studies from our group based on shallow Illumina sequencing resulted in the development of the first molecular markers for the species, as well as in assessments of germplasm diversity and structure. Assembly and analysis of complete plastid genomes for four Urochloa species allowed the characterization of their phylogenetic divergence. Here, we strengthen the set of genomic tools for tropical forage grasses by assembling long reads into a first draft for the nuclear genome of the heterozygous clone C69. We used PacBio Sequel to generate over 13.3 million raw reads (mean size 6.5 kbp), adding up to 87.5 Gbp of raw data (~142x coverage). The current assembly using FALCON contains ~1.02 Gbp in 7,628 primary contigs, with NG50 of 412 kbp. It covers almost twice the size of the estimated haploid genome size of 615 Mbp for ruzigrass, indicating that haplotypes were assembled separately. In addition, RNA-seq data was obtained, totaling 258 million reads and 26 Gbp of raw data. These will allow transcriptome characterization for different tissues and aid gene prediction and annotation. Ongoing research includes haplotype p... Mostrar Tudo |
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Palavras-Chave: |
Bioinformática; De novo Assembly; Montagem de sequência de DNA. |
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Thesagro: |
Brachiaria Ruziziensis; Genoma; Pastagem. |
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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/186953/1/920-apagar.pdf
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Marc: |
LEADER 02571nam a2200229 a 4500
001 2101425
005 2022-06-23
008 2018 bl uuuu u01u1 u #d
100 1 $aPESSOA FILHO, M. A. C. de P.
245 $aA draft genome assembly for the forage grass Urochloa ruziziensis based on single-molecule real-time sequencing.$h[electronic resource]
260 $aIn: BRAZILIAN BIOTECHNOLOGY CONGRESS, 7.; BIOTECHNOLOGY IBERO-AMERICAN CONGRESS, 2., 2018, Brasília, DF. Proceedings... Brasília, DF: SBBiotec$c2018
520 $aABSTRACT: Ruzigrass (Urochloa ruziziensis) is a diploid, tropical forage grass native to Africa, widely planted in Brazil, and known for its high nutritional quality. It is closely related to other important forage species of Urochloa, playing a crucial role in the breeding program of brachiaria grasses, which is mostly focused on inter-specific hybrids. Previous studies from our group based on shallow Illumina sequencing resulted in the development of the first molecular markers for the species, as well as in assessments of germplasm diversity and structure. Assembly and analysis of complete plastid genomes for four Urochloa species allowed the characterization of their phylogenetic divergence. Here, we strengthen the set of genomic tools for tropical forage grasses by assembling long reads into a first draft for the nuclear genome of the heterozygous clone C69. We used PacBio Sequel to generate over 13.3 million raw reads (mean size 6.5 kbp), adding up to 87.5 Gbp of raw data (~142x coverage). The current assembly using FALCON contains ~1.02 Gbp in 7,628 primary contigs, with NG50 of 412 kbp. It covers almost twice the size of the estimated haploid genome size of 615 Mbp for ruzigrass, indicating that haplotypes were assembled separately. In addition, RNA-seq data was obtained, totaling 258 million reads and 26 Gbp of raw data. These will allow transcriptome characterization for different tissues and aid gene prediction and annotation. Ongoing research includes haplotype phasing, polishing, assembly curation and Hi-C scaffolding. A high-quality genome assembly for ruzigrass will aid research groups in the development and application of genomic tools in breeding and genetics of brachiaria grasses.
650 $aBrachiaria Ruziziensis
650 $aGenoma
650 $aPastagem
653 $aBioinformática
653 $aDe novo Assembly
653 $aMontagem de sequência de DNA
700 1 $aSOUZA SOBRINHO, F. de
700 1 $aFRAGOSO, R. da R.
700 1 $aSILVA JUNIOR, O. B. da
700 1 $aFERREIRA, M. E.
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Registro original: |
Embrapa Recursos Genéticos e Biotecnologia (CENARGEN) |
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| Registros recuperados : 9 | |
| 1. |  | SOARES, S.; FÁVARO, C. P.; FARINAS, C. S. Avaliação de Trichoderma spp. e Aspergillus niger como agentes promotores de solubilização de rochas fosfáticas. In: JORNADA CIENTÍFICA - EMBRAPA SÃO CARLOS, 12., 2020, São Carlos, SP. Anais... São Carlos: Embrapa Instrumentação: Embrapa Pecuária Sudeste, 2020. Editores técnicos: Cristiane Sanchez Farinas, Daniel Souza Corrêa, José Manoel Marconcini, Maria Fernanda Berlingieri Durigan, Paulo Sérgio de Paula Herrmann Junior. 53 Embrapa Instrumentação. Documentos, 71.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Instrumentação. |
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| 2. | | FAVARO, C, P.; BARALDI, I. J.; FARINAS, C. S. Produção de beta-mananase utilizando resíduos da indústria de café In: JORNADA CIENTÍFICA - EMBRAPA SÃO CARLOS, 8., 2016, São Carlos, SP. Anais... São Carlos: Embrapa Instrumentação: Embrapa Pecuária Sudeste, 2016. p.121. Editores técnicos: Wilson Tadeu Lopes da Silva, José Manoel Marconcini, Maria Alice Martins, Lucimara Aparecida Forato, Paulino Ribeiro Villas Boas. (Embrapa Instrumentação. Documentos, 61).| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Instrumentação. |
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| 4. | | KLAIC, R.; FÁVARO, C. P.; LODI, L. A.; OLIVEIRA, C. R. de; FARINAS, C. S. Biofertilizantes a partir do uso de fontes de nutrientes de baixa reatividade e microrganismos solubilizadores. In: SIMPÓSIO NACIONAL DE INSTRUMENTAÇÃO AGROPECUÁRIA, 4., 2019, São Carlos, SP. Ciência, inovação e mercado: anais. São Carlos, SP: Embrapa Instrumentação, 2019. Editores: Paulino Ribeiro Villas-Boas, Maria Alice Martins, Débora Marcondes Bastos Pereira Milori, Ladislau Martin Neto. SIAGRO 2019. 375-379| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Instrumentação. |
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| 8. | | MONTEIRO, B. F. C.; RIBEIRO, M. B. M.; FAVARO, C. P.; FREITAS, J. V.; FARINAS, C. S. Avaliação do processo de bioadsorção de compostos fenólicos para aplicação em biorrefinarias. In: JORNADA CIENTÍFICA - EMBRAPA SÃO CARLOS, 11., 2019, São Carlos, SP. Anais... São Carlos: Embrapa Pecuária Sudeste: Embrapa Instrumentação, 2019. Editores técnicos: Alexandre Berndt, Ana Rita de Araujo Nogueira, Lea Chapaval, Marcelo Mattos Cavallari, Manuel Antonio Chagas Jacinto. 38 Embrapa Pecuária Sudeste. Documentos, 134.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Instrumentação. |
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| 9. | | FLORENCIO, C.; BORTOLETTO-SANTOS, R.; FAVARO, C. P.; BRONDI, M. G.; VELLOSO, C. C. V.; KLAIC, R.; RIBEIRO, C.; FARINAS, C. S.; MATTOSO, L. H. C. Avanços na produção e formulação de inoculantes microbianos visando uma agricultura mais sustentável. Química Nova, v. 45, n. 9, 2022. 1133-1145| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
| Biblioteca(s): Embrapa Instrumentação. |
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| Registros recuperados : 9 | |
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