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Registro Completo |
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Biblioteca(s): |
Embrapa Cerrados. |
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Data corrente: |
23/11/2018 |
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Data da última atualização: |
29/11/2018 |
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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 2099953
005 2018-11-29
008 2018 bl uuuu u00u1 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 Cerrados (CPAC) |
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| Registros recuperados : 12 | |
| 2. |  | NAKASHIMA, T.; PEDROSO, L.; SASSKI, G. L.; ESCRITORE, G.; BOTELHO, S.; MAZZA, M. C. M. Componentes químicos de Rapanea umbellata (Mart) Mez - Myrcinaceae. In: JORNADA CATARINENSE DE PLANTAS MEDICINAIS, 1., 1998, Tubarão. Saúde e sustentabilidade para o 3. milênio: palestras e resumos de trabalhos. Tubarão: Universidade do Sul de Santa Catarina, 1998. p. 156. Painél.| Tipo: Resumo em Anais de Congresso | Circulação/Nível: -- - -- |
| Biblioteca(s): Embrapa Florestas. |
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| 4. | | LAGOS, J. B.; AMARAL, F. M. R.; NAKASHIMA, T.; MAZZA, M. C. M.; MEDRADO, M. J. Estudo fitoquimico e molecular de seis variedades de erva-mate. In: CONGRESSO SUL-AMERICANO DA ERVA MATE, 2.; REUNIAO TECNICA DA ERVA MATE, 3., 2000, Encantado. Anais. Porto Alegre: Comissao dos Organizadores / Universidade do Rio Grande do Sul / Fundacao Estadual de Pesquisa Agropecuaria, 2000. p.403-405.| Biblioteca(s): Embrapa Florestas. |
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| 6. | | NAKASHIMA, T.; TOLEDO, M. G. T.; BRAGA, K. F.; DEL CLARO, L. N.; STINSAK, M. R.; MAZZA, M. C. M. Estudo fitoquímico de Ocotea puberula (canela-guaicá) - Lauraceae. In: JORNADA CATARINENSE DE PLANTAS MEDICINAIS, 1., 1998, Tubarão. Saúde e sustentabilidade para o 3. milênio: palestras e resumos de trabalhos. Tubarão: Universidade do Sul de Santa Catarina, 1998. p. 146. Painél.| Tipo: Resumo em Anais de Congresso | Circulação/Nível: -- - -- |
| Biblioteca(s): Embrapa Florestas. |
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| 8. | | MAZZA, M. C. M.; ZILLER, S. R.; NAKASHIMA, T.; RODIGHERI, H. R.; SOARES, A. O.; BAGGIO, A. J. Importância medicinal de espécies da sub-mata de bracatingais da região metropolitana de Curitiba, Paraná, Brasil. SBPN - Scientific Journal, Curitiba, v. 4, supl. 1, p. 77, 2000. Edição dos Anais da 8ª Reunião Anual da Sociedade Brasileira de Pesquisadores Nikkeis, Curitiba, 2000. Resumos.| Biblioteca(s): Embrapa Florestas. |
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| 9. | | BOBEK, V. B.; HEIDEN, G.; OLIVEIRA, C. F. de; ALMEIDA, V. P. de; PAULA, J. P. de; FARAGO, P. V.; NAKASHIMA, T.; BUDEL, J. M. Comparative analytical micrographs of "vassouras" (Baccharis, Asteraceae). Revista Brasileira de Farmacognosia, v. 26, p. 665?672, 2016.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 1 |
| Biblioteca(s): Embrapa Clima Temperado. |
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| 10. | | BOREK, V. B.; ALMEIDA, V. P. de; PEREIRA, C. B.; HEIDEN, G.; DUARTE, M. do R.; BUDEL, J. M.; NAKASHIMA, T. Comparative Pharmacobotanical Analysis of Baccharis caprariifolia DC. and B. erioclada DC. from Campos Gerais, Paraná, Southern Brazil. Latin American Journal of Pharmacy, v. 34, n. 7, p. 1396-1402, 2015.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 3 |
| Biblioteca(s): Embrapa Clima Temperado. |
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| 11. | | MAZZA, M. C. M.; RODIGHERI, H. R.; NAKASHIMA, T.; ZILLER, S. R.; MAZZA, C. A. da S.; CONTO, A. J. de; SOARES, A. de O.; BAGGIO, A. J. Potencial de aproveitamento medicinal de especies do sub-bosque dos bracatingais da regiao de Curitiba, PR. Colombo: Embrapa Florestas, 2000. 26 p. (Embrapa Florestas. Documentos, 43).| Biblioteca(s): Embrapa Florestas. |
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| 12. | | MAZZA, M. C. M.; ZILLER, S. R.; NAKASHIMA, T.; RODIGHERI, H.; MAZZA, C. A. da S.; CURCIO, G. R.; RACHWAL, M. G.; BAGGIO, A. J.; MAIA, C. M. B. F.; CONTO, A. J. de. Análise do potencial de aproveitamento de espécies medicinais da sub-mata de bracatingais. In: INTERNATIONAL CONGRESS AND EXHIBITION ON FOREST=CONGRESSO E EXPOSIÇÃO INTERNACIONAL SOBRE FLORESTAS, 5., 1999, Curitiba. Forest 99: [resumos]. Rio de Janeiro: BIOSFERA, 1999. 1 CD ROM.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Florestas. |
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| Registros recuperados : 12 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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